forked from lijiext/lammps
Merge branch 'master' of ssh://github.com/lammps/lammps into atomvec-custom
This commit is contained in:
Stan Moore
commit
8301c7a9c6
|
|
@ -425,7 +425,12 @@ if(PKG_USER-ATC)
|
|||
if(LAMMPS_SIZES STREQUAL BIGBIG)
|
||||
message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG")
|
||||
endif()
|
||||
target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES} MPI::MPI_CXX)
|
||||
target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES})
|
||||
if(BUILD_MPI)
|
||||
target_link_libraries(atc PRIVATE MPI::MPI_CXX)
|
||||
else()
|
||||
target_link_libraries(atc PRIVATE mpi_stubs)
|
||||
endif()
|
||||
target_include_directories(atc PRIVATE ${LAMMPS_SOURCE_DIR})
|
||||
target_compile_definitions(atc PRIVATE -DLAMMPS_${LAMMPS_SIZES})
|
||||
endif()
|
||||
|
|
@ -549,10 +554,16 @@ if(BUILD_TOOLS)
|
|||
|
||||
include(CheckGeneratorSupport)
|
||||
if(CMAKE_GENERATOR_SUPPORT_FORTRAN)
|
||||
enable_language(Fortran)
|
||||
add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
|
||||
target_link_libraries(chain.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
|
||||
install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
|
||||
include(CheckLanguage)
|
||||
check_language(Fortran)
|
||||
if(CMAKE_Fortran_COMPILER)
|
||||
enable_language(Fortran)
|
||||
add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
|
||||
target_link_libraries(chain.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
|
||||
install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
|
||||
else()
|
||||
message(WARNING "No suitable Fortran compiler found, skipping building 'chain.x'")
|
||||
endif()
|
||||
else()
|
||||
message(WARNING "CMake build doesn't support fortran, skipping building 'chain.x'")
|
||||
endif()
|
||||
|
|
|
|||
|
|
@ -11,7 +11,8 @@
|
|||
# TBB Malloc
|
||||
|
||||
find_path(TBB_MALLOC_INCLUDE_DIR NAMES tbb/tbb.h PATHS $ENV{TBBROOT}/include)
|
||||
find_library(TBB_MALLOC_LIBRARY NAMES tbbmalloc PATHS $ENV{TBBROOT}/lib/intel64/gcc4.7
|
||||
find_library(TBB_MALLOC_LIBRARY NAMES tbbmalloc PATHS $ENV{TBBROOT}/lib/intel64/gcc4.8
|
||||
$ENV{TBBROOT}/lib/intel64/gcc4.7
|
||||
$ENV{TBBROOT}/lib/intel64/gcc4.4
|
||||
$ENV{TBBROOT}/lib/intel64/gcc4.1)
|
||||
|
||||
|
|
|
|||
|
|
@ -1,5 +1,8 @@
|
|||
enable_language(C)
|
||||
|
||||
if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.12)
|
||||
cmake_policy(SET CMP0074 NEW)
|
||||
endif()
|
||||
find_package(HDF5 REQUIRED)
|
||||
target_link_libraries(h5md PRIVATE ${HDF5_LIBRARIES})
|
||||
target_include_directories(h5md PUBLIC ${HDF5_INCLUDE_DIRS})
|
||||
|
|
|
|||
|
|
@ -1,11 +1,18 @@
|
|||
# USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
|
||||
# NetCDF library enables dump style "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
|
||||
find_package(NetCDF)
|
||||
if(NETCDF_FOUND)
|
||||
find_package(PNetCDF)
|
||||
else(NETCDF_FOUND)
|
||||
find_package(PNetCDF REQUIRED)
|
||||
endif(NETCDF_FOUND)
|
||||
if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.12)
|
||||
cmake_policy(SET CMP0074 NEW)
|
||||
endif()
|
||||
if(NOT BUILD_MPI)
|
||||
find_package(NetCDF REQUIRED)
|
||||
else()
|
||||
find_package(NetCDF)
|
||||
if(NETCDF_FOUND)
|
||||
find_package(PNetCDF)
|
||||
else()
|
||||
find_package(PNetCDF REQUIRED)
|
||||
endif()
|
||||
endif()
|
||||
|
||||
if(NETCDF_FOUND)
|
||||
target_link_libraries(lammps PRIVATE NetCDF::NetCDF)
|
||||
|
|
|
|||
|
|
@ -24,7 +24,11 @@ if(DOWNLOAD_VORO)
|
|||
ExternalProject_Add(voro_build
|
||||
URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
|
||||
URL_MD5 2338b824c3b7b25590e18e8df5d68af9
|
||||
CONFIGURE_COMMAND "" BUILD_COMMAND make ${VORO_BUILD_OPTIONS} BUILD_IN_SOURCE 1 INSTALL_COMMAND ""
|
||||
PATCH_COMMAND patch -b -p0 < ${LAMMPS_LIB_SOURCE_DIR}/voronoi/voro-make.patch
|
||||
CONFIGURE_COMMAND ""
|
||||
BUILD_COMMAND make ${VORO_BUILD_OPTIONS}
|
||||
BUILD_IN_SOURCE 1
|
||||
INSTALL_COMMAND ""
|
||||
BUILD_BYPRODUCTS <SOURCE_DIR>/src/libvoro++.a
|
||||
)
|
||||
ExternalProject_get_property(voro_build SOURCE_DIR)
|
||||
|
|
|
|||
|
|
@ -5,10 +5,10 @@
|
|||
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL
|
||||
DIPOLE GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI
|
||||
POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
|
||||
USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
|
||||
USER-DPD USER-DRUDE USER-FEP USER-MEAMC USER-MESODPD
|
||||
USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
|
||||
USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC USER-MESODPD
|
||||
USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
|
||||
USER-REAXC USER-SPH USER-SMD USER-UEF USER-YAFF)
|
||||
USER-REAXC USER-SDPD USER-SPH USER-SMD USER-UEF USER-YAFF)
|
||||
|
||||
foreach(PKG ${ALL_PACKAGES})
|
||||
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
.TH LAMMPS "15 April 2020" "2020-04-15"
|
||||
.TH LAMMPS "5 May 2020" "2020-05-5"
|
||||
.SH NAME
|
||||
.B LAMMPS
|
||||
\- Molecular Dynamics Simulator.
|
||||
|
|
|
|||
|
|
@ -42,7 +42,7 @@ KOKKOS, o = USER-OMP, t = OPT.
|
|||
* :doc:`com <compute_com>`
|
||||
* :doc:`com/chunk <compute_com_chunk>`
|
||||
* :doc:`contact/atom <compute_contact_atom>`
|
||||
* :doc:`coord/atom <compute_coord_atom>`
|
||||
* :doc:`coord/atom (k) <compute_coord_atom>`
|
||||
* :doc:`damage/atom <compute_damage_atom>`
|
||||
* :doc:`dihedral <compute_dihedral>`
|
||||
* :doc:`dihedral/local <compute_dihedral_local>`
|
||||
|
|
@ -161,5 +161,6 @@ KOKKOS, o = USER-OMP, t = OPT.
|
|||
* :doc:`torque/chunk <compute_torque_chunk>`
|
||||
* :doc:`vacf <compute_vacf>`
|
||||
* :doc:`vcm/chunk <compute_vcm_chunk>`
|
||||
* :doc:`viscosity/cos <compute_viscosity_cos>`
|
||||
* :doc:`voronoi/atom <compute_voronoi_atom>`
|
||||
* :doc:`xrd <compute_xrd>`
|
||||
|
|
|
|||
|
|
@ -22,6 +22,7 @@ OPT.
|
|||
.. table_from_list::
|
||||
:columns: 5
|
||||
|
||||
* :doc:`accelerate/cos <fix_accelerate_cos>`
|
||||
* :doc:`adapt <fix_adapt>`
|
||||
* :doc:`adapt/fep <fix_adapt_fep>`
|
||||
* :doc:`addforce <fix_addforce>`
|
||||
|
|
|
|||
|
|
@ -1,10 +1,11 @@
|
|||
Calculate viscosity
|
||||
===================
|
||||
|
||||
The shear viscosity eta of a fluid can be measured in at least 5 ways
|
||||
The shear viscosity eta of a fluid can be measured in at least 6 ways
|
||||
using various options in LAMMPS. See the examples/VISCOSITY directory
|
||||
for scripts that implement the 5 methods discussed here for a simple
|
||||
Lennard-Jones fluid model. Also, see the :doc:`Howto kappa <Howto_kappa>` doc page for an analogous discussion for
|
||||
Lennard-Jones fluid model and 1 method for SPC/E water model.
|
||||
Also, see the :doc:`Howto kappa <Howto_kappa>` doc page for an analogous discussion for
|
||||
thermal conductivity.
|
||||
|
||||
Eta is a measure of the propensity of a fluid to transmit momentum in
|
||||
|
|
@ -130,9 +131,25 @@ time-integrated momentum fluxes play the role of Cartesian
|
|||
coordinates, whose mean-square displacement increases linearly
|
||||
with time at sufficiently long times.
|
||||
|
||||
The sixth is periodic perturbation method. It is also a non-equilibrium MD method.
|
||||
However, instead of measure the momentum flux in response of applied velocity gradient,
|
||||
it measures the velocity profile in response of applied stress.
|
||||
A cosine-shaped periodic acceleration is added to the system via the
|
||||
:doc:`fix accelerate/cos <fix_accelerate_cos>` command,
|
||||
and the :doc:`compute viscosity/cos<compute_viscosity_cos>` command is used to monitor the
|
||||
generated velocity profile and remove the velocity bias before thermostatting.
|
||||
|
||||
.. note::
|
||||
|
||||
An article by :ref:`(Hess) <Hess3>` discussed the accuracy and efficiency of these methods.
|
||||
|
||||
----------
|
||||
|
||||
.. _Daivis-viscosity:
|
||||
|
||||
**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
|
||||
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
|
||||
|
||||
.. _Hess3:
|
||||
|
||||
**(Hess)** Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209-217.
|
||||
|
|
|
|||
|
|
@ -307,6 +307,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
|
|||
* :doc:`torque/chunk <compute_torque_chunk>` - torque applied on each chunk
|
||||
* :doc:`vacf <compute_vacf>` - velocity auto-correlation function of group of atoms
|
||||
* :doc:`vcm/chunk <compute_vcm_chunk>` - velocity of center-of-mass for each chunk
|
||||
* :doc:`viscosity/cos <compute_viscosity_cos>` - velocity profile under cosine-shaped acceleration
|
||||
* :doc:`voronoi/atom <compute_voronoi_atom>` - Voronoi volume and neighbors for each atom
|
||||
* :doc:`xrd <compute_xrd>` - x-ray diffraction intensity on a mesh of reciprocal lattice nodes
|
||||
|
||||
|
|
|
|||
|
|
@ -3,6 +3,9 @@
|
|||
compute coord/atom command
|
||||
==========================
|
||||
|
||||
compute coord/atom/kk command
|
||||
===================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
|
@ -109,6 +112,30 @@ too frequently.
|
|||
:doc:`special_bonds <special_bonds>` command that includes all pairs in
|
||||
the neighbor list.
|
||||
|
||||
----------
|
||||
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
|
||||
----------
|
||||
|
||||
**Output info:**
|
||||
|
||||
For *cstyle* cutoff, this compute can calculate a per-atom vector or
|
||||
|
|
|
|||
|
|
@ -19,13 +19,14 @@ Syntax
|
|||
|
||||
.. parsed-literal::
|
||||
|
||||
keyword = *cutoff* or *nnn* or *degrees* or *components*
|
||||
keyword = *cutoff* or *nnn* or *degrees* or *components* or *chunksize*
|
||||
*cutoff* value = distance cutoff
|
||||
*nnn* value = number of nearest neighbors
|
||||
*degrees* values = nlvalues, l1, l2,...
|
||||
*wl* value = yes or no
|
||||
*wl/hat* value = yes or no
|
||||
*components* value = ldegree
|
||||
*chunksize* value = number of atoms in each pass
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
|
@ -107,6 +108,14 @@ in conjunction with :doc:`compute coord_atom <compute_coord_atom>` to
|
|||
calculate the ten Wolde's criterion to identify crystal-like
|
||||
particles, as discussed in :ref:`ten Wolde <tenWolde2>`.
|
||||
|
||||
The optional keyword *chunksize* is only applicable when using the
|
||||
the KOKKOS package and is ignored otherwise. This keyword controls
|
||||
the number of atoms in each pass used to compute the bond-orientational
|
||||
order parameters and is used to avoid running out of memory. For example
|
||||
if there are 4000 atoms in the simulation and the *chunksize*
|
||||
is set to 2000, the parameter calculation will be broken up
|
||||
into two passes.
|
||||
|
||||
The value of :math:`Q_l` is set to zero for atoms not in the
|
||||
specified compute group, as well as for atoms that have less than
|
||||
*nnn* neighbors within the distance cutoff, unless *nnn* is NULL.
|
||||
|
|
@ -192,7 +201,7 @@ Default
|
|||
|
||||
The option defaults are *cutoff* = pair style cutoff, *nnn* = 12,
|
||||
*degrees* = 5 4 6 8 10 12 i.e. :math:`Q_4`, :math:`Q_6`, :math:`Q_8`, :math:`Q_{10}`, and :math:`Q_{12}`,
|
||||
*wl* = no, *wl/hat* = no, and *components* off
|
||||
*wl* = no, *wl/hat* = no, *components* off, and *chunksize* = 2000
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,156 @@
|
|||
.. index:: compute viscosity/cos
|
||||
|
||||
compute viscosity/cos command
|
||||
=============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
compute ID group-ID viscosity/cos
|
||||
|
||||
* ID, group-ID are documented in :doc:`compute <compute>` command
|
||||
* viscosity/cos = style name of this compute command
|
||||
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
compute cos all viscosity/cos
|
||||
variable V equal c_cos[7]
|
||||
variable A equal 0.02E-5
|
||||
variable density equal density
|
||||
variable lz equal lz
|
||||
variable reciprocalViscosity equal v_V/${A}/v_density*39.4784/v_lz/v_lz*100
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Define a computation that calculates the velocity amplitude of a group of atoms
|
||||
with an cosine-shaped velocity profile and the temperature of them
|
||||
after subtracting out the velocity profile before computing the kinetic energy.
|
||||
A compute of this style can be used by any command that computes a temperature,
|
||||
e.g. :doc:`thermo_modify <thermo_modify>`, :doc:`fix npt <fix_nh>`, etc.
|
||||
|
||||
This command together with :doc:`fix_accelerate/cos<fix_accelerate_cos>`
|
||||
enables viscosity calculation with periodic perturbation method,
|
||||
as described by :ref:`Hess<Hess1>`.
|
||||
An acceleration along the x-direction is applied to the simulation system
|
||||
by using :doc:`fix_accelerate/cos<fix_accelerate_cos>` command.
|
||||
The acceleration is a periodic function along the z-direction:
|
||||
|
||||
.. math::
|
||||
|
||||
a_{x}(z) = A \cos \left(\frac{2 \pi z}{l_{z}}\right)
|
||||
|
||||
where :math:`A` is the acceleration amplitude, :math:`l_z` is the z-length
|
||||
of the simulation box. At steady state, the acceleration generates
|
||||
a velocity profile:
|
||||
|
||||
.. math::
|
||||
|
||||
v_{x}(z) = V \cos \left(\frac{2 \pi z}{l_{z}}\right)
|
||||
|
||||
The generated velocity amplitude :math:`V` is related to the
|
||||
shear viscosity :math:`\eta` by:
|
||||
|
||||
.. math::
|
||||
|
||||
V = \frac{A \rho}{\eta}\left(\frac{l_{z}}{2 \pi}\right)^{2}
|
||||
|
||||
|
||||
and it can be obtained from ensemble average of the velocity profile:
|
||||
|
||||
.. math::
|
||||
|
||||
V = \frac{\sum_i 2 m_{i} v_{i, x} \cos \left(\frac{2 \pi z_i}{l_{z}}\right)}{\sum_i m_{i}}
|
||||
|
||||
|
||||
where :math:`m_i`, :math:`v_{i,x}` and :math:`z_i` are the mass,
|
||||
x-component velocity and z coordinate of a particle.
|
||||
|
||||
After the cosine-shaped collective velocity in :math:`x` direction
|
||||
has been subtracted for each atom, the temperature is calculated by the formula
|
||||
KE = dim/2 N k T, where KE = total kinetic energy of the group of
|
||||
atoms (sum of 1/2 m v\^2), dim = 2 or 3 = dimensionality of the
|
||||
simulation, N = number of atoms in the group, k = Boltzmann constant,
|
||||
and T = temperature.
|
||||
|
||||
A kinetic energy tensor, stored as a 6-element vector, is also
|
||||
calculated by this compute for use in the computation of a pressure
|
||||
tensor. The formula for the components of the tensor is the same as
|
||||
the above formula, except that v\^2 is replaced by vx\*vy for the xy
|
||||
component, etc. The 6 components of the vector are ordered xx, yy,
|
||||
zz, xy, xz, yz.
|
||||
|
||||
The number of atoms contributing to the temperature is assumed to be
|
||||
constant for the duration of the run; use the *dynamic* option of the
|
||||
:doc:`compute_modify <compute_modify>` command if this is not the case.
|
||||
However, in order to get meaningful result, the group ID of this compute should be all.
|
||||
|
||||
The removal of the cosine-shaped velocity component by this command is
|
||||
essentially computing the temperature after a "bias" has been removed
|
||||
from the velocity of the atoms. If this compute is used with a fix
|
||||
command that performs thermostatting then this bias will be subtracted
|
||||
from each atom, thermostatting of the remaining thermal velocity will
|
||||
be performed, and the bias will be added back in. Thermostatting
|
||||
fixes that work in this way include :doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix temp/berendsen <fix_temp_berendsen>`, and :doc:`fix langevin <fix_langevin>`.
|
||||
|
||||
This compute subtracts out degrees-of-freedom due to fixes that
|
||||
constrain molecular motion, such as :doc:`fix shake <fix_shake>` and
|
||||
:doc:`fix rigid <fix_rigid>`. This means the temperature of groups of
|
||||
atoms that include these constraints will be computed correctly. If
|
||||
needed, the subtracted degrees-of-freedom can be altered using the
|
||||
*extra* option of the :doc:`compute_modify <compute_modify>` command.
|
||||
|
||||
See the :doc:`Howto thermostat <Howto_thermostat>` doc page for a
|
||||
discussion of different ways to compute temperature and perform
|
||||
thermostatting.
|
||||
|
||||
----------
|
||||
|
||||
**Output info:**
|
||||
|
||||
This compute calculates a global scalar (the temperature) and a global
|
||||
vector of length 7, which can be accessed by indices 1-7.
|
||||
The first 6 elements of the vector are the KE tensor,
|
||||
and the 7-th is the cosine-shaped velocity amplitude :math:`V`,
|
||||
which can be used to calculate the reciprocal viscosity, as shown in the example.
|
||||
These values can be used by any command that uses global scalar or
|
||||
vector values from a compute as input.
|
||||
See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
first 6 elements of vector values are "extensive",
|
||||
and the 7-th element of vector values is "intensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
first 6 elements of vector values will be in energy :doc:`units <units>`.
|
||||
The 7-th element of vector value will be in velocity :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This command is only available when LAMMPS was built with the USER-MISC package.
|
||||
Since this compute depends on :doc:`fix accelerate/cos <fix_accelerate_cos>` which can
|
||||
only work for 3d systems, it cannot be used for 2d systems.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`fix accelerate/cos <fix_accelerate_cos>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
.. _Hess1:
|
||||
|
||||
**(Hess)** Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209-217.
|
||||
|
|
@ -165,6 +165,7 @@ The individual style names on the :doc:`Commands fix <Commands_fix>` doc
|
|||
page are followed by one or more of (g,i,k,o,t) to indicate which
|
||||
accelerated styles exist.
|
||||
|
||||
* :doc:`accelerate/cos <fix_accelerate_cos>` - apply cosine-shaped acceleration to atoms
|
||||
* :doc:`adapt <fix_adapt>` - change a simulation parameter over time
|
||||
* :doc:`adapt/fep <fix_adapt_fep>` - enhanced version of fix adapt
|
||||
* :doc:`addforce <fix_addforce>` - add a force to each atom
|
||||
|
|
|
|||
|
|
@ -0,0 +1,104 @@
|
|||
.. index:: fix accelerate/cos
|
||||
|
||||
fix accelerate/cos command
|
||||
==========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
fix ID group-ID accelerate value
|
||||
|
||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||
* accelerate/cos = style name of this fix command
|
||||
* value = amplitude of acceleration (in unit of force/mass)
|
||||
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix 1 all accelerate/cos 0.02e-5
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Give each atom a acceleration in x-direction based on its z coordinate.
|
||||
The acceleration is a periodic function along the z-direction:
|
||||
|
||||
.. math::
|
||||
|
||||
a_{x}(z) = A \cos \left(\frac{2 \pi z}{l_{z}}\right)
|
||||
|
||||
where :math:`A` is the acceleration amplitude, :math:`l_z` is the z-length
|
||||
of the simulation box.
|
||||
At steady state, the acceleration generates a velocity profile:
|
||||
|
||||
.. math::
|
||||
|
||||
v_{x}(z) = V \cos \left(\frac{2 \pi z}{l_{z}}\right)
|
||||
|
||||
The generated velocity amplitude :math:`V` is related to the
|
||||
shear viscosity :math:`\eta` by:
|
||||
|
||||
.. math::
|
||||
|
||||
V = \frac{A \rho}{\eta}\left(\frac{l_{z}}{2 \pi}\right)^{2}
|
||||
|
||||
|
||||
and it can be obtained from ensemble average of the velocity profile:
|
||||
|
||||
.. math::
|
||||
|
||||
V = \frac{\sum_i 2 m_{i} v_{i, x} \cos \left(\frac{2 \pi z_i}{l_{z}}\right)}{\sum_i m_{i}}
|
||||
|
||||
where :math:`m_i`, :math:`v_{i,x}` and :math:`z_i` are the mass,
|
||||
x-component velocity and z coordinate of a particle.
|
||||
|
||||
The velocity amplitude :math:`V` can be calculated with :doc:`compute viscosity/cos <compute_viscosity_cos>`,
|
||||
which enables viscosity calculation with periodic perturbation method,
|
||||
as described by :ref:`Hess<Hess2>`.
|
||||
Because the applied acceleration drives the system away from equilibration,
|
||||
the calculated shear viscosity is lower than the intrinsic viscosity
|
||||
due to the shear-thinning effect.
|
||||
Extrapolation to zero acceleration should generally be performed to
|
||||
predict the zero-shear viscosity.
|
||||
As the shear stress decreases, the signal-noise ratio decreases rapidly,
|
||||
the simulation time must be extended accordingly to get converged result.
|
||||
|
||||
In order to get meaningful result, the group ID of this fix should be all.
|
||||
|
||||
----------
|
||||
|
||||
**Restart, fix_modify, output, run start/stop, minimize info:**
|
||||
|
||||
No information about this fix is written to binary restart files.
|
||||
None of the fix_modify options are relevant to this fix.
|
||||
No global or per-atom quantities are stored by this fix for access by various output commands.
|
||||
No parameter of this fix can be used with the start/stop keywords of the run command.
|
||||
This fix is not invoked during energy minimization.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This command is only available when LAMMPS was built with the USER-MISC package.
|
||||
Since this fix depends on the z-coordinate of atoms, it cannot be used in 2d simulations.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`compute viscosity/cos <compute_viscosity_cos>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
.. _Hess2:
|
||||
|
||||
**(Hess)** Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209-217.
|
||||
|
|
@ -26,7 +26,7 @@ Syntax
|
|||
v_name = global value calculated by an equal-style variable with name
|
||||
|
||||
* zero or more keyword/arg pairs may be appended
|
||||
* keyword = *type* or *start* or *file* or *overwrite* or *title1* or *title2* or *ncorr* or *p* or *m*
|
||||
* keyword = *type* or *start* or *file* or *overwrite* or *title1* or *title2* or *ncorr* or *nlen* or *ncount*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
|
|
|
|||
|
|
@ -160,7 +160,7 @@ the :doc:`run <run>` command.
|
|||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
The *diskfree* attribute is currently only supported on Linux and MacOS.
|
||||
The *diskfree* attribute is currently only supported on Linux, MacOSX, and BSD.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
|
|
|||
|
|
@ -21,12 +21,13 @@ Syntax
|
|||
|
||||
.. parsed-literal::
|
||||
|
||||
keyword = *checkqeq* or *lgvdw* or *safezone* or *mincap*
|
||||
keyword = *checkqeq* or *lgvdw* or *safezone* or *mincap* or *minhbonds*
|
||||
*checkqeq* value = *yes* or *no* = whether or not to require qeq/reax fix
|
||||
*enobonds* value = *yes* or *no* = whether or not to tally energy of atoms with no bonds
|
||||
*lgvdw* value = *yes* or *no* = whether or not to use a low gradient vdW correction
|
||||
*safezone* = factor used for array allocation
|
||||
*mincap* = minimum size for array allocation
|
||||
*minhbonds* = minimum size use for storing hydrogen bonds
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
|
@ -146,11 +147,11 @@ zero. The latter behavior is usual not desired, as it causes
|
|||
discontinuities in the potential energy when the bonding of an atom
|
||||
drops to zero.
|
||||
|
||||
Optional keywords *safezone* and *mincap* are used for allocating
|
||||
reax/c arrays. Increasing these values can avoid memory problems,
|
||||
such as segmentation faults and bondchk failed errors, that could
|
||||
occur under certain conditions. These keywords are not used by the
|
||||
Kokkos version, which instead uses a more robust memory allocation
|
||||
Optional keywords *safezone*\ , *mincap*\ , and *minhbonds* are used
|
||||
for allocating reax/c arrays. Increasing these values can avoid memory
|
||||
problems, such as segmentation faults and bondchk failed errors, that
|
||||
could occur under certain conditions. These keywords are not used by
|
||||
the Kokkos version, which instead uses a more robust memory allocation
|
||||
scheme that checks if the sizes of the arrays have been exceeded and
|
||||
automatically allocates more memory.
|
||||
|
||||
|
|
@ -352,7 +353,7 @@ Default
|
|||
"""""""
|
||||
|
||||
The keyword defaults are checkqeq = yes, enobonds = yes, lgvdw = no,
|
||||
safezone = 1.2, mincap = 50.
|
||||
safezone = 1.2, mincap = 50, minhbonds = 25.
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -1789,6 +1789,7 @@ Militzer
|
|||
Minary
|
||||
mincap
|
||||
Mindlin
|
||||
minhbonds
|
||||
mingw
|
||||
minima
|
||||
minimizations
|
||||
|
|
|
|||
|
|
@ -1,5 +1,6 @@
|
|||
This directory has 5 scripts that compute the viscosity (eta) of a
|
||||
Lennard-Jones fluid using 5 different methods. See the discussion in
|
||||
This directory has 6 scripts that compute the viscosity (eta) of fluid
|
||||
using 6 different methods. 5 of them are for a Lennard-Jones fluid
|
||||
and the last one is for SPC/E water model. See the discussion in
|
||||
Section 6.21 of the manual for an overview of the methods and pointers
|
||||
to doc pages for the commands which implement them. Citations for the
|
||||
various methods can also be found in the manual.
|
||||
|
|
@ -10,7 +11,7 @@ enough to generate good statistics and highly accurate results.
|
|||
|
||||
-------------
|
||||
|
||||
These are the 5 methods for computing viscosity. The first 3 are
|
||||
These are the 5 methods for computing viscosity of a LJ fluid. The first 3 are
|
||||
non-equilibrium methods; the last 2 are equilibrium methods.
|
||||
|
||||
in.wall = move a wall to shear the fluid between two walls
|
||||
|
|
@ -89,3 +90,18 @@ heat/flux doc page - the resulting value prints at the end of the run
|
|||
and is in the log file
|
||||
|
||||
eta = 1.07
|
||||
|
||||
-------------
|
||||
|
||||
in.cos.1000SPCE is an example script of using cosine periodic perturbation method
|
||||
to calculate the viscosity of SPC/E water model.
|
||||
|
||||
The reciprocal of eta is computed within the script, and printed out as v_invVis
|
||||
in thermo_style command. The result will converge after hundreds of picoseconds.
|
||||
Then eta is obtained from the reciprocal of time average of v_invVis.
|
||||
|
||||
eta = 0.75 mPa*s
|
||||
|
||||
Note that the calculated viscosity by this method decreases with increased acceleration.
|
||||
It is therefore generally necessary to perform calculation at different accelerations
|
||||
and extrapolate the viscosity to zero shear.
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,53 @@
|
|||
# DFF generated Lammps input file
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
boundary p p p
|
||||
|
||||
pair_style lj/cut/coul/long 10.0
|
||||
pair_modify mix arithmetic
|
||||
pair_modify tail yes
|
||||
kspace_style pppm 1.0e-4
|
||||
dielectric 1.0
|
||||
special_bonds amber
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
read_data data.cos.1000SPCE
|
||||
|
||||
variable T equal 300
|
||||
variable P equal 1.0
|
||||
|
||||
velocity all create ${T} 12345 mom yes rot yes dist gaussian
|
||||
|
||||
timestep 1.0
|
||||
|
||||
# Constraint ##################################
|
||||
fix com all momentum 100 linear 1 1 1
|
||||
fix rigid all shake 1e-4 20 0 b 1 a 1
|
||||
|
||||
# Viscosity ##################################
|
||||
variable A equal 0.05e-5 # angstrom/fs^2
|
||||
|
||||
fix cos all accelerate/cos ${A}
|
||||
compute cos all viscosity/cos
|
||||
|
||||
variable density equal density
|
||||
variable lz equal lz
|
||||
variable vMax equal c_cos[7] # velocity of atoms at z=0
|
||||
variable invVis equal v_vMax/${A}/v_density*39.4784/v_lz/v_lz*100 # reciprocal of viscosity 1/Pa/s
|
||||
|
||||
fix npt all npt temp ${T} ${T} 100 iso ${P} ${P} 1000
|
||||
fix_modify npt temp cos
|
||||
|
||||
thermo_style custom step cpu temp press pe density v_vMax v_invVis
|
||||
thermo_modify temp cos
|
||||
thermo 100
|
||||
################################################
|
||||
|
||||
dump 1 all custom 10000 dump.lammpstrj id mol type element q xu yu zu
|
||||
dump_modify 1 sort id element O H
|
||||
|
||||
run 2000
|
||||
|
|
@ -0,0 +1,160 @@
|
|||
LAMMPS (3 Mar 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# DFF generated Lammps input file
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
boundary p p p
|
||||
|
||||
pair_style lj/cut/coul/long 10.0
|
||||
pair_modify mix arithmetic
|
||||
pair_modify tail yes
|
||||
kspace_style pppm 1.0e-4
|
||||
dielectric 1.0
|
||||
special_bonds amber
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
read_data data.1000SPCE.lmp
|
||||
orthogonal box = (0 0 0) to (31.043 31.043 31.043)
|
||||
2 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
2000 bonds
|
||||
reading angles ...
|
||||
1000 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.00114917 secs
|
||||
read_data CPU = 0.00953543 secs
|
||||
|
||||
variable T equal 300
|
||||
variable P equal 1.0
|
||||
|
||||
velocity all create ${T} 12345 mom yes rot yes dist gaussian
|
||||
velocity all create 300 12345 mom yes rot yes dist gaussian
|
||||
|
||||
timestep 1.0
|
||||
|
||||
# Constraint ##################################
|
||||
fix com all momentum 100 linear 1 1 1
|
||||
fix rigid all shake 1e-4 20 0 b 1 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
1000 = # of frozen angles
|
||||
find clusters CPU = 0.000442737 secs
|
||||
|
||||
# Viscosity ##################################
|
||||
variable A equal 0.02e-5 # angstrom/fs^2
|
||||
|
||||
fix cos all accelerate/cos ${A}
|
||||
fix cos all accelerate/cos 2e-07
|
||||
compute cos all viscosity/cos
|
||||
|
||||
variable density equal density
|
||||
variable lz equal lz
|
||||
variable vMax equal c_cos[7] # velocity of atoms at z=0
|
||||
variable invVis equal v_vMax/${A}/v_density*39.4784/v_lz/v_lz*100 # reciprocal of viscosity 1/Pa/s
|
||||
variable invVis equal v_vMax/2e-07/v_density*39.4784/v_lz/v_lz*100
|
||||
|
||||
fix npt all npt temp ${T} ${T} 100 iso ${P} ${P} 1000
|
||||
fix npt all npt temp 300 ${T} 100 iso ${P} ${P} 1000
|
||||
fix npt all npt temp 300 300 100 iso ${P} ${P} 1000
|
||||
fix npt all npt temp 300 300 100 iso 1 ${P} 1000
|
||||
fix npt all npt temp 300 300 100 iso 1 1 1000
|
||||
fix_modify npt temp cos
|
||||
|
||||
thermo_style custom step cpu temp press pe density v_vMax v_invVis
|
||||
thermo_modify temp cos
|
||||
thermo 100
|
||||
################################################
|
||||
|
||||
dump 1 all custom 10000 dump.lammpstrj id mol type element q xu yu zu
|
||||
dump_modify 1 sort id element O H
|
||||
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.263539
|
||||
grid = 16 16 16
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0325342
|
||||
estimated relative force accuracy = 9.79757e-05
|
||||
using double precision MKL FFT
|
||||
3d grid and FFT values/proc = 3375 512
|
||||
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 = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, 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) = 10.14 | 10.14 | 10.14 Mbytes
|
||||
Step CPU Temp Press PotEng Density v_vMax v_invVis
|
||||
0 0 450.04468 9838.6886 -7651.736 0.99999331 0.0001293705 2649.9663
|
||||
100 0.33736925 497.65155 2024.4827 -8342.2499 0.98595028 0.00019602427 4034.2452
|
||||
200 0.67116638 446.48518 27.075082 -8908.9684 0.9652009 0.00027615455 5723.7907
|
||||
300 0.99760895 401.79875 -776.99871 -9381.8986 0.95205822 0.00019626685 4086.6103
|
||||
400 1.3239019 369.65373 -510.5336 -9803.6463 0.94817309 0.00022998514 4795.2142
|
||||
500 1.6488092 343.35807 -936.31982 -10146.023 0.94840581 0.0001434423 2990.5423
|
||||
600 1.9826063 319.86131 -1381.3302 -10405.812 0.95459202 6.6411532e-05 1381.5767
|
||||
700 2.3172637 307.74606 -98.775733 -10643.5 0.96669652 0.00010446317 2164.0664
|
||||
800 2.6562841 305.14214 -540.57804 -10865.742 0.97808367 5.4381233e-05 1122.1765
|
||||
900 2.9938415 288.01316 639.00486 -10925.39 0.98686357 0.00010878474 2238.1355
|
||||
1000 3.327893 295.07773 -226.06503 -11033.826 0.99128496 0.00011935058 2451.8608
|
||||
1100 3.6618862 299.21578 306.34231 -11049.152 0.99552203 8.9538943e-05 1836.8166
|
||||
1200 3.9984287 301.82462 85.804646 -11013.564 0.99713434 0.00015912276 3262.51
|
||||
1300 4.3320735 308.6009 268.08897 -11009.836 0.99695358 0.00026212596 5374.72
|
||||
1400 4.668875 298.36903 -258.75495 -10962.299 0.99503447 0.00033087355 6788.7027
|
||||
1500 5.0003694 299.96073 99.512082 -10980.551 0.99315631 0.00033996557 6979.6425
|
||||
1600 5.3367337 304.18018 -500.65441 -11002.054 0.9914558 0.00039075642 8026.9849
|
||||
1700 5.6780828 301.63978 -499.07458 -10992.88 0.99234354 0.00038101175 7824.4738
|
||||
1800 6.0140638 303.25858 640.03432 -11053.335 0.99553958 0.00041336203 8479.7267
|
||||
1900 6.3532521 301.40882 208.28331 -11119.481 0.99534534 0.00032474734 6662.3144
|
||||
2000 6.6938104 298.0462 -236.47954 -11162.212 0.99421846 0.00023869721 4898.8129
|
||||
Loop time of 6.69387 on 8 procs for 2000 steps with 3000 atoms
|
||||
|
||||
Performance: 25.815 ns/day, 0.930 hours/ns, 298.781 timesteps/s
|
||||
99.7% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.36 | 4.4981 | 4.6781 | 5.1 | 67.20
|
||||
Bond | 0.00074545 | 0.00088463 | 0.0012464 | 0.0 | 0.01
|
||||
Kspace | 0.86696 | 1.0476 | 1.1863 | 10.5 | 15.65
|
||||
Neigh | 0.37733 | 0.37785 | 0.3784 | 0.1 | 5.64
|
||||
Comm | 0.19874 | 0.20168 | 0.20729 | 0.6 | 3.01
|
||||
Output | 0.0015529 | 0.0015803 | 0.0017546 | 0.2 | 0.02
|
||||
Modify | 0.54083 | 0.55143 | 0.55445 | 0.6 | 8.24
|
||||
Other | | 0.01483 | | | 0.22
|
||||
|
||||
Nlocal: 375 ave 385 max 361 min
|
||||
Histogram: 1 1 0 0 1 0 2 0 1 2
|
||||
Nghost: 5772.25 ave 5789 max 5757 min
|
||||
Histogram: 1 1 2 0 0 0 2 0 0 2
|
||||
Neighs: 135285 ave 144189 max 127550 min
|
||||
Histogram: 1 2 1 1 0 0 0 0 1 2
|
||||
|
||||
Total # of neighbors = 1082280
|
||||
Ave neighs/atom = 360.76
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 101
|
||||
Dangerous builds = 1
|
||||
Total wall time: 0:00:06
|
||||
|
|
@ -1,5 +1,11 @@
|
|||
#ifndef _WIN32
|
||||
#if !defined(_WIN32)
|
||||
|
||||
#if defined(__FreeBSD__) || defined(__DragonFly__) || defined(__OpenBSD__) || defined(__NetBSD__)
|
||||
#include <cstdlib>
|
||||
#else
|
||||
#include <alloca.h>
|
||||
#endif
|
||||
|
||||
#endif
|
||||
#include "Function.h"
|
||||
#include "ATC_Error.h"
|
||||
|
|
|
|||
|
|
@ -0,0 +1,30 @@
|
|||
--- src/Makefile.orig 2020-05-03 03:50:23.501557199 -0400
|
||||
+++ src/Makefile 2020-05-03 03:53:32.147681674 -0400
|
||||
@@ -10,10 +10,10 @@
|
||||
# List of the common source files
|
||||
objs=cell.o common.o container.o unitcell.o v_compute.o c_loops.o \
|
||||
v_base.o wall.o pre_container.o container_prd.o
|
||||
-src=$(patsubst %.o,%.cc,$(objs))
|
||||
+src=$(objs:.o=.cc)
|
||||
|
||||
# Makefile rules
|
||||
-all: libvoro++.a voro++
|
||||
+all: depend libvoro++.a voro++
|
||||
|
||||
depend:
|
||||
$(CXX) -MM $(src) >Makefile.dep
|
||||
@@ -22,12 +22,12 @@
|
||||
|
||||
libvoro++.a: $(objs)
|
||||
rm -f libvoro++.a
|
||||
- ar rs libvoro++.a $^
|
||||
+ $(AR) rs libvoro++.a $(objs)
|
||||
|
||||
voro++: libvoro++.a cmd_line.cc
|
||||
$(CXX) $(CFLAGS) -L. -o voro++ cmd_line.cc -lvoro++
|
||||
|
||||
-%.o: %.cc
|
||||
+.cc.o:
|
||||
$(CXX) $(CFLAGS) -c $<
|
||||
|
||||
help: Doxyfile $(SOURCE)
|
||||
|
|
@ -926,7 +926,7 @@ void PairKIM::set_argument_pointers()
|
|||
kimerror = kimerror ||
|
||||
KIM_ComputeArguments_SetArgumentPointerDouble(
|
||||
pargs,KIM_COMPUTE_ARGUMENT_NAME_partialEnergy,
|
||||
reinterpret_cast<double * const>(NULL));
|
||||
static_cast<double * const>(NULL));
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -947,7 +947,7 @@ void PairKIM::set_argument_pointers()
|
|||
kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble(
|
||||
pargs,
|
||||
KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy,
|
||||
reinterpret_cast<double * const>(NULL));
|
||||
static_cast<double * const>(NULL));
|
||||
} else if (KIM_SupportStatus_NotEqual(kim_model_support_for_particleEnergy,
|
||||
KIM_SUPPORT_STATUS_notSupported)) {
|
||||
kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble(
|
||||
|
|
@ -960,7 +960,7 @@ void PairKIM::set_argument_pointers()
|
|||
kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble(
|
||||
pargs,
|
||||
KIM_COMPUTE_ARGUMENT_NAME_partialForces,
|
||||
reinterpret_cast<double * const>(NULL));
|
||||
static_cast<double * const>(NULL));
|
||||
} else {
|
||||
kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble(
|
||||
pargs, KIM_COMPUTE_ARGUMENT_NAME_partialForces, &(atom->f[0][0]));
|
||||
|
|
@ -983,7 +983,7 @@ void PairKIM::set_argument_pointers()
|
|||
kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble(
|
||||
pargs,
|
||||
KIM_COMPUTE_ARGUMENT_NAME_partialParticleVirial,
|
||||
reinterpret_cast<double * const>(NULL));
|
||||
static_cast<double * const>(NULL));
|
||||
} else if (KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial,
|
||||
KIM_SUPPORT_STATUS_notSupported)) {
|
||||
kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble(
|
||||
|
|
|
|||
|
|
@ -85,6 +85,8 @@ action comm_kokkos.cpp
|
|||
action comm_kokkos.h
|
||||
action comm_tiled_kokkos.cpp
|
||||
action comm_tiled_kokkos.h
|
||||
action compute_coord_atom_kokkos.cpp
|
||||
action compute_coord_atom_kokkos.h
|
||||
action compute_orientorder_atom_kokkos.cpp
|
||||
action compute_orientorder_atom_kokkos.h
|
||||
action compute_temp_kokkos.cpp
|
||||
|
|
|
|||
|
|
@ -0,0 +1,249 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
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_coord_atom_kokkos.h"
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
#include "compute_orientorder_atom_kokkos.h"
|
||||
#include "atom_kokkos.h"
|
||||
#include "update.h"
|
||||
#include "modify.h"
|
||||
#include "neighbor_kokkos.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neigh_request.h"
|
||||
#include "force.h"
|
||||
#include "pair.h"
|
||||
#include "comm.h"
|
||||
#include "group.h"
|
||||
#include "memory_kokkos.h"
|
||||
#include "error.h"
|
||||
#include "atom_masks.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define INVOKED_PERATOM 8
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template<class DeviceType>
|
||||
ComputeCoordAtomKokkos<DeviceType>::ComputeCoordAtomKokkos(LAMMPS *lmp, int narg, char **arg) :
|
||||
ComputeCoordAtom(lmp, narg, arg)
|
||||
{
|
||||
kokkosable = 1;
|
||||
atomKK = (AtomKokkos *) atom;
|
||||
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
|
||||
datamask_read = EMPTY_MASK;
|
||||
datamask_modify = EMPTY_MASK;
|
||||
|
||||
d_typelo = typename AT::t_int_1d("coord/atom:typelo",ncol);
|
||||
d_typehi = typename AT::t_int_1d("coord/atom:typehi",ncol);
|
||||
|
||||
auto h_typelo = Kokkos::create_mirror_view(d_typelo);
|
||||
auto h_typehi = Kokkos::create_mirror_view(d_typehi);
|
||||
|
||||
for (int i = 0; i < ncol; i++) {
|
||||
h_typelo(i) = typelo[i];
|
||||
h_typehi(i) = typehi[i];
|
||||
}
|
||||
|
||||
Kokkos::deep_copy(d_typelo,h_typelo);
|
||||
Kokkos::deep_copy(d_typehi,h_typehi);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template<class DeviceType>
|
||||
ComputeCoordAtomKokkos<DeviceType>::~ComputeCoordAtomKokkos<DeviceType>()
|
||||
{
|
||||
if (copymode) return;
|
||||
|
||||
memoryKK->destroy_kokkos(k_cvec,cvec);
|
||||
memoryKK->destroy_kokkos(k_carray,carray);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template<class DeviceType>
|
||||
void ComputeCoordAtomKokkos<DeviceType>::init()
|
||||
{
|
||||
ComputeCoordAtom::init();
|
||||
|
||||
// need an occasional full neighbor list
|
||||
|
||||
// irequest = neigh request made by parent class
|
||||
|
||||
int irequest = neighbor->nrequest - 1;
|
||||
|
||||
neighbor->requests[irequest]->
|
||||
kokkos_host = std::is_same<DeviceType,LMPHostType>::value &&
|
||||
!std::is_same<DeviceType,LMPDeviceType>::value;
|
||||
neighbor->requests[irequest]->
|
||||
kokkos_device = std::is_same<DeviceType,LMPDeviceType>::value;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template<class DeviceType>
|
||||
void ComputeCoordAtomKokkos<DeviceType>::compute_peratom()
|
||||
{
|
||||
invoked_peratom = update->ntimestep;
|
||||
|
||||
// grow coordination array if necessary
|
||||
|
||||
if (atom->nmax > nmax) {
|
||||
if (ncol == 1) {
|
||||
memoryKK->destroy_kokkos(k_cvec,cvec);
|
||||
nmax = atom->nmax;
|
||||
memoryKK->create_kokkos(k_cvec,cvec,nmax,"coord/atom:cvec");
|
||||
vector_atom = cvec;
|
||||
d_cvec = k_cvec.template view<DeviceType>();
|
||||
} else {
|
||||
memoryKK->destroy_kokkos(k_carray,carray);
|
||||
nmax = atom->nmax;
|
||||
memoryKK->create_kokkos(k_carray,carray,nmax,ncol,"coord/atom:carray");
|
||||
array_atom = carray;
|
||||
d_carray = k_carray.template view<DeviceType>();
|
||||
}
|
||||
}
|
||||
|
||||
if (cstyle == ORIENT) {
|
||||
if (!(c_orientorder->invoked_flag & INVOKED_PERATOM)) {
|
||||
c_orientorder->compute_peratom();
|
||||
c_orientorder->invoked_flag |= INVOKED_PERATOM;
|
||||
}
|
||||
nqlist = c_orientorder->nqlist;
|
||||
normv = c_orientorder->array_atom;
|
||||
comm->forward_comm_compute(this);
|
||||
|
||||
if (!c_orientorder->kokkosable)
|
||||
error->all(FLERR,"Must use compute orientorder/atom/kk with compute coord/atom/kk");
|
||||
|
||||
if (c_orientorder->execution_space == Host) {
|
||||
ComputeOrientOrderAtomKokkos<LMPHostType>* c_orientorder_kk;
|
||||
c_orientorder_kk = (ComputeOrientOrderAtomKokkos<LMPHostType>*) c_orientorder;
|
||||
c_orientorder_kk->k_qnarray.modify<LMPHostType>();
|
||||
c_orientorder_kk->k_qnarray.sync<DeviceType>();
|
||||
d_normv = c_orientorder_kk->k_qnarray.view<DeviceType>();
|
||||
} else {
|
||||
ComputeOrientOrderAtomKokkos<LMPDeviceType>* c_orientorder_kk;
|
||||
c_orientorder_kk = (ComputeOrientOrderAtomKokkos<LMPDeviceType>*) c_orientorder;
|
||||
c_orientorder_kk->k_qnarray.modify<LMPHostType>();
|
||||
c_orientorder_kk->k_qnarray.sync<DeviceType>();
|
||||
d_normv = c_orientorder_kk->k_qnarray.view<DeviceType>();
|
||||
}
|
||||
}
|
||||
|
||||
// invoke full neighbor list (will copy or build if necessary)
|
||||
|
||||
neighbor->build_one(list);
|
||||
|
||||
inum = list->inum;
|
||||
NeighListKokkos<DeviceType>* k_list = static_cast<NeighListKokkos<DeviceType>*>(list);
|
||||
d_numneigh = k_list->d_numneigh;
|
||||
d_neighbors = k_list->d_neighbors;
|
||||
d_ilist = k_list->d_ilist;
|
||||
|
||||
// compute coordination number(s) for each atom in group
|
||||
// use full neighbor list to count atoms less than cutoff
|
||||
|
||||
atomKK->sync(execution_space,X_MASK|TYPE_MASK|MASK_MASK);
|
||||
x = atomKK->k_x.view<DeviceType>();
|
||||
type = atomKK->k_type.view<DeviceType>();
|
||||
mask = atomKK->k_mask.view<DeviceType>();
|
||||
|
||||
copymode = 1;
|
||||
if (cstyle == CUTOFF) {
|
||||
if (ncol == 1) {
|
||||
typename Kokkos::RangePolicy<DeviceType, TagComputeCoordAtom<CUTOFF,1> > policy(0,inum);
|
||||
Kokkos::parallel_for("ComputeCoordAtom",policy,*this);
|
||||
} else {
|
||||
typename Kokkos::RangePolicy<DeviceType, TagComputeCoordAtom<CUTOFF,0> > policy(0,inum);
|
||||
Kokkos::parallel_for("ComputeCoordAtom",policy,*this);
|
||||
}
|
||||
} else if (cstyle == ORIENT) {
|
||||
typename Kokkos::RangePolicy<DeviceType, TagComputeCoordAtom<ORIENT,1> > policy(0,inum);
|
||||
Kokkos::parallel_for("ComputeCoordAtom",policy,*this);
|
||||
}
|
||||
copymode = 0;
|
||||
|
||||
if (ncol == 1 || cstyle == ORIENT) {
|
||||
k_cvec.modify<DeviceType>();
|
||||
k_cvec.sync<LMPHostType>();
|
||||
} else {
|
||||
k_carray.modify<DeviceType>();
|
||||
k_carray.sync<LMPHostType>();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
template<class DeviceType>
|
||||
template<int CSTYLE, int NCOL>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void ComputeCoordAtomKokkos<DeviceType>::operator()(TagComputeCoordAtom<CSTYLE,NCOL>, const int &ii) const
|
||||
{
|
||||
const int i = d_ilist[ii];
|
||||
if (NCOL == 1 || CSTYLE == ORIENT)
|
||||
d_cvec(i) = 0.0;
|
||||
else
|
||||
for (int m = 0; m < ncol; m++) d_carray(i,m) = 0.0;
|
||||
if (mask[i] & groupbit) {
|
||||
const X_FLOAT xtmp = x(i,0);
|
||||
const X_FLOAT ytmp = x(i,1);
|
||||
const X_FLOAT ztmp = x(i,2);
|
||||
const int jnum = d_numneigh[i];
|
||||
|
||||
int n = 0;
|
||||
for (int jj = 0; jj < jnum; jj++) {
|
||||
int j = d_neighbors(i,jj);
|
||||
j &= NEIGHMASK;
|
||||
|
||||
if (NCOL == 1)
|
||||
if (!(mask[j] & jgroupbit)) continue;
|
||||
|
||||
const int jtype = type[j];
|
||||
const F_FLOAT delx = x(j,0) - xtmp;
|
||||
const F_FLOAT dely = x(j,1) - ytmp;
|
||||
const F_FLOAT delz = x(j,2) - ztmp;
|
||||
const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
|
||||
if (rsq < cutsq) {
|
||||
if (CSTYLE == CUTOFF) {
|
||||
if (NCOL == 1) {
|
||||
if (jtype >= d_typelo[0] && jtype <= d_typehi[0])
|
||||
n++;
|
||||
} else {
|
||||
for (int m = 0; m < ncol; m++)
|
||||
if (jtype >= d_typelo[m] && jtype <= d_typehi[m])
|
||||
d_carray(i,m) += 1.0;
|
||||
}
|
||||
} else if (CSTYLE == ORIENT) {
|
||||
double dot_product = 0.0;
|
||||
for (int m=0; m < 2*(2*l+1); m++) {
|
||||
dot_product += d_normv(i,nqlist+m)*d_normv(j,nqlist+m);
|
||||
}
|
||||
if (dot_product > threshold) n++;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (NCOL == 1 || CSTYLE == ORIENT)
|
||||
d_cvec[i] = n;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
template class ComputeCoordAtomKokkos<LMPDeviceType>;
|
||||
#ifdef KOKKOS_ENABLE_CUDA
|
||||
template class ComputeCoordAtomKokkos<LMPHostType>;
|
||||
#endif
|
||||
}
|
||||
|
|
@ -0,0 +1,78 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
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
|
||||
|
||||
ComputeStyle(coord/atom/kk,ComputeCoordAtomKokkos<LMPDeviceType>)
|
||||
ComputeStyle(coord/atom/kk/device,ComputeCoordAtomKokkos<LMPDeviceType>)
|
||||
ComputeStyle(coord/atom/kk/host,ComputeCoordAtomKokkos<LMPHostType>)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_COMPUTE_COORD_ATOM_KOKKOS_H
|
||||
#define LMP_COMPUTE_COORD_ATOM_KOKKOS_H
|
||||
|
||||
#include "compute_coord_atom.h"
|
||||
#include "kokkos_type.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
template<int CSTYLE, int NCOL>
|
||||
struct TagComputeCoordAtom{};
|
||||
|
||||
template<class DeviceType>
|
||||
class ComputeCoordAtomKokkos : public ComputeCoordAtom {
|
||||
public:
|
||||
typedef DeviceType device_type;
|
||||
typedef ArrayTypes<DeviceType> AT;
|
||||
|
||||
ComputeCoordAtomKokkos(class LAMMPS *, int, char **);
|
||||
virtual ~ComputeCoordAtomKokkos();
|
||||
void init();
|
||||
void compute_peratom();
|
||||
enum {NONE,CUTOFF,ORIENT};
|
||||
|
||||
template<int CSTYLE, int NCOL>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void operator()(TagComputeCoordAtom<CSTYLE,NCOL>, const int&) const;
|
||||
|
||||
private:
|
||||
int inum;
|
||||
|
||||
typename AT::t_x_array_randomread x;
|
||||
typename ArrayTypes<DeviceType>::t_int_1d_randomread type;
|
||||
typename ArrayTypes<DeviceType>::t_int_1d mask;
|
||||
|
||||
typename AT::t_neighbors_2d d_neighbors;
|
||||
typename AT::t_int_1d_randomread d_ilist;
|
||||
typename AT::t_int_1d_randomread d_numneigh;
|
||||
|
||||
typename AT::t_int_1d d_typelo;
|
||||
typename AT::t_int_1d d_typehi;
|
||||
|
||||
DAT::tdual_float_1d k_cvec;
|
||||
typename AT::t_float_1d d_cvec;
|
||||
DAT::tdual_float_2d k_carray;
|
||||
typename AT::t_float_2d d_carray;
|
||||
|
||||
typename AT::t_float_2d d_normv;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
*/
|
||||
|
|
@ -38,7 +38,8 @@ FFT3dKokkos<DeviceType>::FFT3dKokkos(LAMMPS *lmp, MPI_Comm comm, int nfast, int
|
|||
int in_klo, int in_khi,
|
||||
int out_ilo, int out_ihi, int out_jlo, int out_jhi,
|
||||
int out_klo, int out_khi,
|
||||
int scaled, int permute, int *nbuf, int usecollective) :
|
||||
int scaled, int permute, int *nbuf, int usecollective,
|
||||
int usecuda_aware) :
|
||||
Pointers(lmp)
|
||||
{
|
||||
int nthreads = lmp->kokkos->nthreads;
|
||||
|
|
@ -70,7 +71,7 @@ FFT3dKokkos<DeviceType>::FFT3dKokkos(LAMMPS *lmp, MPI_Comm comm, int nfast, int
|
|||
plan = fft_3d_create_plan_kokkos(comm,nfast,nmid,nslow,
|
||||
in_ilo,in_ihi,in_jlo,in_jhi,in_klo,in_khi,
|
||||
out_ilo,out_ihi,out_jlo,out_jhi,out_klo,out_khi,
|
||||
scaled,permute,nbuf,usecollective,nthreads);
|
||||
scaled,permute,nbuf,usecollective,nthreads,usecuda_aware);
|
||||
if (plan == NULL) error->one(FLERR,"Could not create 3d FFT plan");
|
||||
}
|
||||
|
||||
|
|
@ -368,6 +369,7 @@ void FFT3dKokkos<DeviceType>::fft_3d_kokkos(typename FFT_AT::t_FFT_DATA_1d d_in,
|
|||
2 = permute twice = slow->fast, fast->mid, mid->slow
|
||||
nbuf returns size of internal storage buffers used by FFT
|
||||
usecollective use collective MPI operations for remapping data
|
||||
usecuda_aware use CUDA-Aware MPI or not
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
template<class DeviceType>
|
||||
|
|
@ -378,7 +380,7 @@ struct fft_plan_3d_kokkos<DeviceType>* FFT3dKokkos<DeviceType>::fft_3d_create_pl
|
|||
int out_ilo, int out_ihi, int out_jlo, int out_jhi,
|
||||
int out_klo, int out_khi,
|
||||
int scaled, int permute, int *nbuf, int usecollective,
|
||||
int nthreads)
|
||||
int nthreads, int usecuda_aware)
|
||||
{
|
||||
struct fft_plan_3d_kokkos<DeviceType> *plan;
|
||||
int me,nprocs;
|
||||
|
|
@ -435,7 +437,8 @@ struct fft_plan_3d_kokkos<DeviceType>* FFT3dKokkos<DeviceType>::fft_3d_create_pl
|
|||
plan->pre_plan =
|
||||
remapKK->remap_3d_create_plan_kokkos(comm,in_ilo,in_ihi,in_jlo,in_jhi,in_klo,in_khi,
|
||||
first_ilo,first_ihi,first_jlo,first_jhi,
|
||||
first_klo,first_khi,2,0,0,FFT_PRECISION,0);
|
||||
first_klo,first_khi,2,0,0,FFT_PRECISION,
|
||||
usecollective,usecuda_aware);
|
||||
if (plan->pre_plan == NULL) return NULL;
|
||||
}
|
||||
|
||||
|
|
@ -460,7 +463,7 @@ struct fft_plan_3d_kokkos<DeviceType>* FFT3dKokkos<DeviceType>::fft_3d_create_pl
|
|||
first_klo,first_khi,
|
||||
second_ilo,second_ihi,second_jlo,second_jhi,
|
||||
second_klo,second_khi,2,1,0,FFT_PRECISION,
|
||||
usecollective);
|
||||
usecollective,usecuda_aware);
|
||||
if (plan->mid1_plan == NULL) return NULL;
|
||||
|
||||
// 1d FFTs along mid axis
|
||||
|
|
@ -500,7 +503,8 @@ struct fft_plan_3d_kokkos<DeviceType>* FFT3dKokkos<DeviceType>::fft_3d_create_pl
|
|||
second_jlo,second_jhi,second_klo,second_khi,
|
||||
second_ilo,second_ihi,
|
||||
third_jlo,third_jhi,third_klo,third_khi,
|
||||
third_ilo,third_ihi,2,1,0,FFT_PRECISION,usecollective);
|
||||
third_ilo,third_ihi,2,1,0,FFT_PRECISION,
|
||||
usecollective,usecuda_aware);
|
||||
if (plan->mid2_plan == NULL) return NULL;
|
||||
|
||||
// 1d FFTs along slow axis
|
||||
|
|
@ -527,7 +531,8 @@ struct fft_plan_3d_kokkos<DeviceType>* FFT3dKokkos<DeviceType>::fft_3d_create_pl
|
|||
third_klo,third_khi,third_ilo,third_ihi,
|
||||
third_jlo,third_jhi,
|
||||
out_klo,out_khi,out_ilo,out_ihi,
|
||||
out_jlo,out_jhi,2,(permute+1)%3,0,FFT_PRECISION,0);
|
||||
out_jlo,out_jhi,2,(permute+1)%3,0,FFT_PRECISION,
|
||||
usecollective,usecuda_aware);
|
||||
if (plan->post_plan == NULL) return NULL;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -77,7 +77,7 @@ class FFT3dKokkos : protected Pointers {
|
|||
|
||||
FFT3dKokkos(class LAMMPS *, MPI_Comm,
|
||||
int,int,int,int,int,int,int,int,int,int,int,int,int,int,int,
|
||||
int,int,int *,int);
|
||||
int,int,int *,int,int);
|
||||
~FFT3dKokkos();
|
||||
void compute(typename FFT_AT::t_FFT_SCALAR_1d, typename FFT_AT::t_FFT_SCALAR_1d, int);
|
||||
void timing1d(typename FFT_AT::t_FFT_SCALAR_1d, int, int);
|
||||
|
|
@ -95,7 +95,7 @@ class FFT3dKokkos : protected Pointers {
|
|||
struct fft_plan_3d_kokkos<DeviceType> *fft_3d_create_plan_kokkos(MPI_Comm, int, int, int,
|
||||
int, int, int, int, int,
|
||||
int, int, int, int, int, int, int,
|
||||
int, int, int *, int, int);
|
||||
int, int, int *, int, int, int);
|
||||
|
||||
void fft_3d_destroy_plan_kokkos(struct fft_plan_3d_kokkos<DeviceType> *);
|
||||
|
||||
|
|
|
|||
|
|
@ -289,7 +289,10 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI,SIZE>::build(NeighList *list_)
|
|||
if (team_size <= team_size_max) {
|
||||
Kokkos::TeamPolicy<DeviceType> config((mbins+factor-1)/factor,team_size);
|
||||
Kokkos::parallel_for(config, f);
|
||||
} else Kokkos::parallel_for(nall, f); // fall back to flat method
|
||||
} else { // fall back to flat method
|
||||
f.sharedsize = 0;
|
||||
Kokkos::parallel_for(nall, f);
|
||||
}
|
||||
} else
|
||||
Kokkos::parallel_for(nall, f);
|
||||
#else
|
||||
|
|
|
|||
|
|
@ -840,21 +840,23 @@ void PPPMKokkos<DeviceType>::allocate()
|
|||
// 2nd FFT returns data in 3d brick decomposition
|
||||
// remap takes data from 3d brick to FFT decomposition
|
||||
|
||||
int collective_flag = 0; // not yet supported in Kokkos version
|
||||
int cuda_aware_flag = lmp->kokkos->cuda_aware_flag;
|
||||
int tmp;
|
||||
|
||||
fft1 = new FFT3dKokkos<DeviceType>(lmp,world,nx_pppm,ny_pppm,nz_pppm,
|
||||
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
|
||||
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
|
||||
0,0,&tmp,collective_flag);
|
||||
0,0,&tmp,collective_flag,cuda_aware_flag);
|
||||
|
||||
fft2 = new FFT3dKokkos<DeviceType>(lmp,world,nx_pppm,ny_pppm,nz_pppm,
|
||||
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
|
||||
nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
|
||||
0,0,&tmp,collective_flag);
|
||||
0,0,&tmp,collective_flag,cuda_aware_flag);
|
||||
remap = new RemapKokkos<DeviceType>(lmp,world,
|
||||
nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
|
||||
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
|
||||
1,0,0,FFT_PRECISION,collective_flag);
|
||||
1,0,0,FFT_PRECISION,collective_flag,cuda_aware_flag);
|
||||
|
||||
// create ghost grid object for rho and electric field communication
|
||||
|
||||
|
|
|
|||
|
|
@ -38,12 +38,14 @@ RemapKokkos<DeviceType>::RemapKokkos(LAMMPS *lmp, MPI_Comm comm,
|
|||
int out_ilo, int out_ihi, int out_jlo, int out_jhi,
|
||||
int out_klo, int out_khi,
|
||||
int nqty, int permute, int memory,
|
||||
int precision, int usecollective) : Pointers(lmp)
|
||||
int precision, int usecollective,
|
||||
int usecuda_aware) : Pointers(lmp)
|
||||
{
|
||||
plan = remap_3d_create_plan_kokkos(comm,
|
||||
in_ilo,in_ihi,in_jlo,in_jhi,in_klo,in_khi,
|
||||
out_ilo,out_ihi,out_jlo,out_jhi,out_klo,out_khi,
|
||||
nqty,permute,memory,precision,usecollective);
|
||||
nqty,permute,memory,precision,usecollective,
|
||||
usecuda_aware);
|
||||
if (plan == NULL) error->one(FLERR,"Could not create 3d remap plan");
|
||||
}
|
||||
|
||||
|
|
@ -119,20 +121,36 @@ void RemapKokkos<DeviceType>::remap_3d_kokkos(typename FFT_AT::t_FFT_SCALAR_1d d
|
|||
|
||||
// post all recvs into scratch space
|
||||
|
||||
FFT_SCALAR* v_scratch = d_scratch.data();
|
||||
if (!plan->usecuda_aware) {
|
||||
plan->h_scratch = Kokkos::create_mirror_view(d_scratch);
|
||||
v_scratch = plan->h_scratch.data();
|
||||
}
|
||||
|
||||
for (irecv = 0; irecv < plan->nrecv; irecv++) {
|
||||
FFT_SCALAR* scratch = d_scratch.data() + plan->recv_bufloc[irecv];
|
||||
FFT_SCALAR* scratch = v_scratch + plan->recv_bufloc[irecv];
|
||||
MPI_Irecv(scratch,plan->recv_size[irecv],
|
||||
MPI_FFT_SCALAR,plan->recv_proc[irecv],0,
|
||||
plan->comm,&plan->request[irecv]);
|
||||
}
|
||||
|
||||
FFT_SCALAR* v_sendbuf = plan->d_sendbuf.data();
|
||||
if (!plan->usecuda_aware) {
|
||||
plan->h_sendbuf = Kokkos::create_mirror_view(plan->d_sendbuf);
|
||||
v_sendbuf = plan->h_sendbuf.data();
|
||||
}
|
||||
|
||||
// send all messages to other procs
|
||||
|
||||
for (isend = 0; isend < plan->nsend; isend++) {
|
||||
int in_offset = plan->send_offset[isend];
|
||||
plan->pack(d_in,in_offset,
|
||||
plan->d_sendbuf,0,&plan->packplan[isend]);
|
||||
MPI_Send(plan->d_sendbuf.data(),plan->send_size[isend],MPI_FFT_SCALAR,
|
||||
|
||||
if (!plan->usecuda_aware)
|
||||
Kokkos::deep_copy(plan->h_sendbuf,plan->d_sendbuf);
|
||||
|
||||
MPI_Send(v_sendbuf,plan->send_size[isend],MPI_FFT_SCALAR,
|
||||
plan->send_proc[isend],0,plan->comm);
|
||||
}
|
||||
|
||||
|
|
@ -161,6 +179,9 @@ void RemapKokkos<DeviceType>::remap_3d_kokkos(typename FFT_AT::t_FFT_SCALAR_1d d
|
|||
int scratch_offset = plan->recv_bufloc[irecv];
|
||||
int out_offset = plan->recv_offset[irecv];
|
||||
|
||||
if (!plan->usecuda_aware)
|
||||
Kokkos::deep_copy(d_scratch,plan->h_scratch);
|
||||
|
||||
plan->unpack(d_scratch,scratch_offset,
|
||||
d_out,out_offset,&plan->unpackplan[irecv]);
|
||||
}
|
||||
|
|
@ -189,6 +210,7 @@ void RemapKokkos<DeviceType>::remap_3d_kokkos(typename FFT_AT::t_FFT_SCALAR_1d d
|
|||
1 = single precision (4 bytes per datum)
|
||||
2 = double precision (8 bytes per datum)
|
||||
usecollective whether to use collective MPI or point-to-point
|
||||
usecuda_aware whether to use CUDA-Aware MPI or not
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
template<class DeviceType>
|
||||
|
|
@ -198,7 +220,8 @@ struct remap_plan_3d_kokkos<DeviceType>* RemapKokkos<DeviceType>::remap_3d_creat
|
|||
int in_klo, int in_khi,
|
||||
int out_ilo, int out_ihi, int out_jlo, int out_jhi,
|
||||
int out_klo, int out_khi,
|
||||
int nqty, int permute, int memory, int precision, int usecollective)
|
||||
int nqty, int permute, int memory, int precision,
|
||||
int usecollective, int usecuda_aware)
|
||||
{
|
||||
|
||||
struct remap_plan_3d_kokkos<DeviceType> *plan;
|
||||
|
|
@ -216,6 +239,7 @@ struct remap_plan_3d_kokkos<DeviceType>* RemapKokkos<DeviceType>::remap_3d_creat
|
|||
plan = new struct remap_plan_3d_kokkos<DeviceType>;
|
||||
if (plan == NULL) return NULL;
|
||||
plan->usecollective = usecollective;
|
||||
plan->usecuda_aware = usecuda_aware;
|
||||
|
||||
// store parameters in local data structs
|
||||
|
||||
|
|
|
|||
|
|
@ -28,7 +28,9 @@ struct remap_plan_3d_kokkos {
|
|||
typedef DeviceType device_type;
|
||||
typedef FFTArrayTypes<DeviceType> FFT_AT;
|
||||
typename FFT_AT::t_FFT_SCALAR_1d d_sendbuf; // buffer for MPI sends
|
||||
FFT_HAT::t_FFT_SCALAR_1d h_sendbuf; // host buffer for MPI sends
|
||||
typename FFT_AT::t_FFT_SCALAR_1d d_scratch; // scratch buffer for MPI recvs
|
||||
FFT_HAT::t_FFT_SCALAR_1d h_scratch; // host scratch buffer for MPI recvs
|
||||
void (*pack)(typename FFT_AT::t_FFT_SCALAR_1d_um, int, typename FFT_AT::t_FFT_SCALAR_1d_um, int, struct pack_plan_3d *);
|
||||
// which pack function to use
|
||||
void (*unpack)(typename FFT_AT::t_FFT_SCALAR_1d_um, int, typename FFT_AT::t_FFT_SCALAR_1d_um, int, struct pack_plan_3d *);
|
||||
|
|
@ -51,6 +53,7 @@ struct remap_plan_3d_kokkos {
|
|||
int usecollective; // use collective or point-to-point MPI
|
||||
int commringlen; // length of commringlist
|
||||
int *commringlist; // ranks on communication ring of this plan
|
||||
int usecuda_aware; // use CUDA-Aware MPI or not
|
||||
};
|
||||
|
||||
template<class DeviceType>
|
||||
|
|
@ -60,7 +63,7 @@ class RemapKokkos : protected Pointers {
|
|||
typedef FFTArrayTypes<DeviceType> FFT_AT;
|
||||
RemapKokkos(class LAMMPS *);
|
||||
RemapKokkos(class LAMMPS *, MPI_Comm,int,int,int,int,int,int,
|
||||
int,int,int,int,int,int,int,int,int,int,int);
|
||||
int,int,int,int,int,int,int,int,int,int,int,int);
|
||||
~RemapKokkos();
|
||||
void perform(typename FFT_AT::t_FFT_SCALAR_1d, typename FFT_AT::t_FFT_SCALAR_1d, typename FFT_AT::t_FFT_SCALAR_1d);
|
||||
|
||||
|
|
@ -70,7 +73,7 @@ class RemapKokkos : protected Pointers {
|
|||
struct remap_plan_3d_kokkos<DeviceType> *remap_3d_create_plan_kokkos(MPI_Comm,
|
||||
int, int, int, int, int, int,
|
||||
int, int, int, int, int, int,
|
||||
int, int, int, int, int);
|
||||
int, int, int, int, int, int);
|
||||
void remap_3d_destroy_plan_kokkos(struct remap_plan_3d_kokkos<DeviceType> *);
|
||||
};
|
||||
|
||||
|
|
|
|||
|
|
@ -59,7 +59,7 @@ extern "C" {
|
|||
|
||||
typedef int bool_t;
|
||||
|
||||
#if defined(__MINGW32__) || defined(__APPLE__)
|
||||
#if defined(__MINGW32__) || defined(__APPLE__) || defined(__FreeBSD__) || defined(__DragonFly__) || defined(__OpenBSD__) || defined(__NetBSD__)
|
||||
typedef char * caddr_t;
|
||||
typedef unsigned int u_int;
|
||||
#endif
|
||||
|
|
|
|||
|
|
@ -102,7 +102,7 @@ void VerletLRTIntel::setup(int flag)
|
|||
}
|
||||
|
||||
#if defined(_LMP_INTEL_LRT_PTHREAD)
|
||||
#if defined(__linux)
|
||||
#if defined(__linux__)
|
||||
if (comm->me == 0) {
|
||||
cpu_set_t cpuset;
|
||||
sched_getaffinity(0, sizeof(cpuset), &cpuset);
|
||||
|
|
|
|||
|
|
@ -67,8 +67,15 @@ MEAM::meam_setup_global(int nelt, lattice_t* lat, int* ielement, double* /*atwt*
|
|||
case DIA3:
|
||||
this->re_meam[i][i] = tmplat[i] * sqrt(3.0) / 4.0;
|
||||
break;
|
||||
//default:
|
||||
// error
|
||||
case B1:
|
||||
case B2:
|
||||
case C11:
|
||||
case L12:
|
||||
// do nothing
|
||||
break;
|
||||
default:
|
||||
;
|
||||
// error
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -38,6 +38,7 @@ compute momentum, Rupert Nash (University of Edinburgh), r.nash at epcc.ed.ac.uk
|
|||
compute stress/mop, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18
|
||||
compute stress/mop/profile, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18
|
||||
compute temp/rotate, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
|
||||
compute viscosity/cos, Zheng Gong (ENS de Lyon), z.gong@outlook.com, 24 Apr 20
|
||||
compute PRESSURE/GREM, David Stelter, dstelter@bu.edu, 22 Nov 16
|
||||
dihedral_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
|
||||
dihedral_style fourier, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
|
||||
|
|
@ -46,6 +47,7 @@ dihedral_style quadratic, Loukas Peristeras, loukas.peristeras at scienomics.com
|
|||
dihedral_style spherical, Andrew Jewett, jewett.aij@gmail.com, 15 Jul 16
|
||||
dihedral_style table, Andrew Jewett, jewett.aij@gmail.com, 10 Jan 12
|
||||
dihedral_style table/cut, Mike Salerno, ksalerno@pha.jhu.edu, 11 May 18
|
||||
fix accelerate/cos, Zheng Gong (ENS de Lyon), z.gong@outlook.com, 24 Apr 20
|
||||
fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
|
||||
fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015
|
||||
fix electron/stopping, Konstantin Avchaciov, k.avchachov at gmail.com, 26 Feb 2019
|
||||
|
|
|
|||
|
|
@ -0,0 +1,293 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Zheng GONG (ENS de Lyon, z.gong@outlook.com)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <mpi.h>
|
||||
#include "compute_viscosity_cos.h"
|
||||
#include "atom.h"
|
||||
#include "update.h"
|
||||
#include "force.h"
|
||||
#include "domain.h"
|
||||
#include "comm.h"
|
||||
#include "group.h"
|
||||
#include "error.h"
|
||||
#include "math_const.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputeViscosityCos::ComputeViscosityCos(LAMMPS *lmp, int narg, char **arg) :
|
||||
Compute(lmp, narg, arg) {
|
||||
if (narg != 3) error->all(FLERR, "Illegal compute viscosity/cos command");
|
||||
|
||||
scalar_flag = vector_flag = 1;
|
||||
size_vector = 7;
|
||||
extscalar = 0;
|
||||
extvector = -1;
|
||||
extlist = new int[7]{1,1,1,1,1,1,0};
|
||||
tempflag = 1;
|
||||
tempbias = 1;
|
||||
|
||||
maxbias = 0;
|
||||
vbiasall = NULL;
|
||||
|
||||
vector = new double[7];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputeViscosityCos::~ComputeViscosityCos() {
|
||||
if (!copymode)
|
||||
delete[] vector;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeViscosityCos::setup() {
|
||||
dynamic = 0;
|
||||
if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
|
||||
dof_compute();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeViscosityCos::dof_compute() {
|
||||
adjust_dof_fix();
|
||||
natoms_temp = group->count(igroup);
|
||||
dof = domain->dimension * natoms_temp;
|
||||
dof -= extra_dof + fix_dof;
|
||||
if (dof > 0.0) tfactor = force->mvv2e / (dof * force->boltz);
|
||||
else tfactor = 0.0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
void ComputeViscosityCos::calc_V() {
|
||||
double zlo = domain->boxlo[2];
|
||||
double zhi = domain->boxhi[2];
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double *mass = atom->mass;
|
||||
double *rmass = atom->rmass;
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double massone;
|
||||
|
||||
double V_m[2];
|
||||
double V_m_local[2] = {0, 0};
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
if (rmass) massone = rmass[i];
|
||||
else massone = mass[type[i]];
|
||||
|
||||
V_m_local[0] +=
|
||||
2 * massone * v[i][0] * cos(MY_2PI * (x[i][2] - zlo) / (zhi - zlo));
|
||||
V_m_local[1] += massone;
|
||||
}
|
||||
|
||||
MPI_Allreduce(V_m_local, V_m, 2, MPI_DOUBLE, MPI_SUM, world);
|
||||
V = V_m[0] / V_m[1];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double ComputeViscosityCos::compute_scalar() {
|
||||
invoked_scalar = update->ntimestep;
|
||||
|
||||
double zlo = domain->boxlo[2];
|
||||
double zhi = domain->boxhi[2];
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double *mass = atom->mass;
|
||||
double *rmass = atom->rmass;
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double t = 0.0;
|
||||
double vx_acc;
|
||||
double massone;
|
||||
|
||||
calc_V();
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
if (rmass) massone = rmass[i];
|
||||
else massone = mass[type[i]];
|
||||
|
||||
vx_acc = V * cos(MY_2PI * (x[i][2] - zlo) / (zhi - zlo));
|
||||
t += ((v[i][0] - vx_acc) * (v[i][0] - vx_acc) + v[i][1] * v[i][1] +
|
||||
v[i][2] * v[i][2]) * massone;
|
||||
}
|
||||
|
||||
MPI_Allreduce(&t, &scalar, 1, MPI_DOUBLE, MPI_SUM, world);
|
||||
if (dynamic) dof_compute();
|
||||
if (dof < 0.0 && natoms_temp > 0.0)
|
||||
error->all(FLERR, "Temperature compute degrees of freedom < 0");
|
||||
scalar *= tfactor;
|
||||
return scalar;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeViscosityCos::compute_vector() {
|
||||
int i;
|
||||
|
||||
invoked_vector = update->ntimestep;
|
||||
|
||||
double zlo = domain->boxlo[2];
|
||||
double zhi = domain->boxhi[2];
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double *mass = atom->mass;
|
||||
double *rmass = atom->rmass;
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double vx_acc;
|
||||
|
||||
double massone, t[6];
|
||||
for (i = 0; i < 6; i++) t[i] = 0.0;
|
||||
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
if (rmass) massone = rmass[i];
|
||||
else massone = mass[type[i]];
|
||||
|
||||
vx_acc = V * cos(MY_2PI * (x[i][2] - zlo) / (zhi - zlo));
|
||||
t[0] += massone * (v[i][0] - vx_acc) * (v[i][0] - vx_acc);
|
||||
t[1] += massone * v[i][1] * v[i][1];
|
||||
t[2] += massone * v[i][2] * v[i][2];
|
||||
t[3] += massone * (v[i][0] - vx_acc) * v[i][1];
|
||||
t[4] += massone * (v[i][0] - vx_acc) * v[i][2];
|
||||
t[5] += massone * v[i][1] * v[i][2];
|
||||
}
|
||||
|
||||
MPI_Allreduce(t, vector, 6, MPI_DOUBLE, MPI_SUM, world);
|
||||
for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
|
||||
vector[6] = V;
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
remove velocity bias from atom I to leave thermal velocity
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputeViscosityCos::remove_bias(int i, double *v) {
|
||||
|
||||
double zlo = domain->boxlo[2];
|
||||
double zhi = domain->boxhi[2];
|
||||
|
||||
double **x = atom->x;
|
||||
|
||||
vbias[0] = V * cos(MY_2PI * (x[i][2] - zlo) / (zhi - zlo));
|
||||
vbias[1] = 0;
|
||||
vbias[2] = 0;
|
||||
v[0] -= vbias[0];
|
||||
// v[1] -= vbias[1];
|
||||
// v[2] -= vbias[2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
remove velocity bias from atom I to leave thermal velocity
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputeViscosityCos::remove_bias_thr(int i, double *v, double *b) {
|
||||
double zlo = domain->boxlo[2];
|
||||
double zhi = domain->boxhi[2];
|
||||
|
||||
double **x = atom->x;
|
||||
|
||||
b[0] = V * cos(MY_2PI * (x[i][2] - zlo) / (zhi - zlo));
|
||||
b[1] = 0;
|
||||
b[2] = 0;
|
||||
v[0] -= b[0];
|
||||
// v[1] -= b[1];
|
||||
// v[2] -= b[2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
remove velocity bias from all atoms to leave thermal velocity
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputeViscosityCos::remove_bias_all() {
|
||||
double zlo = domain->boxlo[2];
|
||||
double zhi = domain->boxhi[2];
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
vbiasall[i][0] = V * cos(MY_2PI * (x[i][2] - zlo) / (zhi - zlo));
|
||||
vbiasall[i][1] = 0;
|
||||
vbiasall[i][2] = 0;
|
||||
v[i][0] -= vbiasall[i][0];
|
||||
// v[i][1] -= vbiasall[i][1];
|
||||
// v[i][2] -= vbiasall[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
add back in velocity bias to atom I removed by remove_bias()
|
||||
assume remove_bias() was previously called
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputeViscosityCos::restore_bias(int i, double *v) {
|
||||
v[0] += vbias[0];
|
||||
v[1] += vbias[1];
|
||||
v[2] += vbias[2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
add back in velocity bias to atom I removed by remove_bias_thr()
|
||||
assume remove_bias_thr() was previously called with the same buffer b
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputeViscosityCos::restore_bias_thr(int i, double *v, double *b) {
|
||||
v[0] += b[0];
|
||||
v[1] += b[1];
|
||||
v[2] += b[2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
add back in velocity bias to all atoms removed by remove_bias_all()
|
||||
assume remove_bias_all() was previously called
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputeViscosityCos::restore_bias_all() {
|
||||
double **v = atom->v;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
v[i][0] += vbiasall[i][0];
|
||||
v[i][1] += vbiasall[i][1];
|
||||
v[i][2] += vbiasall[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,73 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Zheng GONG (ENS de Lyon, z.gong@outlook.com)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef COMPUTE_CLASS
|
||||
|
||||
ComputeStyle(viscosity/cos,ComputeViscosityCos)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_COMPUTE_VISCOSITY_COS_H
|
||||
#define LMP_COMPUTE_VISCOSITY_COS_H
|
||||
|
||||
#include "compute.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class ComputeViscosityCos : public Compute {
|
||||
public:
|
||||
ComputeViscosityCos(class LAMMPS *, int, char **);
|
||||
virtual ~ComputeViscosityCos();
|
||||
void init() {}
|
||||
void setup();
|
||||
virtual double compute_scalar();
|
||||
virtual void compute_vector();
|
||||
|
||||
void remove_bias(int, double *);
|
||||
void remove_bias_thr(int, double *, double *);
|
||||
void remove_bias_all();
|
||||
void restore_bias(int, double *);
|
||||
void restore_bias_thr(int, double *, double *);
|
||||
void restore_bias_all();
|
||||
|
||||
protected:
|
||||
double tfactor;
|
||||
double V;
|
||||
|
||||
void dof_compute();
|
||||
void calc_V();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Temperature compute degrees of freedom < 0
|
||||
|
||||
This should not happen if you are calculating the temperature
|
||||
on a valid set of atoms.
|
||||
|
||||
*/
|
||||
|
|
@ -0,0 +1,85 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Zheng GONG (ENS de Lyon, z.gong@outlook.com)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "fix_accelerate_cos.h"
|
||||
#include "atom.h"
|
||||
#include "update.h"
|
||||
#include "modify.h"
|
||||
#include "domain.h"
|
||||
#include "region.h"
|
||||
#include "respa.h"
|
||||
#include "input.h"
|
||||
#include "variable.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "math_const.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixAccelerateCos::FixAccelerateCos(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg) {
|
||||
if (narg < 4) error->all(FLERR, "Illegal fix accelerate/cos command");
|
||||
acceleration = force->numeric(FLERR, arg[3]);
|
||||
if (domain->dimension == 2)
|
||||
error->all(FLERR,"Fix accelerate/cos cannot be used with 2d systems");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixAccelerateCos::setmask() {
|
||||
int mask = 0;
|
||||
mask |= POST_FORCE;
|
||||
return mask;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixAccelerateCos::setup(int vflag) {
|
||||
post_force(vflag);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixAccelerateCos::post_force(int vflag) {
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *type = atom->type;
|
||||
double *mass = atom->mass;
|
||||
double *rmass = atom->rmass;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double massone, force_x, acc_x;
|
||||
double zlo = domain->boxlo[2];
|
||||
double zhi = domain->boxhi[2];
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
if (rmass) massone = rmass[i];
|
||||
else massone = mass[type[i]];
|
||||
|
||||
acc_x = acceleration *
|
||||
cos(MathConst::MY_2PI * (x[i][2] - zlo) / (zhi - zlo));
|
||||
force_x = acc_x * massone * force->mvv2e;
|
||||
|
||||
f[i][0] += force_x;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,61 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Zheng GONG (ENS de Lyon, z.gong@outlook.com)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(accelerate/cos,FixAccelerateCos)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_ACCELERATE_COS_H
|
||||
#define LMP_FIX_ACCELERATE_COS_H
|
||||
|
||||
#include "fix.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixAccelerateCos: public Fix {
|
||||
public:
|
||||
FixAccelerateCos(class LAMMPS *, int, char **);
|
||||
virtual ~FixAccelerateCos() {};
|
||||
int setmask();
|
||||
virtual void init() {};
|
||||
void setup(int);
|
||||
virtual void post_force(int);
|
||||
|
||||
protected:
|
||||
double acceleration;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Fix accelerate/cos cannot be used with 2d systems
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
*/
|
||||
|
|
@ -495,7 +495,7 @@ void FixAveCorrelateLong::end_of_step()
|
|||
if(overwrite) fseek(fp,filepos,SEEK_SET);
|
||||
fprintf(fp,"# Timestep: " BIGINT_FORMAT "\n", ntimestep);
|
||||
for (unsigned int i=0;i<npcorr;++i) {
|
||||
fprintf(fp, "%lg ", t[i]*update->dt);
|
||||
fprintf(fp, "%lg ", t[i]*update->dt*nevery);
|
||||
for (int j=0;j<npair;++j) {
|
||||
fprintf(fp, "%lg ", f[j][i]);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1237,7 +1237,7 @@ void *imdsock_accept(void * v) {
|
|||
#elif defined(SOCKLEN_T)
|
||||
SOCKLEN_T len;
|
||||
#define _SOCKLEN_TYPE SOCKLEN_T
|
||||
#elif defined(_POSIX_SOURCE) || (defined(__APPLE__) && defined(__MACH__)) || defined(__linux)
|
||||
#elif defined(_POSIX_SOURCE) || (defined(__APPLE__) && defined(__MACH__)) || defined(__linux__) || defined(__FreeBSD__) || defined(__DragonFly__) || defined(__OpenBSD__) || defined(__NetBSD__)
|
||||
socklen_t len;
|
||||
#define _SOCKLEN_TYPE socklen_t
|
||||
#else
|
||||
|
|
|
|||
|
|
@ -717,6 +717,7 @@ void PairMEAMSpline::SplineFunction::prepareSpline(Error* error)
|
|||
Y2[i] /= h*6.0;
|
||||
#endif
|
||||
}
|
||||
inv_h = (1/h);
|
||||
xmax_shifted = xmax - xmin;
|
||||
}
|
||||
|
||||
|
|
@ -732,6 +733,7 @@ void PairMEAMSpline::SplineFunction::communicate(MPI_Comm& world, int me)
|
|||
MPI_Bcast(&isGridSpline, 1, MPI_INT, 0, world);
|
||||
MPI_Bcast(&h, 1, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&hsq, 1, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&inv_h, 1, MPI_DOUBLE, 0, world);
|
||||
if(me != 0) {
|
||||
X = new double[N];
|
||||
Xs = new double[N];
|
||||
|
|
|
|||
|
|
@ -142,7 +142,7 @@ protected:
|
|||
((a*a*a - a) * Y2[klo] + (b*b*b - b) * Y2[khi])*(h*h)/6.0;
|
||||
#else
|
||||
// For a spline with regular grid, we directly calculate the interval X is in.
|
||||
int klo = (int)(x / h);
|
||||
int klo = (int)(x*inv_h);
|
||||
int khi = klo + 1;
|
||||
double a = Xs[khi] - x;
|
||||
double b = h - a;
|
||||
|
|
@ -186,7 +186,7 @@ protected:
|
|||
(b*b*b - b) * Y2[khi]) * (h*h) / 6.0;
|
||||
#else
|
||||
// For a spline with regular grid, we directly calculate the interval X is in.
|
||||
int klo = (int)(x / h);
|
||||
int klo = (int)(x*inv_h);
|
||||
int khi = klo + 1;
|
||||
double a = Xs[khi] - x;
|
||||
double b = h - a;
|
||||
|
|
@ -224,6 +224,7 @@ protected:
|
|||
int isGridSpline;// Indicates that all spline knots are on a regular grid.
|
||||
double h; // The distance between knots if this is a grid spline with equidistant knots.
|
||||
double hsq; // The squared distance between knots if this is a grid spline with equidistant knots.
|
||||
double inv_h; // (1/h), used to avoid numerical errors in binnning for grid spline with equidistant knots.
|
||||
double xmax_shifted; // The end of the spline interval after it has been shifted to begin at X=0.
|
||||
};
|
||||
|
||||
|
|
|
|||
|
|
@ -674,6 +674,7 @@ void PairMEAMSWSpline::SplineFunction::prepareSpline(Error* error)
|
|||
Y2[i] /= h*6.0;
|
||||
#endif
|
||||
}
|
||||
inv_h = 1/h;
|
||||
xmax_shifted = xmax - xmin;
|
||||
}
|
||||
|
||||
|
|
@ -689,6 +690,7 @@ void PairMEAMSWSpline::SplineFunction::communicate(MPI_Comm& world, int me)
|
|||
MPI_Bcast(&isGridSpline, 1, MPI_INT, 0, world);
|
||||
MPI_Bcast(&h, 1, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&hsq, 1, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&inv_h, 1, MPI_DOUBLE, 0, world);
|
||||
if(me != 0) {
|
||||
X = new double[N];
|
||||
Xs = new double[N];
|
||||
|
|
|
|||
|
|
@ -130,7 +130,7 @@ protected:
|
|||
#else
|
||||
// For a spline with grid points, we can directly calculate the interval X is in.
|
||||
//
|
||||
int klo = (int)(x / h);
|
||||
int klo = (int)(x*inv_h);
|
||||
if ( klo > N - 2 ) klo = N - 2;
|
||||
int khi = klo + 1;
|
||||
double a = Xs[khi] - x;
|
||||
|
|
@ -170,7 +170,7 @@ protected:
|
|||
return a * Y[klo] + b * Y[khi] + ((a*a*a - a) * Y2[klo] + (b*b*b - b) * Y2[khi]) * (h*h) / 6.0;
|
||||
#else
|
||||
// For a spline with grid points, we can directly calculate the interval X is in.
|
||||
int klo = (int)(x / h);
|
||||
int klo = (int)(x*inv_h);
|
||||
if ( klo > N - 2 ) klo = N - 2;
|
||||
int khi = klo + 1;
|
||||
double a = Xs[khi] - x;
|
||||
|
|
@ -207,6 +207,7 @@ protected:
|
|||
int isGridSpline; // Indicates that all spline knots are on a regular grid.
|
||||
double h; // The distance between knots if this is a grid spline with equidistant knots.
|
||||
double hsq; // The squared distance between knots if this is a grid spline with equidistant knots.
|
||||
double inv_h; // (1/h), used to avoid numerical errors in binnning for grid spline with equidistant knots.
|
||||
double xmax_shifted; // The end of the spline interval after it has been shifted to begin at X=0.
|
||||
};
|
||||
|
||||
|
|
|
|||
|
|
@ -508,7 +508,7 @@ int PairReaxCOMP::estimate_reax_lists()
|
|||
num_nbrs += numneigh[i];
|
||||
}
|
||||
|
||||
int new_estimate = MAX (num_nbrs, mincap*MIN_NBRS);
|
||||
int new_estimate = MAX(num_nbrs, mincap*REAX_MIN_NBRS);
|
||||
|
||||
return new_estimate;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -310,7 +310,7 @@ void Validate_ListsOMP(reax_system *system, storage * /*workspace*/, reax_list *
|
|||
Hindex = system->my_atoms[i].Hindex;
|
||||
if (Hindex > -1) {
|
||||
system->my_atoms[i].num_hbonds =
|
||||
(int)(MAX( Num_Entries(Hindex, hbonds)*saferzone, MIN_HBONDS ));
|
||||
(int)(MAX(Num_Entries(Hindex,hbonds)*saferzone,system->minhbonds));
|
||||
|
||||
if (Hindex < numH-1)
|
||||
comp = Start_Index(Hindex+1, hbonds);
|
||||
|
|
|
|||
|
|
@ -68,7 +68,7 @@ int Init_ListsOMP(reax_system *system, control_params *control,
|
|||
system->my_atoms[i].num_hbonds = hb_top[i];
|
||||
total_hbonds += hb_top[i];
|
||||
}
|
||||
total_hbonds = (int)(MAX( total_hbonds*saferzone, mincap*MIN_HBONDS ));
|
||||
total_hbonds = (int)(MAX(total_hbonds*saferzone,mincap*system->minhbonds));
|
||||
|
||||
if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND,
|
||||
*lists+HBONDS ) ) {
|
||||
|
|
|
|||
|
|
@ -43,11 +43,8 @@ using namespace LAMMPS_NS;
|
|||
using namespace FixConst;
|
||||
|
||||
#define EV_TO_KCAL_PER_MOL 14.4
|
||||
//#define DANGER_ZONE 0.95
|
||||
//#define LOOSE_ZONE 0.7
|
||||
#define SQR(x) ((x)*(x))
|
||||
#define CUBE(x) ((x)*(x)*(x))
|
||||
#define MIN_NBRS 100
|
||||
|
||||
static const char cite_fix_qeq_reax[] =
|
||||
"fix qeq/reax command:\n\n"
|
||||
|
|
@ -300,8 +297,8 @@ void FixQEqReax::allocate_matrix()
|
|||
mincap = reaxc->system->mincap;
|
||||
safezone = reaxc->system->safezone;
|
||||
} else {
|
||||
mincap = MIN_CAP;
|
||||
safezone = SAFE_ZONE;
|
||||
mincap = REAX_MIN_CAP;
|
||||
safezone = REAX_SAFE_ZONE;
|
||||
}
|
||||
|
||||
n = atom->nlocal;
|
||||
|
|
@ -324,7 +321,7 @@ void FixQEqReax::allocate_matrix()
|
|||
i = ilist[ii];
|
||||
m += numneigh[i];
|
||||
}
|
||||
m_cap = MAX( (int)(m * safezone), mincap * MIN_NBRS);
|
||||
m_cap = MAX( (int)(m * safezone), mincap * REAX_MIN_NBRS);
|
||||
|
||||
H.n = n_cap;
|
||||
H.m = m_cap;
|
||||
|
|
|
|||
|
|
@ -244,9 +244,10 @@ void PairReaxC::settings(int narg, char **arg)
|
|||
qeqflag = 1;
|
||||
control->lgflag = 0;
|
||||
control->enobondsflag = 1;
|
||||
system->mincap = MIN_CAP;
|
||||
system->safezone = SAFE_ZONE;
|
||||
system->saferzone = SAFER_ZONE;
|
||||
system->mincap = REAX_MIN_CAP;
|
||||
system->minhbonds = REAX_MIN_HBONDS;
|
||||
system->safezone = REAX_SAFE_ZONE;
|
||||
system->saferzone = REAX_SAFER_ZONE;
|
||||
|
||||
// process optional keywords
|
||||
|
||||
|
|
@ -265,7 +266,7 @@ void PairReaxC::settings(int narg, char **arg)
|
|||
else if (strcmp(arg[iarg+1],"no") == 0) control->enobondsflag = 0;
|
||||
else error->all(FLERR,"Illegal pair_style reax/c command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"lgvdw") == 0) {
|
||||
} else if (strcmp(arg[iarg],"lgvdw") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style reax/c command");
|
||||
if (strcmp(arg[iarg+1],"yes") == 0) control->lgflag = 1;
|
||||
else if (strcmp(arg[iarg+1],"no") == 0) control->lgflag = 0;
|
||||
|
|
@ -284,6 +285,12 @@ void PairReaxC::settings(int narg, char **arg)
|
|||
if (system->mincap < 0)
|
||||
error->all(FLERR,"Illegal pair_style reax/c mincap command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"minhbonds") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style reax/c command");
|
||||
system->minhbonds = force->inumeric(FLERR,arg[iarg+1]);
|
||||
if (system->minhbonds < 0)
|
||||
error->all(FLERR,"Illegal pair_style reax/c minhbonds command");
|
||||
iarg += 2;
|
||||
} else error->all(FLERR,"Illegal pair_style reax/c command");
|
||||
}
|
||||
|
||||
|
|
@ -712,7 +719,7 @@ int PairReaxC::estimate_reax_lists()
|
|||
|
||||
free( marked );
|
||||
|
||||
return static_cast<int> (MAX( num_nbrs*safezone, mincap*MIN_NBRS ));
|
||||
return static_cast<int> (MAX(num_nbrs*safezone, mincap*REAX_MIN_NBRS));
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
|
|
|||
|
|
@ -340,7 +340,7 @@ static int Reallocate_HBonds_List( reax_system *system, reax_list *hbonds )
|
|||
if ((system->my_atoms[i].Hindex) >= 0) {
|
||||
total_hbonds += system->my_atoms[i].num_hbonds;
|
||||
}
|
||||
total_hbonds = (int)(MAX( total_hbonds*saferzone, mincap*MIN_HBONDS ));
|
||||
total_hbonds = (int)(MAX(total_hbonds*saferzone, mincap*system->minhbonds));
|
||||
|
||||
Delete_List( hbonds);
|
||||
if (!Make_List( system->Hcap, total_hbonds, TYP_HBOND, hbonds )) {
|
||||
|
|
@ -456,7 +456,7 @@ void ReAllocate( reax_system *system, control_params *control,
|
|||
}
|
||||
|
||||
newsize = static_cast<int>
|
||||
(MAX( realloc->num_far*safezone, mincap*MIN_NBRS ));
|
||||
(MAX( realloc->num_far*safezone, mincap*REAX_MIN_NBRS));
|
||||
|
||||
Reallocate_Neighbor_List( far_nbrs, system->total_cap, newsize);
|
||||
realloc->num_far = 0;
|
||||
|
|
|
|||
|
|
@ -75,37 +75,32 @@
|
|||
#define MAX_TOKENS 1024
|
||||
#define MAX_TOKEN_LEN 1024
|
||||
|
||||
#define MAX_ATOM_ID 100000
|
||||
#define MAX_RESTRICT 15
|
||||
#define MAX_MOLECULE_SIZE 20
|
||||
#define MAX_ATOM_TYPES 25
|
||||
|
||||
#define NUM_INTRS 10
|
||||
#define ALMOST_ZERO 1e-10
|
||||
#define NEG_INF -1e10
|
||||
#define NO_BOND 1e-3 // 0.001
|
||||
#define HB_THRESHOLD 1e-2 // 0.01
|
||||
|
||||
#define MIN_CAP 50
|
||||
#define MIN_NBRS 100
|
||||
#define MIN_HENTRIES 100
|
||||
#define MAX_BONDS 30
|
||||
#define MIN_BONDS 25
|
||||
#define MIN_HBONDS 25
|
||||
#define MIN_3BODIES 1000
|
||||
#define MIN_GCELL_POPL 50
|
||||
#define MIN_SEND 100
|
||||
#define SAFE_ZONE 1.2
|
||||
#define SAFER_ZONE 1.4
|
||||
#define DANGER_ZONE 0.90
|
||||
#define LOOSE_ZONE 0.75
|
||||
#define MAX_3BODY_PARAM 5
|
||||
#define MAX_4BODY_PARAM 5
|
||||
#define REAX_MIN_CAP 50
|
||||
#define REAX_MIN_NBRS 100
|
||||
#define MIN_HENTRIES 100
|
||||
#define MAX_BONDS 30
|
||||
#define MIN_BONDS 25
|
||||
#define REAX_MIN_HBONDS 25
|
||||
#define MIN_3BODIES 1000
|
||||
#define MIN_GCELL_POPL 50
|
||||
#define MIN_SEND 100
|
||||
#define REAX_SAFE_ZONE 1.2
|
||||
#define REAX_SAFER_ZONE 1.4
|
||||
#define DANGER_ZONE 0.90
|
||||
#define LOOSE_ZONE 0.75
|
||||
#define MAX_3BODY_PARAM 5
|
||||
#define MAX_4BODY_PARAM 5
|
||||
|
||||
#define MAX_dV 1.01
|
||||
#define MIN_dV 0.99
|
||||
#define MAX_dT 4.00
|
||||
#define MIN_dT 0.00
|
||||
#define MAX_dV 1.01
|
||||
#define MIN_dV 0.99
|
||||
#define MAX_dT 4.00
|
||||
#define MIN_dT 0.00
|
||||
|
||||
#define MASTER_NODE 0
|
||||
#define MAX_NBRS 6 //27
|
||||
|
|
|
|||
|
|
@ -152,7 +152,7 @@ void Validate_Lists( reax_system *system, storage * /*workspace*/, reax_list **l
|
|||
Hindex = system->my_atoms[i].Hindex;
|
||||
if (Hindex > -1) {
|
||||
system->my_atoms[i].num_hbonds =
|
||||
(int)(MAX( Num_Entries(Hindex, hbonds)*saferzone, MIN_HBONDS ));
|
||||
(int)(MAX(Num_Entries(Hindex, hbonds)*saferzone, system->minhbonds));
|
||||
|
||||
//if( Num_Entries(i, hbonds) >=
|
||||
//(Start_Index(i+1,hbonds)-Start_Index(i,hbonds))*0.90/*DANGER_ZONE*/){
|
||||
|
|
@ -423,7 +423,7 @@ void Estimate_Storages( reax_system *system, control_params *control,
|
|||
|
||||
*Htop = (int)(MAX( *Htop * safezone, mincap * MIN_HENTRIES ));
|
||||
for( i = 0; i < system->n; ++i )
|
||||
hb_top[i] = (int)(MAX( hb_top[i] * saferzone, MIN_HBONDS ));
|
||||
hb_top[i] = (int)(MAX(hb_top[i] * saferzone, system->minhbonds));
|
||||
|
||||
for( i = 0; i < system->N; ++i ) {
|
||||
*num_3body += SQR(bond_top[i]);
|
||||
|
|
|
|||
|
|
@ -179,7 +179,7 @@ int Init_Lists( reax_system *system, control_params *control,
|
|||
system->my_atoms[i].num_hbonds = hb_top[i];
|
||||
total_hbonds += hb_top[i];
|
||||
}
|
||||
total_hbonds = (int)(MAX( total_hbonds*saferzone, mincap*MIN_HBONDS ));
|
||||
total_hbonds = (int)(MAX(total_hbonds*saferzone,mincap*system->minhbonds));
|
||||
|
||||
if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND,
|
||||
*lists+HBONDS ) ) {
|
||||
|
|
|
|||
|
|
@ -27,7 +27,6 @@
|
|||
#include "reaxc_lookup.h"
|
||||
#include <mpi.h>
|
||||
#include <cstdlib>
|
||||
#include "reaxc_defs.h"
|
||||
#include "reaxc_nonbonded.h"
|
||||
#include "reaxc_tool_box.h"
|
||||
|
||||
|
|
@ -153,7 +152,7 @@ int Init_Lookup_Tables( reax_system *system, control_params *control,
|
|||
{
|
||||
int i, j, r;
|
||||
int num_atom_types;
|
||||
int existing_types[MAX_ATOM_TYPES], aggregated[MAX_ATOM_TYPES];
|
||||
int existing_types[REAX_MAX_ATOM_TYPES], aggregated[REAX_MAX_ATOM_TYPES];
|
||||
double dr;
|
||||
double *h, *fh, *fvdw, *fele, *fCEvd, *fCEclmb;
|
||||
double v0_vdw, v0_ele, vlast_vdw, vlast_ele;
|
||||
|
|
@ -186,12 +185,12 @@ int Init_Lookup_Tables( reax_system *system, control_params *control,
|
|||
LR[i] = (LR_lookup_table*)
|
||||
scalloc(system->error_ptr, num_atom_types, sizeof(LR_lookup_table), "lookup:LR[i]");
|
||||
|
||||
for( i = 0; i < MAX_ATOM_TYPES; ++i )
|
||||
for( i = 0; i < REAX_MAX_ATOM_TYPES; ++i )
|
||||
existing_types[i] = 0;
|
||||
for( i = 0; i < system->n; ++i )
|
||||
existing_types[ system->my_atoms[i].type ] = 1;
|
||||
|
||||
MPI_Allreduce( existing_types, aggregated, MAX_ATOM_TYPES,
|
||||
MPI_Allreduce( existing_types, aggregated, REAX_MAX_ATOM_TYPES,
|
||||
MPI_INT, MPI_SUM, mpi_data->world );
|
||||
|
||||
for( i = 0; i < num_atom_types; ++i ) {
|
||||
|
|
|
|||
|
|
@ -39,11 +39,11 @@ int Reallocate_Output_Buffer( LAMMPS_NS::Error *error_ptr, output_controls *out_
|
|||
if (out_control->buffer_len > 0)
|
||||
free( out_control->buffer );
|
||||
|
||||
out_control->buffer_len = (int)(req_space*SAFE_ZONE);
|
||||
out_control->buffer_len = (int)(req_space*REAX_SAFE_ZONE);
|
||||
out_control->buffer = (char*) malloc(out_control->buffer_len*sizeof(char));
|
||||
if (out_control->buffer == NULL) {
|
||||
char errmsg[256];
|
||||
snprintf(errmsg, 256, "Insufficient memory for required buffer size %d", (int) (req_space*SAFE_ZONE));
|
||||
snprintf(errmsg, 256, "Insufficient memory for required buffer size %d", (int) (req_space*REAX_SAFE_ZONE));
|
||||
error_ptr->one(FLERR,errmsg);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -409,7 +409,7 @@ struct _reax_system
|
|||
class LAMMPS_NS::Error *error_ptr;
|
||||
class LAMMPS_NS::Pair *pair_ptr;
|
||||
int my_bonds;
|
||||
int mincap;
|
||||
int mincap,minhbonds;
|
||||
double safezone, saferzone;
|
||||
|
||||
_LR_lookup_table **LR;
|
||||
|
|
|
|||
|
|
@ -27,6 +27,7 @@
|
|||
#include "group.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "utils.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -93,7 +94,7 @@ ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
|
|||
int iorientorder = modify->find_compute(id_orientorder);
|
||||
if (iorientorder < 0)
|
||||
error->all(FLERR,"Could not find compute coord/atom compute ID");
|
||||
if (strcmp(modify->compute[iorientorder]->style,"orientorder/atom") != 0)
|
||||
if (!utils::strmatch(modify->compute[iorientorder]->style,"^orientorder/atom"))
|
||||
error->all(FLERR,"Compute coord/atom compute ID is not orientorder/atom");
|
||||
|
||||
threshold = force->numeric(FLERR,arg[5]);
|
||||
|
|
@ -119,6 +120,8 @@ ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
|
|||
|
||||
ComputeCoordAtom::~ComputeCoordAtom()
|
||||
{
|
||||
if (copymode) return;
|
||||
|
||||
delete [] group2;
|
||||
delete [] typelo;
|
||||
delete [] typehi;
|
||||
|
|
@ -138,7 +141,7 @@ void ComputeCoordAtom::init()
|
|||
l = c_orientorder->qlcomp;
|
||||
// communicate real and imaginary 2*l+1 components of the normalized vector
|
||||
comm_forward = 2*(2*l+1);
|
||||
if (c_orientorder->iqlcomp < 0)
|
||||
if (!(c_orientorder->qlcompflag))
|
||||
error->all(FLERR,"Compute coord/atom requires components "
|
||||
"option in compute orientorder/atom");
|
||||
}
|
||||
|
|
|
|||
|
|
@ -27,16 +27,16 @@ namespace LAMMPS_NS {
|
|||
class ComputeCoordAtom : public Compute {
|
||||
public:
|
||||
ComputeCoordAtom(class LAMMPS *, int, char **);
|
||||
~ComputeCoordAtom();
|
||||
void init();
|
||||
virtual ~ComputeCoordAtom();
|
||||
virtual void init();
|
||||
void init_list(int, class NeighList *);
|
||||
void compute_peratom();
|
||||
virtual void compute_peratom();
|
||||
int pack_forward_comm(int, int *, double *, int, int *);
|
||||
void unpack_forward_comm(int, int, double *);
|
||||
double memory_usage();
|
||||
enum {NONE,CUTOFF,ORIENT};
|
||||
|
||||
private:
|
||||
protected:
|
||||
int nmax,ncol;
|
||||
double cutsq;
|
||||
class NeighList *list;
|
||||
|
|
|
|||
|
|
@ -306,12 +306,12 @@ double FixHalt::tlimit()
|
|||
/* ----------------------------------------------------------------------
|
||||
determine available disk space, if supported. Return -1 if not.
|
||||
------------------------------------------------------------------------- */
|
||||
#if defined(__linux) || defined(__APPLE__)
|
||||
#if defined(__linux__) || defined(__APPLE__) || defined(__FreeBSD__) || defined(__DragonFly__) || defined(__OpenBSD__) || defined(__NetBSD__)
|
||||
#include <sys/statvfs.h>
|
||||
#endif
|
||||
double FixHalt::diskfree()
|
||||
{
|
||||
#if defined(__linux) || defined(__APPLE__)
|
||||
#if defined(__linux__) || defined(__APPLE__) || defined(__FreeBSD__) || defined(__DragonFly__) || defined(__OpenBSD__) || defined(__NetBSD__)
|
||||
struct statvfs fs;
|
||||
double disk_free = -1.0;
|
||||
|
||||
|
|
@ -319,9 +319,9 @@ double FixHalt::diskfree()
|
|||
disk_free = 1.0e100;
|
||||
int rv = statvfs(dlimit_path,&fs);
|
||||
if (rv == 0) {
|
||||
#if defined(__linux)
|
||||
#if defined(__linux__)
|
||||
disk_free = fs.f_bavail*fs.f_bsize/1048576.0;
|
||||
#elif defined(__APPLE__)
|
||||
#elif defined(__APPLE__) || defined(__FreeBSD__) || defined(__DragonFly__) || defined(__OpenBSD__) || defined(__NetBSD__)
|
||||
disk_free = fs.f_bavail*fs.f_frsize/1048576.0;
|
||||
#endif
|
||||
} else
|
||||
|
|
|
|||
|
|
@ -44,8 +44,9 @@ enum{BOND,LBOUND,ANGLE,DIHEDRAL};
|
|||
|
||||
FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg),
|
||||
rstyle(NULL), mult(NULL), ids(NULL), kstart(NULL), kstop(NULL), target(NULL),
|
||||
deqstart(NULL), deqstop(NULL), cos_target(NULL), sin_target(NULL)
|
||||
rstyle(NULL), mult(NULL), ids(NULL), kstart(NULL), kstop(NULL),
|
||||
deqstart(NULL), deqstop(NULL), target(NULL), cos_target(NULL),
|
||||
sin_target(NULL)
|
||||
{
|
||||
if (narg < 4) error->all(FLERR,"Illegal fix restrain command");
|
||||
|
||||
|
|
|
|||
|
|
@ -60,7 +60,7 @@
|
|||
#include <sys/utsname.h>
|
||||
#endif
|
||||
|
||||
#if defined(__linux)
|
||||
#if defined(__linux__)
|
||||
#include <malloc.h>
|
||||
#endif
|
||||
|
||||
|
|
@ -345,7 +345,7 @@ void Info::command(int narg, char **arg)
|
|||
fprintf(out,"Maximum working set size: %.4g Mbyte\n",
|
||||
(double)pmc.PeakWorkingSetSize/1048576.0);
|
||||
#else
|
||||
#if defined(__linux)
|
||||
#if defined(__linux__)
|
||||
struct mallinfo mi;
|
||||
mi = mallinfo();
|
||||
fprintf(out,"Current reserved memory pool size: %.4g Mbyte\n",
|
||||
|
|
|
|||
|
|
@ -201,7 +201,7 @@ void RanMars::select_subset(bigint ntarget, int nmine, int *mark, int *next)
|
|||
|
||||
for (int i = 0; i < nmine; i++) mark[i] = 0;
|
||||
for (int i = 0; i < nmine; i++) next[i] = i+1;
|
||||
next[nmine-1] = -1;
|
||||
if (nmine > 0) next[nmine-1] = -1;
|
||||
|
||||
nmark = 0;
|
||||
niter = 0;
|
||||
|
|
@ -241,7 +241,7 @@ void RanMars::select_subset(bigint ntarget, int nmine, int *mark, int *next)
|
|||
// flip each value based on RN < thresh
|
||||
|
||||
nflip = 0;
|
||||
while (index >= 0) {
|
||||
while ((nmine > 0) && (index >= 0)) {
|
||||
if (uniform() < thresh) {
|
||||
mark[index] = newvalue;
|
||||
nflip++;
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@
|
|||
#include "lammps.h"
|
||||
#include "error.h"
|
||||
|
||||
#if defined(__linux)
|
||||
#if defined(__linux__)
|
||||
#include <unistd.h> // for readlink
|
||||
#endif
|
||||
|
||||
|
|
@ -95,7 +95,7 @@ static const char *guesspath(char *buf, int len, FILE *fp)
|
|||
{
|
||||
memset(buf,0,len);
|
||||
|
||||
#if defined(__linux)
|
||||
#if defined(__linux__)
|
||||
char procpath[32];
|
||||
int fd = fileno(fp);
|
||||
snprintf(procpath,32,"/proc/self/fd/%d",fd);
|
||||
|
|
|
|||
|
|
@ -1 +1 @@
|
|||
#define LAMMPS_VERSION "15 Apr 2020"
|
||||
#define LAMMPS_VERSION "5 May 2020"
|
||||
|
|
|
|||
|
|
@ -7,16 +7,35 @@ From: centos:7
|
|||
yum -y install vim-enhanced \
|
||||
ccache gcc-c++ gcc-gfortran clang gdb valgrind-openmpi \
|
||||
make cmake cmake3 ninja-build patch which file git Lmod \
|
||||
libpng-devel libjpeg-devel openmpi-devel mpich-devel python-devel \
|
||||
python-virtualenv fftw-devel voro++-devel eigen3-devel gsl-devel openblas-devel enchant
|
||||
libpng-devel libjpeg-devel openmpi-devel mpich-devel python-devel python36-devel \
|
||||
hdf5-devel python36-virtualenv python36-pip python-pip \
|
||||
netcdf-devel netcdf-cxx-devel netcdf-mpich-devel netcdf-openmpi-devel \
|
||||
python-virtualenv fftw-devel voro++-devel eigen3-devel gsl-devel openblas-devel enchant \
|
||||
blas-devel lapack-devel
|
||||
yum clean all
|
||||
|
||||
%environment
|
||||
LC_ALL=C
|
||||
export LC_ALL
|
||||
|
||||
# we need to reset any module variables
|
||||
# inherited from the host.
|
||||
unset __LMOD_REF_COUNT__LMFILES_
|
||||
unset __LMOD_REF_COUNT_PATH
|
||||
unset __LMOD_REF_COUNT_LD_LIBRARY_PATH
|
||||
unset __LMOD_REF_COUNT_MANPATH
|
||||
unset __LMOD_REF_COUNT_MODULEPATH
|
||||
unset __LMOD_REF_COUNT_LOADEDMODULES
|
||||
unset _LMFILES_
|
||||
unset MODULEPATH
|
||||
unset MODULESHOME
|
||||
unset MODULEPATH_ROOT
|
||||
unset LOADEDMODULES
|
||||
. /etc/profile.d/z00_lmod.sh
|
||||
module purge
|
||||
unset LMOD_SYSTEM_DEFAULT_MODULES
|
||||
|
||||
# load MPI by default
|
||||
. /etc/profile
|
||||
module load mpi
|
||||
|
||||
%labels
|
||||
Author akohlmey
|
||||
Author akohlmey, rbberger
|
||||
|
|
|
|||
|
|
@ -8,21 +8,39 @@ From: centos:8
|
|||
dnf -y install vim-enhanced git file make cmake patch which file ninja-build \
|
||||
ccache gcc-c++ gcc-gfortran clang gdb valgrind libubsan libasan libtsan \
|
||||
eigen3-devel openblas-devel libpng-devel libjpeg-devel platform-python-devel \
|
||||
openmpi-devel mpich-devel fftw-devel voro++-devel gsl-devel \
|
||||
openmpi-devel mpich-devel fftw-devel voro++-devel gsl-devel hdf5-devel \
|
||||
netcdf-devel netcdf-cxx-devel netcdf-mpich-devel netcdf-openmpi-devel \
|
||||
enchant python3-virtualenv doxygen \
|
||||
texlive-latex-fonts texlive-pslatex texlive-collection-latexrecommended \
|
||||
texlive-latex texlive-latexconfig doxygen-latex texlive-collection-latex \
|
||||
texlive-latex-bin texlive-lualatex-math texlive-fncychap texlive-tabulary \
|
||||
texlive-framed texlive-wrapfig texlive-upquote texlive-capt-of \
|
||||
texlive-needspace texlive-titlesec texlive-anysize texlive-dvipng
|
||||
texlive-needspace texlive-titlesec texlive-anysize texlive-dvipng \
|
||||
blas-devel lapack-devel
|
||||
dnf clean all
|
||||
|
||||
%environment
|
||||
LC_ALL=C
|
||||
export LC_ALL
|
||||
|
||||
# we need to reset any module variables
|
||||
# inherited from the host.
|
||||
unset __LMOD_REF_COUNT__LMFILES_
|
||||
unset __LMOD_REF_COUNT_PATH
|
||||
unset __LMOD_REF_COUNT_LD_LIBRARY_PATH
|
||||
unset __LMOD_REF_COUNT_MANPATH
|
||||
unset __LMOD_REF_COUNT_MODULEPATH
|
||||
unset __LMOD_REF_COUNT_LOADEDMODULES
|
||||
unset _LMFILES_
|
||||
unset MODULEPATH
|
||||
unset MODULESHOME
|
||||
unset MODULEPATH_ROOT
|
||||
unset LOADEDMODULES
|
||||
. /etc/profile.d/modules.sh
|
||||
module purge
|
||||
unset LMOD_SYSTEM_DEFAULT_MODULES
|
||||
|
||||
# load MPI by default
|
||||
. /etc/profile
|
||||
module load mpi
|
||||
|
||||
%labels
|
||||
Author akohlmey
|
||||
Author akohlmey, rbberger
|
||||
|
|
|
|||
|
|
@ -7,7 +7,8 @@ From: fedora:30
|
|||
ninja-build clang libomp-devel libubsan libasan libtsan \
|
||||
dos2unix findutils rsync python-devel libjpeg-devel libpng-devel \
|
||||
ccache gcc-c++ gcc-gfortran gdb valgrind eigen3-devel openblas-devel \
|
||||
openmpi-devel mpich-devel fftw-devel voro++-devel gsl-devel \
|
||||
openmpi-devel mpich-devel fftw-devel voro++-devel gsl-devel hdf5-devel \
|
||||
netcdf-devel netcdf-cxx-devel netcdf-mpich-devel netcdf-openmpi-devel \
|
||||
mingw-filesystem-base mingw32-nsis mingw-binutils-generic \
|
||||
mingw32-filesystem mingw32-pkg-config \
|
||||
mingw64-filesystem mingw64-pkg-config \
|
||||
|
|
@ -33,17 +34,32 @@ From: fedora:30
|
|||
texlive-latex texlive-latexconfig doxygen-latex texlive-collection-latex \
|
||||
texlive-latex-bin texlive-lualatex-math texlive-fncychap texlive-tabulary \
|
||||
texlive-framed texlive-wrapfig texlive-upquote texlive-capt-of \
|
||||
texlive-needspace texlive-titlesec texlive-anysize texlive-dvipng
|
||||
texlive-needspace texlive-titlesec texlive-anysize texlive-dvipng \
|
||||
blas-devel lapack-devel
|
||||
dnf clean all
|
||||
|
||||
%environment
|
||||
LC_ALL=C
|
||||
export LC_ALL
|
||||
|
||||
# we need to reset any module variables
|
||||
# inherited from the host.
|
||||
unset __LMOD_REF_COUNT__LMFILES_
|
||||
unset __LMOD_REF_COUNT_PATH
|
||||
unset __LMOD_REF_COUNT_LD_LIBRARY_PATH
|
||||
unset __LMOD_REF_COUNT_MANPATH
|
||||
unset __LMOD_REF_COUNT_MODULEPATH
|
||||
unset __LMOD_REF_COUNT_LOADEDMODULES
|
||||
unset _LMFILES_
|
||||
unset MODULEPATH
|
||||
unset MODULESHOME
|
||||
unset MODULEPATH_ROOT
|
||||
unset LOADEDMODULES
|
||||
. /etc/profile.d/modules.sh
|
||||
module purge
|
||||
unset LMOD_SYSTEM_DEFAULT_MODULES
|
||||
|
||||
# load MPI by default
|
||||
. /etc/profile
|
||||
module load mpi
|
||||
|
||||
%labels
|
||||
Author akohlmey
|
||||
Author akohlmey, rbberger
|
||||
|
|
|
|||
|
|
@ -7,7 +7,8 @@ From: fedora:32
|
|||
ninja-build clang libomp-devel libubsan libasan libtsan \
|
||||
dos2unix findutils rsync python-devel libjpeg-devel libpng-devel \
|
||||
ccache gcc-c++ gcc-gfortran gdb valgrind eigen3-devel openblas-devel \
|
||||
openmpi-devel mpich-devel fftw-devel voro++-devel gsl-devel \
|
||||
openmpi-devel mpich-devel fftw-devel voro++-devel gsl-devel hdf5-devel \
|
||||
netcdf-devel netcdf-cxx-devel netcdf-mpich-devel netcdf-openmpi-devel \
|
||||
mingw-filesystem-base mingw32-nsis mingw-binutils-generic \
|
||||
mingw32-filesystem mingw32-pkg-config \
|
||||
mingw64-filesystem mingw64-pkg-config \
|
||||
|
|
@ -33,17 +34,29 @@ From: fedora:32
|
|||
texlive-latex texlive-latexconfig doxygen-latex texlive-collection-latex \
|
||||
texlive-latex-bin texlive-lualatex-math texlive-fncychap texlive-tabulary \
|
||||
texlive-framed texlive-wrapfig texlive-upquote texlive-capt-of \
|
||||
texlive-needspace texlive-titlesec texlive-anysize texlive-dvipng
|
||||
texlive-needspace texlive-titlesec texlive-anysize texlive-dvipng \
|
||||
blas-devel lapack-devel diffutils
|
||||
dnf clean all
|
||||
|
||||
%environment
|
||||
LC_ALL=C
|
||||
export LC_ALL
|
||||
# we need to reset any module variables
|
||||
# inherited from the host.
|
||||
unset __LMOD_REF_COUNT__LMFILES_
|
||||
unset __LMOD_REF_COUNT_PATH
|
||||
unset __LMOD_REF_COUNT_LD_LIBRARY_PATH
|
||||
unset __LMOD_REF_COUNT_MANPATH
|
||||
unset __LMOD_REF_COUNT_MODULEPATH
|
||||
unset __LMOD_REF_COUNT_LOADEDMODULES
|
||||
unset _LMFILES_
|
||||
unset MODULEPATH
|
||||
unset MODULESHOME
|
||||
unset MODULEPATH_ROOT
|
||||
unset LOADEDMODULES
|
||||
. /etc/profile.d/modules.sh
|
||||
module purge
|
||||
unset LMOD_SYSTEM_DEFAULT_MODULES
|
||||
|
||||
# load MPI by default
|
||||
. /etc/profile
|
||||
module load mpi
|
||||
|
||||
%labels
|
||||
Author akohlmey
|
||||
Author akohlmey, rbberger
|
||||
|
|
|
|||
|
|
@ -30,6 +30,7 @@ From: ubuntu:18.04
|
|||
libhwloc-dev \
|
||||
libjpeg-dev \
|
||||
liblapack-dev \
|
||||
libnetcdf-dev \
|
||||
libomp-dev \
|
||||
libopenblas-dev \
|
||||
libnuma-dev \
|
||||
|
|
@ -61,11 +62,17 @@ From: ubuntu:18.04
|
|||
virtualenv \
|
||||
voro++-dev \
|
||||
wget \
|
||||
xxd
|
||||
xxd \
|
||||
valgrind \
|
||||
gdb
|
||||
|
||||
# clean cache
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
%environment
|
||||
LC_ALL=C
|
||||
export LC_ALL
|
||||
LC_ALL=C
|
||||
export LC_ALL
|
||||
export PATH=/usr/lib/ccache:$PATH
|
||||
|
||||
%labels
|
||||
Author akohlmey, rbberger
|
||||
|
|
|
|||
|
|
@ -61,7 +61,9 @@ From: rocm/dev-ubuntu-18.04
|
|||
virtualenv \
|
||||
voro++-dev \
|
||||
wget \
|
||||
xxd
|
||||
xxd \
|
||||
valgrind \
|
||||
gdb
|
||||
|
||||
export PATH=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
|
||||
git clone -b master-rocm-3.3 https://github.com/ROCmSoftwarePlatform/hipCUB.git
|
||||
|
|
@ -72,6 +74,9 @@ From: rocm/dev-ubuntu-18.04
|
|||
make package
|
||||
make install
|
||||
|
||||
# clean cache
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
%environment
|
||||
LC_ALL=C
|
||||
export LC_ALL
|
||||
|
|
|
|||
|
|
@ -2,11 +2,11 @@ BootStrap: library
|
|||
From: lammps/default/lammps_development:ubuntu18.04_amd_rocm
|
||||
|
||||
%environment
|
||||
export PATH=/usr/local/nvidia/bin:/usr/local/cuda/bin:${PATH}
|
||||
export CUDADIR=/usr/local/cuda
|
||||
export CUDA_PATH=/usr/local/cuda
|
||||
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/nvidia/lib:/usr/local/nvidia/lib64
|
||||
export LIBRARY_PATH=/usr/local/cuda/lib64/stubs
|
||||
export PATH=/usr/local/cuda-10.2/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
|
||||
export CUDADIR=/usr/local/cuda-10.2
|
||||
export CUDA_PATH=/usr/local/cuda-10.2
|
||||
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-10.2/lib64
|
||||
export LIBRARY_PATH=/usr/local/cuda-10.2/lib64/stubs
|
||||
|
||||
%post
|
||||
export DEBIAN_FRONTEND=noninteractive
|
||||
|
|
@ -15,11 +15,24 @@ From: lammps/default/lammps_development:ubuntu18.04_amd_rocm
|
|||
apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/7fa2af80.pub
|
||||
add-apt-repository "deb http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/ /"
|
||||
apt-get update
|
||||
apt-get -y install cuda cuda-compiler-10-2
|
||||
|
||||
export CUDA_PKG_VERSION=10.2
|
||||
|
||||
apt-get install -y --no-install-recommends \
|
||||
cuda-libraries-$CUDA_PKG_VERSION \
|
||||
cuda-command-line-tools-$CUDA_PKG_VERSION \
|
||||
cuda-libraries-dev-$CUDA_PKG_VERSION \
|
||||
cuda-minimal-build-$CUDA_PKG_VERSION \
|
||||
cuda-compat-$CUDA_PKG_VERSION \
|
||||
libcublas10 \
|
||||
libcublas-dev
|
||||
|
||||
|
||||
echo "/usr/local/nvidia/lib" >> /etc/ld.so.conf.d/nvidia.conf
|
||||
echo "/usr/local/nvidia/lib64" >> /etc/ld.so.conf.d/nvidia.conf
|
||||
|
||||
# clean cache
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
%labels
|
||||
Author rbberger
|
||||
|
|
|
|||
|
|
@ -2,11 +2,11 @@ BootStrap: docker
|
|||
From: rocm/dev-ubuntu-18.04
|
||||
|
||||
%environment
|
||||
export PATH=/usr/local/nvidia/bin:/usr/local/cuda/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
|
||||
export CUDADIR=/usr/local/cuda
|
||||
export CUDA_PATH=/usr/local/cuda
|
||||
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/nvidia/lib:/usr/local/nvidia/lib64
|
||||
export LIBRARY_PATH=/usr/local/cuda/lib64/stubs
|
||||
export PATH=/usr/lib/ccache:/usr/local/cuda-10.2/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
|
||||
export CUDADIR=/usr/local/cuda-10.2
|
||||
export CUDA_PATH=/usr/local/cuda-10.2
|
||||
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-10.2/lib64
|
||||
export LIBRARY_PATH=/usr/local/cuda-10.2/lib64/stubs
|
||||
%post
|
||||
export DEBIAN_FRONTEND=noninteractive
|
||||
apt-get update
|
||||
|
|
@ -64,15 +64,26 @@ From: rocm/dev-ubuntu-18.04
|
|||
virtualenv \
|
||||
voro++-dev \
|
||||
wget \
|
||||
xxd
|
||||
xxd \
|
||||
valgrind \
|
||||
gdb
|
||||
|
||||
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-ubuntu1804.pin
|
||||
mv cuda-ubuntu1804.pin /etc/apt/preferences.d/cuda-repository-pin-600
|
||||
apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/7fa2af80.pub
|
||||
add-apt-repository "deb http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/ /"
|
||||
apt-get update
|
||||
apt-get install --no-install-recommends -y \
|
||||
cuda \
|
||||
cuda-compiler-10-2 \
|
||||
|
||||
export CUDA_PKG_VERSION=10.2
|
||||
|
||||
apt-get install -y --no-install-recommends \
|
||||
cuda-libraries-$CUDA_PKG_VERSION \
|
||||
cuda-command-line-tools-$CUDA_PKG_VERSION \
|
||||
cuda-libraries-dev-$CUDA_PKG_VERSION \
|
||||
cuda-minimal-build-$CUDA_PKG_VERSION \
|
||||
cuda-compat-$CUDA_PKG_VERSION \
|
||||
libcublas10 \
|
||||
libcublas-dev
|
||||
|
||||
export PATH=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
|
||||
git clone -b master-rocm-3.3 https://github.com/ROCmSoftwarePlatform/hipCUB.git
|
||||
|
|
@ -86,6 +97,13 @@ From: rocm/dev-ubuntu-18.04
|
|||
echo "/usr/local/nvidia/lib" >> /etc/ld.so.conf.d/nvidia.conf
|
||||
echo "/usr/local/nvidia/lib64" >> /etc/ld.so.conf.d/nvidia.conf
|
||||
|
||||
# clean cache
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
# add missing symlink
|
||||
ln -s /usr/local/cuda-10.2 /usr/local/cuda
|
||||
ln -s /usr/local/cuda-10.2/lib64/stubs/libcuda.so /usr/local/cuda-10.2/lib64/stubs/libcuda.so.1
|
||||
|
||||
%environment
|
||||
LC_ALL=C
|
||||
export LC_ALL
|
||||
|
|
|
|||
|
|
@ -59,12 +59,17 @@ From: ubuntu:18.04
|
|||
virtualenv \
|
||||
voro++-dev \
|
||||
wget \
|
||||
xxd
|
||||
xxd \
|
||||
valgrind \
|
||||
gdb
|
||||
|
||||
add-apt-repository ppa:intel-opencl/intel-opencl
|
||||
apt-get update
|
||||
apt-get install -y intel-opencl-icd
|
||||
|
||||
# clean cache
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
%environment
|
||||
LC_ALL=C
|
||||
export LC_ALL
|
||||
|
|
|
|||
|
|
@ -59,11 +59,16 @@ From: nvidia/cuda:10.2-devel-ubuntu18.04
|
|||
virtualenv \
|
||||
voro++-dev \
|
||||
wget \
|
||||
xxd
|
||||
xxd \
|
||||
valgrind \
|
||||
gdb
|
||||
|
||||
mkdir -p /etc/OpenCL/vendors
|
||||
echo "libnvidia-opencl.so.1" > /etc/OpenCL/vendors/nvidia.icd
|
||||
|
||||
# clean cache
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
%environment
|
||||
LC_ALL=C
|
||||
export LC_ALL
|
||||
|
|
|
|||
|
|
@ -30,6 +30,7 @@ From: ubuntu:20.04
|
|||
libhwloc-dev \
|
||||
libjpeg-dev \
|
||||
liblapack-dev \
|
||||
libnetcdf-dev \
|
||||
libomp-dev \
|
||||
libopenblas-dev \
|
||||
libnuma-dev \
|
||||
|
|
@ -57,11 +58,16 @@ From: ubuntu:20.04
|
|||
virtualenv \
|
||||
voro++-dev \
|
||||
wget \
|
||||
xxd
|
||||
xxd \
|
||||
valgrind \
|
||||
gdb
|
||||
|
||||
# clean cache
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
%environment
|
||||
LC_ALL=C
|
||||
export LC_ALL
|
||||
LC_ALL=C
|
||||
export LC_ALL
|
||||
|
||||
%labels
|
||||
Author akohlmey, rbberger
|
||||
|
|
|
|||
Loading…
Reference in New Issue