Merge branch 'lammps:develop' into fortran-expansion
This commit is contained in:
hammondkd
@ -7,6 +7,10 @@ cmake_minimum_required(VERSION 3.10)
|
||||
if(POLICY CMP0074)
|
||||
cmake_policy(SET CMP0074 NEW)
|
||||
endif()
|
||||
# set policy to silence warnings about ignoring ${CMAKE_REQUIRED_LIBRARIES} but use it
|
||||
if(POLICY CMP0075)
|
||||
cmake_policy(SET CMP0075 NEW)
|
||||
endif()
|
||||
# set policy to silence warnings about missing executable permissions in
|
||||
# pythonx.y-config when cross-compiling. review occasionally if it may be set to NEW
|
||||
if(POLICY CMP0109)
|
||||
@ -385,9 +389,9 @@ pkg_depends(EXTRA-MOLECULE MOLECULE)
|
||||
|
||||
# detect if we may enable OpenMP support by default
|
||||
set(BUILD_OMP_DEFAULT OFF)
|
||||
find_package(OpenMP QUIET)
|
||||
if(OpenMP_FOUND)
|
||||
check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
|
||||
find_package(OpenMP COMPONENTS CXX QUIET)
|
||||
if(OpenMP_CXX_FOUND)
|
||||
check_omp_h_include()
|
||||
if(HAVE_OMP_H_INCLUDE)
|
||||
set(BUILD_OMP_DEFAULT ON)
|
||||
endif()
|
||||
@ -396,8 +400,8 @@ endif()
|
||||
option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT})
|
||||
|
||||
if(BUILD_OMP)
|
||||
find_package(OpenMP REQUIRED)
|
||||
check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
|
||||
find_package(OpenMP COMPONENTS CXX REQUIRED)
|
||||
check_omp_h_include()
|
||||
if(NOT HAVE_OMP_H_INCLUDE)
|
||||
message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
|
||||
endif()
|
||||
|
||||
@ -24,6 +24,21 @@ function(validate_option name values)
|
||||
endif()
|
||||
endfunction(validate_option)
|
||||
|
||||
# helper function to check for usable omp.h header
|
||||
function(check_omp_h_include)
|
||||
find_package(OpenMP COMPONENTS CXX QUIET)
|
||||
if(OpenMP_CXX_FOUND)
|
||||
set(CMAKE_REQUIRED_FLAGS ${OpenMP_CXX_FLAGS})
|
||||
set(CMAKE_REQUIRED_INCLUDES ${OpenMP_CXX_INCLUDE_DIRS})
|
||||
set(CMAKE_REQUIRED_LINK_OPTIONS ${OpenMP_CXX_FLAGS})
|
||||
set(CMAKE_REQUIRED_LIBRARIES ${OpenMP_CXX_LIBRARIES})
|
||||
check_include_file_cxx(omp.h _have_omp_h)
|
||||
else()
|
||||
set(_have_omp_h FALSE)
|
||||
endif()
|
||||
set(HAVE_OMP_H_INCLUDE ${_have_omp_h} PARENT_SCOPE)
|
||||
endfunction()
|
||||
|
||||
# helper function for getting the most recently modified file or folder from a glob pattern
|
||||
function(get_newest_file path variable)
|
||||
file(GLOB _dirs ${path})
|
||||
|
||||
@ -15,8 +15,9 @@ if(Kokkos_ENABLE_OPENMP)
|
||||
if(NOT BUILD_OMP)
|
||||
message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
|
||||
else()
|
||||
if(LAMMPS_OMP_COMPAT_LEVEL LESS 4)
|
||||
message(FATAL_ERROR "Compiler must support OpenMP 4.0 or later with Kokkos_ENABLE_OPENMP")
|
||||
# NVHPC does not seem to provide a detectable OpenMP version, but is far beyond version 3.1
|
||||
if((OpenMP_CXX_VERSION VERSION_LESS 3.1) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC"))
|
||||
message(FATAL_ERROR "Compiler must support OpenMP 3.1 or later with Kokkos_ENABLE_OPENMP")
|
||||
endif()
|
||||
endif()
|
||||
endif()
|
||||
|
||||
@ -28,10 +28,3 @@ set(MPI_CXX "clang++" CACHE STRING "" FORCE)
|
||||
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
|
||||
|
||||
unset(HAVE_OMP_H_INCLUDE CACHE)
|
||||
set(OpenMP_C "clang" CACHE STRING "" FORCE)
|
||||
set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_CXX "clang++" CACHE STRING "" FORCE)
|
||||
set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)
|
||||
|
||||
@ -19,11 +19,3 @@ set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Og -g -std=f2003" CACHE STRING "" FORCE)
|
||||
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
|
||||
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
|
||||
unset(HAVE_OMP_H_INCLUDE CACHE)
|
||||
|
||||
set(OpenMP_C "gcc" CACHE STRING "" FORCE)
|
||||
set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_C_LIB_NAMES "gomp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_CXX "g++" CACHE STRING "" FORCE)
|
||||
set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_CXX_LIB_NAMES "gomp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_omp_LIBRARY "libgomp.so" CACHE PATH "" FORCE)
|
||||
|
||||
9
cmake/presets/nvhpc.cmake
Normal file
9
cmake/presets/nvhpc.cmake
Normal file
@ -0,0 +1,9 @@
|
||||
# preset that will enable Nvidia HPC SDK compilers with support for MPI and OpenMP (on Linux boxes)
|
||||
|
||||
set(CMAKE_CXX_COMPILER "nvc++" CACHE STRING "" FORCE)
|
||||
set(CMAKE_C_COMPILER "nvc" CACHE STRING "" FORCE)
|
||||
set(CMAKE_Fortran_COMPILER "nvfortran" CACHE STRING "" FORCE)
|
||||
set(MPI_CXX "nvc++" CACHE STRING "" FORCE)
|
||||
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
|
||||
unset(HAVE_OMP_H_INCLUDE CACHE)
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
# preset that will restore gcc/g++ with support for MPI and OpenMP (on Linux boxes)
|
||||
# preset that will set gcc/g++ with extra warnings enabled and support for MPI and OpenMP (on Linux boxes)
|
||||
|
||||
set(CMAKE_CXX_COMPILER "g++" CACHE STRING "" FORCE)
|
||||
set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
|
||||
@ -17,10 +17,3 @@ set(MPI_Fortran "gfortran" CACHE STRING "" FORCE)
|
||||
set(MPI_Fortran_COMPILER "mpifort" CACHE STRING "" FORCE)
|
||||
unset(HAVE_OMP_H_INCLUDE CACHE)
|
||||
|
||||
set(OpenMP_C "gcc" CACHE STRING "" FORCE)
|
||||
set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_C_LIB_NAMES "gomp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_CXX "g++" CACHE STRING "" FORCE)
|
||||
set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_CXX_LIB_NAMES "gomp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_omp_LIBRARY "libgomp.so" CACHE PATH "" FORCE)
|
||||
|
||||
@ -7,10 +7,3 @@ set(MPI_CXX "pgc++" CACHE STRING "" FORCE)
|
||||
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
|
||||
unset(HAVE_OMP_H_INCLUDE CACHE)
|
||||
|
||||
set(OpenMP_C "pgcc" CACHE STRING "" FORCE)
|
||||
set(OpenMP_C_FLAGS "-mp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_CXX "pgc++" CACHE STRING "" FORCE)
|
||||
set(OpenMP_CXX_FLAGS "-mp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)
|
||||
|
||||
@ -295,6 +295,7 @@ OPT.
|
||||
* :doc:`vashishta (gko) <pair_vashishta>`
|
||||
* :doc:`vashishta/table (o) <pair_vashishta>`
|
||||
* :doc:`wf/cut <pair_wf_cut>`
|
||||
* :doc:`ylz <pair_ylz>`
|
||||
* :doc:`yukawa (gko) <pair_yukawa>`
|
||||
* :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
|
||||
* :doc:`zbl (gko) <pair_zbl>`
|
||||
|
||||
@ -200,6 +200,7 @@ particle models including ellipsoids, 2d lines, and 3d triangles.
|
||||
* :doc:`Howto spherical <Howto_spherical>`
|
||||
* :doc:`pair_style gayberne <pair_gayberne>`
|
||||
* :doc:`pair_style resquared <pair_resquared>`
|
||||
* :doc:`pair_style ylz <pair_ylz>`
|
||||
* `doc/PDF/pair_gayberne_extra.pdf <PDF/pair_gayberne_extra.pdf>`_
|
||||
* `doc/PDF/pair_resquared_extra.pdf <PDF/pair_resquared_extra.pdf>`_
|
||||
* examples/ASPHERE
|
||||
|
||||
@ -374,6 +374,7 @@ accelerated styles exist.
|
||||
* :doc:`vashishta <pair_vashishta>` - Vashishta 2-body and 3-body potential
|
||||
* :doc:`vashishta/table <pair_vashishta>` -
|
||||
* :doc:`wf/cut <pair_wf_cut>` - Wang-Frenkel Potential for short-ranged interactions
|
||||
* :doc:`ylz <pair_ylz>` - Yuan-Li-Zhang Potential for anisotropic interactions
|
||||
* :doc:`yukawa <pair_yukawa>` - Yukawa potential
|
||||
* :doc:`yukawa/colloid <pair_yukawa_colloid>` - screened Yukawa potential for finite-size particles
|
||||
* :doc:`zbl <pair_zbl>` - Ziegler-Biersack-Littmark potential
|
||||
|
||||
177
doc/src/pair_ylz.rst
Normal file
177
doc/src/pair_ylz.rst
Normal file
@ -0,0 +1,177 @@
|
||||
.. index:: pair_style ylz
|
||||
|
||||
pair_style ylz command
|
||||
===========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style ylz cutoff
|
||||
|
||||
|
||||
* cutoff = global cutoff for interactions (distance units)
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style ylz 2.6
|
||||
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
|
||||
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
.. versionadded:: TBD
|
||||
|
||||
The *ylz* (Yuan-Li-Zhang) style computes an anisotropic interaction
|
||||
between pairs of coarse-grained particles considering the relative
|
||||
particle orientations. This potential was originally developed as a
|
||||
particle-based solvent-free model for biological membranes
|
||||
:ref:`(Yuan2010a) <Yuan>`. Unlike :doc:`pair_style gayberne
|
||||
<pair_gayberne>`, whose orientation dependence is strictly derived from
|
||||
the closest distance between two ellipsoidal rigid bodies, the
|
||||
orientation-dependence of this pair style is mathematically defined such
|
||||
that the particles can self-assemble into one-particle-thick fluid
|
||||
membranes. The potential of this pair style is described by:
|
||||
|
||||
.. math::
|
||||
|
||||
U ( \mathbf{r}_{ij}, \mathbf{n}_i, \mathbf{n}_j ) =\left\{\begin{matrix} {u}_R(r)+\left [ 1-\phi (\mathbf{\hat{r}}_{ij}, \mathbf{n}_i, \mathbf{n}_j ) \right ]\epsilon, ~~ r<{r}_{min} \\ {u}_A(r)\phi (\mathbf{\hat{r}}_{ij}, \mathbf{n}_i, \mathbf{n}_j ),~~ {r}_{min}<r<{r}_{c} \\ \end{matrix}\right.\\\\ \phi (\mathbf{\hat{r}}_{ij}, \mathbf{n}_i, \mathbf{n}_j )=1+\left [ \mu (a(\mathbf{\hat{r}}_{ij}, \mathbf{n}_i, \mathbf{n}_j )-1) \right ] \\\\a(\mathbf{\hat{r}}_{ij}, \mathbf{n}_i, \mathbf{n}_j )=(\mathbf{n}_i\times\mathbf{\hat{r}}_{ij} )\cdot (\mathbf{n}_j\times\mathbf{\hat{r}}_{ij} )+{\beta}(\mathbf{n}_i-\mathbf{n}_j)\cdot \mathbf{\hat{r}}_{ij}-\beta^{2}\\\\ {u}_R(r)=\epsilon \left [ \left ( \frac{{r}_{min}}{r} \right )^{4}-2\left ( \frac{{r}_{min}}{r}\right )^{2} \right ] \\\\ {u}_A(r)=-\epsilon\;cos^{2\zeta }\left [ \frac{\pi}{2}\frac{\left ( {r}-{r}_{min} \right )}{\left ( {r}_{c}-{r}_{min} \right )} \right ]\\
|
||||
|
||||
where :math:`\mathbf{r}_{i}` and :math:`\mathbf{r}_{j}` are the center
|
||||
position vectors of particles i and j, respectively,
|
||||
:math:`\mathbf{r}_{ij}=\mathbf{r}_{i}-\mathbf{r}_{j}` is the
|
||||
inter-particle distance vector, :math:`r=\left|\mathbf{r}_{ij} \right|`
|
||||
and :math:`{\hat{\mathbf{r}}}_{ij}=\mathbf{r}_{ij}/r`. The unit vectors
|
||||
:math:`\mathbf{n}_{i}` and :math:`\mathbf{n}_{j}` represent the axes of
|
||||
symmetry of particles i and j, respectively, :math:`u_R` and :math:`u_A`
|
||||
are the repulsive and attractive potentials, :math:`\phi` is an angular
|
||||
function which depends on the relative orientation between pair
|
||||
particles, :math:`\mu` is the parameter related to the bending rigidity
|
||||
of the membrane, :math:`\beta` is the parameter related to the
|
||||
spontaneous curvature, and :math:`\epsilon` is the energy unit,
|
||||
respectively. The :math:`\zeta` controls the slope of the attractive
|
||||
branch and hence the diffusivity of the particles in the in-plane
|
||||
direction of the membrane. :math:`{r}_{c}` is the cutoff radius,
|
||||
:math:`r_{min}` is the distance which minimizes the potential energy
|
||||
:math:`u_{A}(r)` and :math:`r_{min}=2^{1/6}\sigma`, where :math:`\sigma`
|
||||
is the length unit.
|
||||
|
||||
This pair style is suited for solvent-free coarse-grained simulations of
|
||||
biological systems involving lipid bilayer membranes, such as vesicle
|
||||
shape transformations :ref:`(Yuan2010b) <Yuan>`, nanoparticle
|
||||
endocytosis :ref:`(Huang) <Huang>`, modeling of red blood cell membranes
|
||||
:ref:`(Fu) <Fu>`, :ref:`(Appshaw) <Appshaw>`, and modeling of cell
|
||||
elasticity :ref:`(Becton) <Becton>`.
|
||||
|
||||
Use of this pair style requires the NVE, NVT, or NPT fixes with the
|
||||
*asphere* extension (e.g. :doc:`fix nve/asphere <fix_nve_asphere>`) in
|
||||
order to integrate particle rotation. Additionally, :doc:`atom_style
|
||||
ellipsoid <atom_style>` should be used since it defines the rotational
|
||||
state of each particle.
|
||||
|
||||
The following coefficients must be defined for each pair of atoms types
|
||||
via the :doc:`pair_coeff <pair_coeff>` command as in the examples above,
|
||||
or in the data file or restart files read by the :doc:`read_data
|
||||
<read_data>` or :doc:`read_restart <read_restart>` commands, or by
|
||||
mixing as described below:
|
||||
|
||||
* :math:`\epsilon` = well depth (energy units)
|
||||
* :math:`\sigma` = minimum effective particle radii (distance units)
|
||||
* :math:`\zeta` = tune parameter for the slope of the attractive branch
|
||||
* :math:`\mu` = parameter related to bending rigidity
|
||||
* :math:`\beta` = parameter related to the spontaneous curvature
|
||||
* cutoff (distance units)
|
||||
|
||||
The last coefficient is optional. If not specified, the global
|
||||
cutoff specified in the pair_style command is used.
|
||||
|
||||
----------
|
||||
|
||||
Mixing, shift, table, tail correction, restart, rRESPA info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
|
||||
and cutoff distance for this pair style can be mixed. The default mix
|
||||
value is *geometric*\ . See the "pair_modify" command for details.
|
||||
|
||||
The :doc:`pair_modify <pair_modify>` table option is not relevant for
|
||||
this pair style.
|
||||
|
||||
This pair style does not support the :doc:`pair_modify <pair_modify>`
|
||||
tail option for adding long-range tail corrections to energy and
|
||||
pressure.
|
||||
|
||||
This pair style writes its information to :doc:`binary restart files
|
||||
<restart>`, so pair_style and pair_coeff commands do not need to be
|
||||
specified in an input script that reads a restart file.
|
||||
|
||||
This pair style can only be used via the *pair* keyword of the
|
||||
:doc:`run_style respa <run_style>` command. It does not support the
|
||||
*inner*, *middle*, *outer* keywords.
|
||||
|
||||
----------
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
The *ylz* style is part of the ASPHERE package. It is only enabled if
|
||||
LAMMPS was built with that package. See the :doc:`Build package
|
||||
<Build_package>` page for more info.
|
||||
|
||||
This pair style requires that atoms store torque and a quaternion to
|
||||
represent their orientation, as defined by the :doc:`atom_style
|
||||
<atom_style>`. It also requires they store a per-atom :doc:`shape
|
||||
<set>`. The particles cannot store a per-particle diameter. To avoid
|
||||
being mistakenly considered as point particles, the shape parameters ought
|
||||
to be non-spherical, like [1 0.99 0.99]. Unlike the :doc:`resquared
|
||||
<pair_resquared>` pair style for which the shape directly determines the
|
||||
mathematical expressions of the potential, the shape parameters for this
|
||||
pair style is only involved in the computation of the moment of inertia
|
||||
and thus only influences the rotational dynamics of individual
|
||||
particles.
|
||||
|
||||
This pair style requires that **all** atoms are ellipsoids as defined by
|
||||
the :doc:`atom_style ellipsoid <atom_style>` command.
|
||||
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair_coeff <pair_coeff>`, :doc:`fix nve/asphere
|
||||
:doc:<fix_nve_asphere>`, `compute temp/asphere <compute_temp_asphere>`,
|
||||
:doc::doc:`pair_style resquared <pair_resquared>`, :doc:`pair_style
|
||||
:doc:gayberne <pair_gayberne>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
.. _Yuan:
|
||||
|
||||
**(Yuan2010a)** Yuan, Huang, Li, Lykotrafitis, Zhang, Phys. Rev. E, 82, 011905(2010).
|
||||
|
||||
**(Yuan2010b)** Yuan, Huang, Zhang, Soft. Matter, 6, 4571(2010).
|
||||
|
||||
.. _Huang:
|
||||
|
||||
**(Huang)** Huang, Zhang, Yuan, Gao, Zhang, Nano Lett. 13, 4546(2013).
|
||||
|
||||
.. _Fu:
|
||||
|
||||
**(Fu)** Fu, Peng, Yuan, Kfoury, Young, Comput. Phys. Commun, 210, 193-203(2017).
|
||||
|
||||
.. _Appshaw:
|
||||
|
||||
**(Appshaw)** Appshaw, Seddon, Hanna, Soft. Matter,18, 1747(2022).
|
||||
|
||||
.. _Becton:
|
||||
|
||||
**(Becton)** Becton, Averett, Wang, Biomech. Model. Mechanobiology, 18, 425-433(2019).
|
||||
@ -123,6 +123,7 @@ Antonelli
|
||||
api
|
||||
Apoorva
|
||||
Appl
|
||||
Appshaw
|
||||
apptainer
|
||||
Apu
|
||||
arallel
|
||||
@ -181,6 +182,7 @@ Avalos
|
||||
avalue
|
||||
aveforce
|
||||
Avendano
|
||||
Averett
|
||||
avi
|
||||
AVX
|
||||
awpmd
|
||||
@ -237,6 +239,7 @@ bcolor
|
||||
bdiam
|
||||
bdw
|
||||
Beckman
|
||||
Becton
|
||||
Belak
|
||||
Bellott
|
||||
bem
|
||||
@ -270,6 +273,7 @@ bilayers
|
||||
binsize
|
||||
binstyle
|
||||
binutils
|
||||
Biomech
|
||||
biomolecular
|
||||
biomolecule
|
||||
Biomolecules
|
||||
@ -924,6 +928,7 @@ Emmrich
|
||||
emol
|
||||
eN
|
||||
endian
|
||||
endocytosis
|
||||
energetics
|
||||
energyCorr
|
||||
eng
|
||||
@ -1155,6 +1160,7 @@ ftm
|
||||
ftol
|
||||
fuer
|
||||
fugacity
|
||||
Fu
|
||||
Fumi
|
||||
func
|
||||
funcs
|
||||
@ -1306,6 +1312,7 @@ Hamaker
|
||||
Hamel
|
||||
Hammerschmidt
|
||||
Hanley
|
||||
Hanna
|
||||
haptic
|
||||
Haque
|
||||
Hara
|
||||
@ -1657,6 +1664,7 @@ kepler
|
||||
keV
|
||||
Keyes
|
||||
keyfile
|
||||
Kfoury
|
||||
Khersonskii
|
||||
Khrapak
|
||||
Khvostov
|
||||
@ -1912,6 +1920,7 @@ lwsock
|
||||
lx
|
||||
ly
|
||||
Lybrand
|
||||
Lykotrafitis
|
||||
lyon
|
||||
Lysogorskiy
|
||||
Lyulin
|
||||
@ -2022,6 +2031,7 @@ MEAM
|
||||
meamf
|
||||
meanDist
|
||||
mech
|
||||
Mechanobiology
|
||||
Mecke
|
||||
mediumaquamarine
|
||||
mediumblue
|
||||
@ -3143,6 +3153,7 @@ seagreen
|
||||
Secor
|
||||
sectoring
|
||||
sed
|
||||
Seddon
|
||||
segmental
|
||||
Seifert
|
||||
Seleson
|
||||
@ -3899,6 +3910,7 @@ yhi
|
||||
yi
|
||||
ylat
|
||||
ylo
|
||||
ylz
|
||||
ymax
|
||||
ymin
|
||||
yml
|
||||
|
||||
@ -29,8 +29,10 @@ stochastic rotation dynamics solvent, using the fix srd command.
|
||||
box = 2d rigid box particles in SRDs, self-diffusion and viscosity
|
||||
dimer = 2d rigid dimers in SRDs, self-diffusion and viscosity
|
||||
ellipsoid = 2d ellipsoids in SRDs, self-diffusion and viscosity
|
||||
flat_membrane = 2d flat membrane in NVE, self-diffusion and viscosity
|
||||
line = 2d line-faceted rigid particles, NEMD shearing for viscosity,
|
||||
implicit and in SRDs
|
||||
poly = 2d poly-disperse spheroids in SRDs, self-diffusion and viscosity
|
||||
star = 2d rigid star particles in SRDs, self-diffusion and viscosity
|
||||
tri = 3d triangle-faceted rigid particles in SRDs, NEMD shearing for viscosity
|
||||
vesicle = 3d vesicle in NVE, self-diffusionand viscosity
|
||||
|
||||
55
examples/ASPHERE/flat_membrane/in.flat_membrane
Normal file
55
examples/ASPHERE/flat_membrane/in.flat_membrane
Normal file
@ -0,0 +1,55 @@
|
||||
# flat membrane demo
|
||||
variable r0 equal 0.97
|
||||
variable d1 equal ${r0}
|
||||
variable d2 equal sqrt(3.0)*${r0}
|
||||
variable d3 equal 3.0*${r0}
|
||||
variable ro equal 2./${d1}/${d2}/${d3}
|
||||
|
||||
variable T equal 0.23
|
||||
variable LD equal 1.0
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice custom ${ro} a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 &
|
||||
a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
|
||||
|
||||
|
||||
region box block 0 40 0 24 -20 20
|
||||
create_box 1 box
|
||||
region membrane block 0 40 0 24 -0.5 0.5
|
||||
create_atoms 1 region membrane
|
||||
|
||||
group membrane region membrane
|
||||
|
||||
set type 1 mass 1.0
|
||||
|
||||
set type 1 shape 1 0.99 0.99
|
||||
|
||||
set group all quat 0 -1 0 90
|
||||
|
||||
#compute memb all temp/com
|
||||
#compute rot all temp/asphere bias memb
|
||||
velocity all create ${T} 87287 loop geom
|
||||
|
||||
pair_style ylz 2.6
|
||||
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
|
||||
neighbor 1.0 bin
|
||||
|
||||
|
||||
thermo_style custom step temp press pxx pyy
|
||||
thermo 200
|
||||
|
||||
timestep 0.01
|
||||
|
||||
#dump 1 all atom 10 dump_onlymembrane.lammpstrj
|
||||
|
||||
fix 1 all langevin ${T} ${T} ${LD} 48279
|
||||
|
||||
|
||||
fix 2 all nve/asphere
|
||||
run 3000
|
||||
|
||||
|
||||
159
examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.1
Normal file
159
examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.1
Normal file
@ -0,0 +1,159 @@
|
||||
LAMMPS (15 Sep 2022)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# flat membrane demo
|
||||
variable r0 equal 0.97
|
||||
variable d1 equal ${r0}
|
||||
variable d1 equal 0.97
|
||||
variable d2 equal sqrt(3.0)*${r0}
|
||||
variable d2 equal sqrt(3.0)*0.97
|
||||
variable d3 equal 3.0*${r0}
|
||||
variable d3 equal 3.0*0.97
|
||||
variable ro equal 2./${d1}/${d2}/${d3}
|
||||
variable ro equal 2./0.97/${d2}/${d3}
|
||||
variable ro equal 2./0.97/1.68008928334181/${d3}
|
||||
variable ro equal 2./0.97/1.68008928334181/2.91
|
||||
|
||||
variable T equal 0.23
|
||||
variable LD equal 1.0
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice custom ${ro} a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
|
||||
lattice custom 0.421728460751825 a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
|
||||
lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
|
||||
lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 1.68008928334181 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
|
||||
lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 1.68008928334181 0.0 a3 0.0 0.0 2.91 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
|
||||
Lattice spacing in x,y,z = 0.97 1.6800893 2.91
|
||||
|
||||
|
||||
region box block 0 40 0 24 -20 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
region membrane block 0 40 0 24 -0.5 0.5
|
||||
create_atoms 1 region membrane
|
||||
Created 1920 atoms
|
||||
using lattice units in orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
group membrane region membrane
|
||||
1920 atoms in group membrane
|
||||
|
||||
set type 1 mass 1.0
|
||||
Setting atom values ...
|
||||
1920 settings made for mass
|
||||
|
||||
set type 1 shape 1 1 1
|
||||
Setting atom values ...
|
||||
1920 settings made for shape
|
||||
|
||||
set group all quat 0 -1 0 90
|
||||
Setting atom values ...
|
||||
1920 settings made for quat
|
||||
|
||||
#compute memb all temp/com
|
||||
#compute rot all temp/asphere bias memb
|
||||
velocity all create ${T} 87287 loop geom
|
||||
velocity all create 0.23 87287 loop geom
|
||||
|
||||
pair_style ylz 2.6
|
||||
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
|
||||
neighbor 1.0 bin
|
||||
|
||||
|
||||
thermo_style custom step temp press pxx pyy
|
||||
thermo 200
|
||||
|
||||
timestep 0.01
|
||||
|
||||
#dump 1 all atom 10 dump_onlymembrane.lammpstrj
|
||||
|
||||
fix 1 all langevin ${T} ${T} ${LD} 48279
|
||||
fix 1 all langevin 0.23 ${T} ${LD} 48279
|
||||
fix 1 all langevin 0.23 0.23 ${LD} 48279
|
||||
fix 1 all langevin 0.23 0.23 1 48279
|
||||
|
||||
|
||||
fix 2 all nve/asphere
|
||||
run 3000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair ylz command:
|
||||
|
||||
@Article{Yuan10,
|
||||
author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
|
||||
title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
|
||||
journal = {Phys. Rev. E},
|
||||
year = 2010,
|
||||
volume = 82,
|
||||
pages = {011905}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 10 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.6
|
||||
ghost atom cutoff = 3.6
|
||||
binsize = 1.8, bins = 22 23 65
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair ylz, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.024 | 5.024 | 5.024 Mbytes
|
||||
Step Temp Press Pxx Pyy
|
||||
0 0.23 -0.0073508785 -0.012283389 -0.012234574
|
||||
200 0.20903886 -0.0010605951 -0.0011885957 -0.00198842
|
||||
400 0.21898026 -0.00069250685 -0.0013217981 -0.00073225707
|
||||
600 0.22689361 -0.00057919328 -0.00076880503 -0.0010242283
|
||||
800 0.22983221 -0.00032145682 -0.00051928834 -0.00059337525
|
||||
1000 0.23819392 -0.00027969126 -0.00088082301 -5.2666567e-05
|
||||
1200 0.22053795 -0.00029571329 -0.0004446455 -0.00035529929
|
||||
1400 0.22285021 -0.0002690371 -0.00068896571 -3.6258442e-05
|
||||
1600 0.22687044 2.8599875e-05 -0.00032651798 0.0004056081
|
||||
1800 0.23356905 -2.28742e-05 -0.00027073251 0.00025081131
|
||||
2000 0.22499821 8.8230586e-06 -7.5750159e-05 0.0001988705
|
||||
2200 0.23162995 -9.026855e-05 -0.00025832535 5.4904927e-05
|
||||
2400 0.22920223 0.00016700455 3.5283125e-05 0.00034955857
|
||||
2600 0.2260299 5.3095557e-05 0.00025691786 0.00013353467
|
||||
2800 0.2296401 0.00043234854 0.00058344966 0.00063645193
|
||||
3000 0.22564577 2.6423111e-05 8.9918406e-05 0.00022146229
|
||||
Loop time of 6.76659 on 1 procs for 3000 steps with 1920 atoms
|
||||
|
||||
Performance: 383058.431 tau/day, 443.355 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.7968 | 5.7968 | 5.7968 | 0.0 | 85.67
|
||||
Neigh | 0.086077 | 0.086077 | 0.086077 | 0.0 | 1.27
|
||||
Comm | 0.034761 | 0.034761 | 0.034761 | 0.0 | 0.51
|
||||
Output | 0.00038014 | 0.00038014 | 0.00038014 | 0.0 | 0.01
|
||||
Modify | 0.8268 | 0.8268 | 0.8268 | 0.0 | 12.22
|
||||
Other | | 0.02181 | | | 0.32
|
||||
|
||||
Nlocal: 1920 ave 1920 max 1920 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 772 ave 772 max 772 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 46804 ave 46804 max 46804 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 46804
|
||||
Ave neighs/atom = 24.377083
|
||||
Neighbor list builds = 99
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Total wall time: 0:00:06
|
||||
159
examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.4
Normal file
159
examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.4
Normal file
@ -0,0 +1,159 @@
|
||||
LAMMPS (15 Sep 2022)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# flat membrane demo
|
||||
variable r0 equal 0.97
|
||||
variable d1 equal ${r0}
|
||||
variable d1 equal 0.97
|
||||
variable d2 equal sqrt(3.0)*${r0}
|
||||
variable d2 equal sqrt(3.0)*0.97
|
||||
variable d3 equal 3.0*${r0}
|
||||
variable d3 equal 3.0*0.97
|
||||
variable ro equal 2./${d1}/${d2}/${d3}
|
||||
variable ro equal 2./0.97/${d2}/${d3}
|
||||
variable ro equal 2./0.97/1.68008928334181/${d3}
|
||||
variable ro equal 2./0.97/1.68008928334181/2.91
|
||||
|
||||
variable T equal 0.23
|
||||
variable LD equal 1.0
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice custom ${ro} a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
|
||||
lattice custom 0.421728460751825 a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
|
||||
lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
|
||||
lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 1.68008928334181 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
|
||||
lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 1.68008928334181 0.0 a3 0.0 0.0 2.91 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
|
||||
Lattice spacing in x,y,z = 0.97 1.6800893 2.91
|
||||
|
||||
|
||||
region box block 0 40 0 24 -20 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
region membrane block 0 40 0 24 -0.5 0.5
|
||||
create_atoms 1 region membrane
|
||||
Created 1920 atoms
|
||||
using lattice units in orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
group membrane region membrane
|
||||
1920 atoms in group membrane
|
||||
|
||||
set type 1 mass 1.0
|
||||
Setting atom values ...
|
||||
1920 settings made for mass
|
||||
|
||||
set type 1 shape 1 1 1
|
||||
Setting atom values ...
|
||||
1920 settings made for shape
|
||||
|
||||
set group all quat 0 -1 0 90
|
||||
Setting atom values ...
|
||||
1920 settings made for quat
|
||||
|
||||
#compute memb all temp/com
|
||||
#compute rot all temp/asphere bias memb
|
||||
velocity all create ${T} 87287 loop geom
|
||||
velocity all create 0.23 87287 loop geom
|
||||
|
||||
pair_style ylz 2.6
|
||||
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
|
||||
neighbor 1.0 bin
|
||||
|
||||
|
||||
thermo_style custom step temp press pxx pyy
|
||||
thermo 200
|
||||
|
||||
timestep 0.01
|
||||
|
||||
#dump 1 all atom 10 dump_onlymembrane.lammpstrj
|
||||
|
||||
fix 1 all langevin ${T} ${T} ${LD} 48279
|
||||
fix 1 all langevin 0.23 ${T} ${LD} 48279
|
||||
fix 1 all langevin 0.23 0.23 ${LD} 48279
|
||||
fix 1 all langevin 0.23 0.23 1 48279
|
||||
|
||||
|
||||
fix 2 all nve/asphere
|
||||
run 3000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair ylz command:
|
||||
|
||||
@Article{Yuan10,
|
||||
author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
|
||||
title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
|
||||
journal = {Phys. Rev. E},
|
||||
year = 2010,
|
||||
volume = 82,
|
||||
pages = {011905}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 10 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.6
|
||||
ghost atom cutoff = 3.6
|
||||
binsize = 1.8, bins = 22 23 65
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair ylz, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.794 | 5.472 Mbytes
|
||||
Step Temp Press Pxx Pyy
|
||||
0 0.23 -0.0073508785 -0.012283389 -0.012234574
|
||||
200 0.20647718 -0.0012368074 -0.0021167303 -0.0015343502
|
||||
400 0.21648371 -0.00085695085 -0.0015627331 -0.0011177093
|
||||
600 0.22929515 -0.00050218657 -0.0008332 -0.00062622609
|
||||
800 0.22062664 -0.00049172378 -0.000611884 -0.00075089294
|
||||
1000 0.22422425 -0.00039405068 -0.00037600355 -0.00070786572
|
||||
1200 0.2298767 -0.00025939082 -0.00021616578 -0.00053125505
|
||||
1400 0.2335927 5.8028332e-05 0.00017530192 -3.1675138e-05
|
||||
1600 0.22884878 -0.0001733902 -0.0008056431 0.00014276754
|
||||
1800 0.22813498 0.00019873459 0.00051040124 5.8860949e-05
|
||||
2000 0.2273166 -3.3595127e-05 0.0001705632 -0.00026498213
|
||||
2200 0.2251643 -2.4517311e-05 -4.0618888e-05 1.066658e-05
|
||||
2400 0.22460629 -4.5661259e-05 -0.00019144039 -1.6649099e-05
|
||||
2600 0.23085675 0.00014029405 0.00017983536 0.00017895001
|
||||
2800 0.22364591 4.2999164e-05 -0.00011000466 0.00024363243
|
||||
3000 0.23421357 0.00023505702 0.00020752013 0.00053567111
|
||||
Loop time of 4.68577 on 4 procs for 3000 steps with 1920 atoms
|
||||
|
||||
Performance: 553164.568 tau/day, 640.237 timesteps/s
|
||||
95.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00015072 | 1.6029 | 3.8573 | 131.7 | 34.21
|
||||
Neigh | 0.00055747 | 0.025423 | 0.065858 | 17.0 | 0.54
|
||||
Comm | 0.0052259 | 0.48173 | 1.624 | 96.5 | 10.28
|
||||
Output | 0.0003894 | 0.023428 | 0.047223 | 15.0 | 0.50
|
||||
Modify | 0.00037337 | 0.2141 | 0.44595 | 46.3 | 4.57
|
||||
Other | | 2.338 | | | 49.90
|
||||
|
||||
Nlocal: 480 ave 1011 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 860 ave 1771 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 11697.8 ave 30095 max 0 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 46791
|
||||
Ave neighs/atom = 24.370313
|
||||
Neighbor list builds = 99
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Total wall time: 0:00:04
|
||||
33
examples/ASPHERE/vesicle/in.vesicle
Normal file
33
examples/ASPHERE/vesicle/in.vesicle
Normal file
@ -0,0 +1,33 @@
|
||||
# Vesicle demo
|
||||
|
||||
variable T equal 0.2
|
||||
variable LD equal 1.0
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
|
||||
boundary p p p
|
||||
|
||||
read_data read_data.vesicle1026
|
||||
|
||||
compute ali all temp/com
|
||||
compute rott all temp/asphere bias ali
|
||||
|
||||
velocity all create ${T} 87287 loop geom
|
||||
|
||||
pair_style ylz 2.6
|
||||
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
|
||||
neighbor 1.0 bin
|
||||
|
||||
thermo_style custom step temp press pxx pyy
|
||||
thermo 200
|
||||
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all atom 10 onlymembrane2.lammpstrj
|
||||
|
||||
fix 1 all langevin ${T} ${T} ${LD} 48279
|
||||
fix 2 all nve/asphere
|
||||
|
||||
run 3000
|
||||
|
||||
122
examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.1
Normal file
122
examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.1
Normal file
@ -0,0 +1,122 @@
|
||||
LAMMPS (15 Sep 2022)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Vesicle demo
|
||||
|
||||
variable T equal 0.2
|
||||
variable LD equal 1.0
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
|
||||
boundary p p p
|
||||
|
||||
read_data read_data.vesicle1026
|
||||
Reading data file ...
|
||||
orthogonal box = (-35 -35 -35) to (35 35 35)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2938 atoms
|
||||
2938 ellipsoids
|
||||
read_data CPU = 0.010 seconds
|
||||
|
||||
compute ali all temp/com
|
||||
compute rott all temp/asphere bias ali
|
||||
|
||||
velocity all create ${T} 87287 loop geom
|
||||
velocity all create 0.2 87287 loop geom
|
||||
|
||||
pair_style ylz 2.6
|
||||
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
|
||||
neighbor 1.0 bin
|
||||
|
||||
thermo_style custom step temp press pxx pyy
|
||||
thermo 200
|
||||
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all atom 10 onlymembrane2.lammpstrj
|
||||
|
||||
fix 1 all langevin ${T} ${T} ${LD} 48279
|
||||
fix 1 all langevin 0.2 ${T} ${LD} 48279
|
||||
fix 1 all langevin 0.2 0.2 ${LD} 48279
|
||||
fix 1 all langevin 0.2 0.2 1 48279
|
||||
fix 2 all nve/asphere
|
||||
|
||||
run 3000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair ylz command:
|
||||
|
||||
@Article{Yuan10,
|
||||
author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
|
||||
title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
|
||||
journal = {Phys. Rev. E},
|
||||
year = 2010,
|
||||
volume = 82,
|
||||
pages = {011905}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 10 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.6
|
||||
ghost atom cutoff = 3.6
|
||||
binsize = 1.8, bins = 39 39 39
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair ylz, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.091 | 5.091 | 5.091 Mbytes
|
||||
Step Temp Press Pxx Pyy
|
||||
0 0.2 -0.0054891414 -0.0052713616 -0.0053641136
|
||||
200 0.12816247 -0.0051288861 -0.0048542514 -0.0049847561
|
||||
400 0.1377632 -0.0048071582 -0.0045651263 -0.0048444087
|
||||
600 0.14983781 -0.0045305725 -0.0043305994 -0.0046127777
|
||||
800 0.16205271 -0.0041176346 -0.0040534483 -0.0041351779
|
||||
1000 0.17462122 -0.0037000069 -0.0034938539 -0.0037915494
|
||||
1200 0.18335448 -0.0032674318 -0.0032790248 -0.0031967931
|
||||
1400 0.19195613 -0.0029332101 -0.0030823703 -0.0028287799
|
||||
1600 0.19261762 -0.0025263447 -0.0025152249 -0.0026205398
|
||||
1800 0.19758674 -0.0021087725 -0.001981333 -0.002309048
|
||||
2000 0.19748896 -0.0017662369 -0.0019316344 -0.0016696035
|
||||
2200 0.20196986 -0.0013363214 -0.0015581191 -0.0013384961
|
||||
2400 0.20109248 -0.0009190831 -0.0010331417 -0.0010664316
|
||||
2600 0.20228664 -0.00053590675 -0.00071808747 -0.00050218533
|
||||
2800 0.20512955 -0.00030845899 -0.00016244901 -0.00047877516
|
||||
3000 0.19855941 -7.9520073e-05 -0.00014969215 -5.4724226e-06
|
||||
Loop time of 9.6866 on 1 procs for 3000 steps with 2938 atoms
|
||||
|
||||
Performance: 26758.610 tau/day, 309.706 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 8.3097 | 8.3097 | 8.3097 | 0.0 | 85.79
|
||||
Neigh | 0.039037 | 0.039037 | 0.039037 | 0.0 | 0.40
|
||||
Comm | 0.0021766 | 0.0021766 | 0.0021766 | 0.0 | 0.02
|
||||
Output | 0.00048628 | 0.00048628 | 0.00048628 | 0.0 | 0.01
|
||||
Modify | 1.3043 | 1.3043 | 1.3043 | 0.0 | 13.47
|
||||
Other | | 0.0309 | | | 0.32
|
||||
|
||||
Nlocal: 2938 ave 2938 max 2938 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 73242 ave 73242 max 73242 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 73242
|
||||
Ave neighs/atom = 24.929204
|
||||
Neighbor list builds = 26
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:09
|
||||
122
examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.4
Normal file
122
examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.4
Normal file
@ -0,0 +1,122 @@
|
||||
LAMMPS (15 Sep 2022)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Vesicle demo
|
||||
|
||||
variable T equal 0.2
|
||||
variable LD equal 1.0
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
|
||||
boundary p p p
|
||||
|
||||
read_data read_data.vesicle1026
|
||||
Reading data file ...
|
||||
orthogonal box = (-35 -35 -35) to (35 35 35)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2938 atoms
|
||||
2938 ellipsoids
|
||||
read_data CPU = 0.137 seconds
|
||||
|
||||
compute ali all temp/com
|
||||
compute rott all temp/asphere bias ali
|
||||
|
||||
velocity all create ${T} 87287 loop geom
|
||||
velocity all create 0.2 87287 loop geom
|
||||
|
||||
pair_style ylz 2.6
|
||||
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
|
||||
neighbor 1.0 bin
|
||||
|
||||
thermo_style custom step temp press pxx pyy
|
||||
thermo 200
|
||||
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all atom 10 onlymembrane2.lammpstrj
|
||||
|
||||
fix 1 all langevin ${T} ${T} ${LD} 48279
|
||||
fix 1 all langevin 0.2 ${T} ${LD} 48279
|
||||
fix 1 all langevin 0.2 0.2 ${LD} 48279
|
||||
fix 1 all langevin 0.2 0.2 1 48279
|
||||
fix 2 all nve/asphere
|
||||
|
||||
run 3000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair ylz command:
|
||||
|
||||
@Article{Yuan10,
|
||||
author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
|
||||
title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
|
||||
journal = {Phys. Rev. E},
|
||||
year = 2010,
|
||||
volume = 82,
|
||||
pages = {011905}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 10 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.6
|
||||
ghost atom cutoff = 3.6
|
||||
binsize = 1.8, bins = 39 39 39
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair ylz, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.899 | 4.9 | 4.902 Mbytes
|
||||
Step Temp Press Pxx Pyy
|
||||
0 0.2 -0.0054891414 -0.0052713616 -0.0053641136
|
||||
200 0.12893798 -0.0051492794 -0.0048734875 -0.0049624005
|
||||
400 0.13798694 -0.004875313 -0.0047071897 -0.0049305051
|
||||
600 0.14725193 -0.0046349542 -0.004719983 -0.0045791451
|
||||
800 0.16146954 -0.0042232199 -0.0040789193 -0.0043672895
|
||||
1000 0.17268468 -0.0037146703 -0.0036270393 -0.0039169034
|
||||
1200 0.18266242 -0.0032749755 -0.0032971704 -0.0033323855
|
||||
1400 0.18500165 -0.0028179031 -0.0030659821 -0.0027519633
|
||||
1600 0.19513132 -0.0023407512 -0.0025109801 -0.0023416835
|
||||
1800 0.19645259 -0.0019995412 -0.0019064341 -0.0021757747
|
||||
2000 0.19658104 -0.0015897919 -0.0015850523 -0.0016828478
|
||||
2200 0.1989936 -0.0011794062 -0.0011779716 -0.0012070706
|
||||
2400 0.20011525 -0.0009147432 -0.00094040885 -0.001073922
|
||||
2600 0.2013975 -0.00059253676 -0.00051920304 -0.00075138934
|
||||
2800 0.19715513 -0.00020995605 -0.00024386426 -0.0005475745
|
||||
3000 0.1976782 -0.0001308553 5.693004e-05 -0.00034478469
|
||||
Loop time of 8.46954 on 4 procs for 3000 steps with 2938 atoms
|
||||
|
||||
Performance: 30603.800 tau/day, 354.211 timesteps/s
|
||||
77.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.1751 | 2.4162 | 2.6707 | 13.2 | 28.53
|
||||
Neigh | 0.0090503 | 0.0098389 | 0.010503 | 0.6 | 0.12
|
||||
Comm | 3.5807 | 4.1526 | 4.9283 | 24.3 | 49.03
|
||||
Output | 0.00032165 | 0.0029648 | 0.010842 | 8.4 | 0.04
|
||||
Modify | 0.34554 | 0.37442 | 0.39198 | 2.8 | 4.42
|
||||
Other | | 1.514 | | | 17.87
|
||||
|
||||
Nlocal: 734.5 ave 739 max 730 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Nghost: 420.25 ave 424 max 415 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
Neighs: 18304.5 ave 19839 max 16636 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 73218
|
||||
Ave neighs/atom = 24.921035
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:08
|
||||
5894
examples/ASPHERE/vesicle/read_data.vesicle1026
Normal file
5894
examples/ASPHERE/vesicle/read_data.vesicle1026
Normal file
File diff suppressed because it is too large
Load Diff
2
src/.gitignore
vendored
2
src/.gitignore
vendored
@ -1336,6 +1336,8 @@
|
||||
/pair_yukawa_colloid.h
|
||||
/pair_wf_cut.cpp
|
||||
/pair_wf_cut.h
|
||||
/pair_ylz.cpp
|
||||
/pair_ylz.h
|
||||
/pair_momb.cpp
|
||||
/pair_momb.h
|
||||
/pppm.cpp
|
||||
|
||||
509
src/ASPHERE/pair_ylz.cpp
Normal file
509
src/ASPHERE/pair_ylz.cpp
Normal file
@ -0,0 +1,509 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS Development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Mehdi Baghaee (SUSTech)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "pair_ylz.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "atom_vec_ellipsoid.h"
|
||||
#include "citeme.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "math_const.h"
|
||||
#include "math_extra.h"
|
||||
#include "memory.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neighbor.h"
|
||||
|
||||
#include <cmath>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using MathConst::MY_4PI;
|
||||
using MathConst::MY_PI2;
|
||||
using MathConst::MY_TWOBYSIXTH;
|
||||
|
||||
static const char cite_pair_ylz[] =
|
||||
"pair ylz command:\n\n"
|
||||
"@Article{Yuan10,\n"
|
||||
" author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},\n"
|
||||
" title = {One-particle-thick, solvent-free, coarse-grained model for biological and "
|
||||
"biomimetic fluid membranes},\n"
|
||||
" journal = {Phys. Rev. E},\n"
|
||||
" year = 2010,\n"
|
||||
" volume = 82,\n"
|
||||
" pages = {011905}\n"
|
||||
"}\n\n";
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairYLZ::PairYLZ(LAMMPS *lmp) :
|
||||
Pair(lmp), epsilon(nullptr), sigma(nullptr), cut(nullptr), zeta(nullptr), mu(nullptr),
|
||||
beta(nullptr)
|
||||
{
|
||||
if (lmp->citeme) lmp->citeme->add(cite_pair_ylz);
|
||||
|
||||
single_enable = 0;
|
||||
writedata = 1;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
free all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
PairYLZ::~PairYLZ()
|
||||
{
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(epsilon);
|
||||
memory->destroy(sigma);
|
||||
memory->destroy(cut);
|
||||
memory->destroy(zeta);
|
||||
memory->destroy(mu);
|
||||
memory->destroy(beta);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairYLZ::compute(int eflag, int vflag)
|
||||
{
|
||||
int i, j, ii, jj, inum, jnum, itype, jtype;
|
||||
double evdwl, one_eng, rsq, factor_lj;
|
||||
double fforce[3], ttor[3], rtor[3], r12[3];
|
||||
double a1[3][3], a2[3][3];
|
||||
int *ilist, *jlist, *numneigh, **firstneigh;
|
||||
double *iquat, *jquat;
|
||||
|
||||
evdwl = 0.0;
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
|
||||
int *ellipsoid = atom->ellipsoid;
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
double **tor = atom->torque;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
double *special_lj = force->special_lj;
|
||||
int newton_pair = force->newton_pair;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
itype = type[i];
|
||||
|
||||
iquat = bonus[ellipsoid[i]].quat;
|
||||
MathExtra::quat_to_mat_trans(iquat, a1);
|
||||
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
// r12 = center to center vector
|
||||
|
||||
r12[0] = x[j][0] - x[i][0];
|
||||
r12[1] = x[j][1] - x[i][1];
|
||||
r12[2] = x[j][2] - x[i][2];
|
||||
rsq = MathExtra::dot3(r12, r12);
|
||||
jtype = type[j];
|
||||
|
||||
// compute if less than cutoff
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
|
||||
jquat = bonus[ellipsoid[j]].quat;
|
||||
MathExtra::quat_to_mat_trans(jquat, a2);
|
||||
one_eng = ylz_analytic(i, j, a1, a2, r12, rsq, fforce, ttor, rtor);
|
||||
|
||||
fforce[0] *= factor_lj;
|
||||
fforce[1] *= factor_lj;
|
||||
fforce[2] *= factor_lj;
|
||||
ttor[0] *= factor_lj;
|
||||
ttor[1] *= factor_lj;
|
||||
ttor[2] *= factor_lj;
|
||||
|
||||
f[i][0] += fforce[0];
|
||||
f[i][1] += fforce[1];
|
||||
f[i][2] += fforce[2];
|
||||
tor[i][0] += ttor[0];
|
||||
tor[i][1] += ttor[1];
|
||||
tor[i][2] += ttor[2];
|
||||
|
||||
if (newton_pair || j < nlocal) {
|
||||
rtor[0] *= factor_lj;
|
||||
rtor[1] *= factor_lj;
|
||||
rtor[2] *= factor_lj;
|
||||
f[j][0] -= fforce[0];
|
||||
f[j][1] -= fforce[1];
|
||||
f[j][2] -= fforce[2];
|
||||
tor[j][0] += rtor[0];
|
||||
tor[j][1] += rtor[1];
|
||||
tor[j][2] += rtor[2];
|
||||
}
|
||||
|
||||
if (eflag) evdwl = factor_lj * one_eng;
|
||||
|
||||
if (evflag)
|
||||
ev_tally_xyz(i, j, nlocal, newton_pair, evdwl, 0.0, fforce[0], fforce[1], fforce[2],
|
||||
-r12[0], -r12[1], -r12[2]);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairYLZ::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int np1 = atom->ntypes + 1;
|
||||
|
||||
memory->create(setflag, np1, np1, "pair:setflag");
|
||||
for (int i = 1; i < np1; i++)
|
||||
for (int j = i; j < np1; j++) setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq, np1, np1, "pair:cutsq");
|
||||
memory->create(epsilon, np1, np1, "pair:epsilon");
|
||||
memory->create(sigma, np1, np1, "pair:sigma");
|
||||
memory->create(cut, np1, np1, "pair:cut");
|
||||
memory->create(zeta, np1, np1, "pair:zeta");
|
||||
memory->create(mu, np1, np1, "pair:mu");
|
||||
memory->create(beta, np1, np1, "pair:beta");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairYLZ::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 1) error->all(FLERR, "Illegal pair_style command");
|
||||
|
||||
cut_global = utils::numeric(FLERR, arg[0], false, lmp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairYLZ::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 8 || narg > 8) error->all(FLERR, "Incorrect args for pair coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo, ihi, jlo, jhi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error);
|
||||
utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error);
|
||||
|
||||
double epsilon_one = utils::numeric(FLERR, arg[2], false, lmp);
|
||||
double sigma_one = utils::numeric(FLERR, arg[3], false, lmp);
|
||||
double zeta_one = utils::numeric(FLERR, arg[4], false, lmp);
|
||||
double mu_one = utils::numeric(FLERR, arg[5], false, lmp);
|
||||
double beta_one = utils::numeric(FLERR, arg[6], false, lmp);
|
||||
double cut_one = utils::numeric(FLERR, arg[7], false, lmp);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo, i); j <= jhi; j++) {
|
||||
epsilon[i][j] = epsilon_one;
|
||||
sigma[i][j] = sigma_one;
|
||||
cut[i][j] = cut_one;
|
||||
zeta[i][j] = zeta_one;
|
||||
mu[i][j] = mu_one;
|
||||
beta[i][j] = beta_one;
|
||||
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairYLZ::init_style()
|
||||
{
|
||||
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
|
||||
if (!avec) error->all(FLERR, "Pair style ylz requires atom style ellipsoid");
|
||||
|
||||
neighbor->request(this, instance_me);
|
||||
|
||||
// check that all atoms are ellipsoids
|
||||
|
||||
int flag_all, flag = 0;
|
||||
const int *ellipsoid = atom->ellipsoid;
|
||||
const int nlocal = atom->nlocal;
|
||||
for (int i = 0; i < nlocal; ++i)
|
||||
if (ellipsoid[i] < 0) flag = 1;
|
||||
MPI_Allreduce(&flag, &flag_all, 1, MPI_INT, MPI_MAX, world);
|
||||
if (flag_all) error->all(FLERR, "All atoms must be ellipsoids for pair style ylz");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairYLZ::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) {
|
||||
epsilon[i][j] = mix_energy(epsilon[i][i], epsilon[j][j], sigma[i][i], sigma[j][j]);
|
||||
sigma[i][j] = mix_distance(sigma[i][i], sigma[j][j]);
|
||||
cut[i][j] = mix_distance(cut[i][i], cut[j][j]);
|
||||
}
|
||||
|
||||
epsilon[j][i] = epsilon[i][j];
|
||||
sigma[j][i] = sigma[i][j];
|
||||
zeta[j][i] = zeta[i][j];
|
||||
mu[j][i] = mu[i][j];
|
||||
beta[j][i] = beta[i][j];
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairYLZ::write_restart(FILE *fp)
|
||||
{
|
||||
write_restart_settings(fp);
|
||||
|
||||
for (int i = 1; i <= atom->ntypes; i++) {
|
||||
for (int j = i; j <= atom->ntypes; j++) {
|
||||
fwrite(&setflag[i][j], sizeof(int), 1, fp);
|
||||
if (setflag[i][j]) {
|
||||
fwrite(&epsilon[i][j], sizeof(double), 1, fp);
|
||||
fwrite(&sigma[i][j], sizeof(double), 1, fp);
|
||||
fwrite(&cut[i][j], sizeof(double), 1, fp);
|
||||
fwrite(&zeta[i][j], sizeof(double), 1, fp);
|
||||
fwrite(&mu[i][j], sizeof(double), 1, fp);
|
||||
fwrite(&beta[i][j], sizeof(double), 1, fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairYLZ::read_restart(FILE *fp)
|
||||
{
|
||||
read_restart_settings(fp);
|
||||
allocate();
|
||||
|
||||
for (int i = 1; i <= atom->ntypes; i++) {
|
||||
for (int j = i; j <= atom->ntypes; j++) {
|
||||
if (comm->me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error);
|
||||
MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
|
||||
if (setflag[i][j]) {
|
||||
if (comm->me == 0) {
|
||||
utils::sfread(FLERR, &epsilon[i][j], sizeof(double), 1, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &sigma[i][j], sizeof(double), 1, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &zeta[i][j], sizeof(double), 1, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &mu[i][j], sizeof(double), 1, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &beta[i][j], sizeof(double), 1, fp, nullptr, error);
|
||||
}
|
||||
|
||||
MPI_Bcast(&epsilon[i][j], 1, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&sigma[i][j], 1, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&zeta[i][j], 1, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&mu[i][j], 1, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&beta[i][j], 1, MPI_DOUBLE, 0, world);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairYLZ::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&cut_global, sizeof(double), 1, fp);
|
||||
fwrite(&offset_flag, sizeof(int), 1, fp);
|
||||
fwrite(&mix_flag, sizeof(int), 1, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairYLZ::read_restart_settings(FILE *fp)
|
||||
{
|
||||
if (comm->me == 0) {
|
||||
|
||||
utils::sfread(FLERR, &cut_global, sizeof(double), 1, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &offset_flag, sizeof(int), 1, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &mix_flag, sizeof(int), 1, fp, nullptr, error);
|
||||
}
|
||||
|
||||
MPI_Bcast(&cut_global, 1, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&offset_flag, 1, MPI_INT, 0, world);
|
||||
MPI_Bcast(&mix_flag, 1, MPI_INT, 0, world);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairYLZ::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
fprintf(fp, "%d %g %g %g %g %g %g\n", i, epsilon[i][i], sigma[i][i], cut[i][i], zeta[i][i],
|
||||
mu[i][i], beta[i][i]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes all pairs to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairYLZ::write_data_all(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
for (int j = i; j <= atom->ntypes; j++)
|
||||
fprintf(fp, "%d %d %g %g %g %g %g %g\n", i, j, epsilon[i][i], sigma[i][i], cut[i][j],
|
||||
zeta[i][j], mu[i][j], beta[i][j]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute analytic energy, force (fforce), and torque (ttor & rtor)
|
||||
based on rotation matrices a
|
||||
if newton is off, rtor is not calculated for ghost atoms
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairYLZ::ylz_analytic(const int i, const int j, double a1[3][3], double a2[3][3],
|
||||
double *r12, const double rsq, double *fforce, double *ttor,
|
||||
double *rtor)
|
||||
|
||||
{
|
||||
int *type = atom->type;
|
||||
int newton_pair = force->newton_pair;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double r12hat[3];
|
||||
MathExtra::normalize3(r12, r12hat);
|
||||
double r = sqrt(rsq);
|
||||
|
||||
double ni1[3], nj1[3], dphi_drhat[3], dUdrhat[3], dUdni1[3], dUdnj1[3];
|
||||
double dphi_dni1[3], dphi_dnj1[3];
|
||||
double t, t1, t2, t4, cos_t, U, uR, uA, dUdr, dUdphi;
|
||||
const double energy_well = epsilon[type[i]][type[j]];
|
||||
const double rmin = MY_TWOBYSIXTH * sigma[type[i]][type[j]];
|
||||
const double rcut = cut[type[i]][type[j]];
|
||||
const double zt = zeta[type[i]][type[j]];
|
||||
const double muu = mu[type[i]][type[j]];
|
||||
const double sint = beta[type[i]][type[j]];
|
||||
|
||||
ni1[0] = a1[0][0];
|
||||
ni1[1] = a1[0][1];
|
||||
ni1[2] = a1[0][2];
|
||||
|
||||
nj1[0] = a2[0][0];
|
||||
nj1[1] = a2[0][1];
|
||||
nj1[2] = a2[0][2];
|
||||
|
||||
const double ninj = MathExtra::dot3(ni1, nj1);
|
||||
const double ni1rhat = MathExtra::dot3(ni1, r12hat);
|
||||
const double nj1rhat = MathExtra::dot3(nj1, r12hat);
|
||||
|
||||
const double a = ninj + (sint - ni1rhat) * (sint + nj1rhat) - 2.0 * sint * sint;
|
||||
const double phi = 1.0 + (a - 1.0) * muu;
|
||||
|
||||
dphi_drhat[0] = muu * ((sint - ni1rhat) * nj1[0] - ni1[0] * (sint + nj1rhat));
|
||||
dphi_drhat[1] = muu * ((sint - ni1rhat) * nj1[1] - ni1[1] * (sint + nj1rhat));
|
||||
dphi_drhat[2] = muu * ((sint - ni1rhat) * nj1[2] - ni1[2] * (sint + nj1rhat));
|
||||
|
||||
dphi_dni1[0] = muu * (nj1[0] - r12hat[0] * (sint + nj1rhat));
|
||||
dphi_dni1[1] = muu * (nj1[1] - r12hat[1] * (sint + nj1rhat));
|
||||
dphi_dni1[2] = muu * (nj1[2] - r12hat[2] * (sint + nj1rhat));
|
||||
|
||||
dphi_dnj1[0] = muu * (ni1[0] + r12hat[0] * (sint - ni1rhat));
|
||||
dphi_dnj1[1] = muu * (ni1[1] + r12hat[1] * (sint - ni1rhat));
|
||||
dphi_dnj1[2] = muu * (ni1[2] + r12hat[2] * (sint - ni1rhat));
|
||||
|
||||
if (r < rmin) {
|
||||
t = rmin / r;
|
||||
t2 = t * t;
|
||||
t4 = t2 * t2;
|
||||
uR = (t4 - 2.0 * t2) * energy_well;
|
||||
U = uR + (1.0 - phi) * energy_well;
|
||||
dUdr = 4.0 * (t2 - t4) / r * energy_well;
|
||||
dUdphi = -energy_well;
|
||||
} else {
|
||||
t = MY_PI2 * (r - rmin) / (rcut - rmin);
|
||||
cos_t = cos(t);
|
||||
t1 = cos_t;
|
||||
|
||||
for (int k = 1; k <= 2 * zt - 2; k++) t1 *= cos_t; // get cos()^(2zt-1)
|
||||
|
||||
uA = -energy_well * t1 * cos_t;
|
||||
U = uA * phi;
|
||||
dUdr = MY_4PI / (rcut - rmin) * (t1) *sin(t) * phi * energy_well;
|
||||
dUdphi = uA;
|
||||
}
|
||||
|
||||
dUdrhat[0] = dUdphi * dphi_drhat[0];
|
||||
dUdrhat[1] = dUdphi * dphi_drhat[1];
|
||||
dUdrhat[2] = dUdphi * dphi_drhat[2];
|
||||
|
||||
double dUdrhatrhat = MathExtra::dot3(dUdrhat, r12hat);
|
||||
|
||||
fforce[0] = dUdr * r12hat[0] + (dUdrhat[0] - dUdrhatrhat * r12hat[0]) / r;
|
||||
fforce[1] = dUdr * r12hat[1] + (dUdrhat[1] - dUdrhatrhat * r12hat[1]) / r;
|
||||
fforce[2] = dUdr * r12hat[2] + (dUdrhat[2] - dUdrhatrhat * r12hat[2]) / r;
|
||||
|
||||
// torque i
|
||||
|
||||
dUdni1[0] = dUdphi * dphi_dni1[0];
|
||||
dUdni1[1] = dUdphi * dphi_dni1[1];
|
||||
dUdni1[2] = dUdphi * dphi_dni1[2];
|
||||
|
||||
MathExtra::cross3(dUdni1, ni1, ttor); //minus sign is replace by swapping ni1 and dUdni1
|
||||
|
||||
if (newton_pair || j < nlocal) {
|
||||
|
||||
dUdnj1[0] = dUdphi * dphi_dnj1[0];
|
||||
dUdnj1[1] = dUdphi * dphi_dnj1[1];
|
||||
dUdnj1[2] = dUdphi * dphi_dnj1[2];
|
||||
|
||||
MathExtra::cross3(dUdnj1, nj1, rtor); //minus sign is replace by swapping ni1 and dUdni1
|
||||
}
|
||||
return U;
|
||||
}
|
||||
56
src/ASPHERE/pair_ylz.h
Normal file
56
src/ASPHERE/pair_ylz.h
Normal file
@ -0,0 +1,56 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/ Sandia National Laboratories
|
||||
LAMMPS Development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
// clang-format off
|
||||
PairStyle(ylz,PairYLZ);
|
||||
// clang-format on
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_YLZ_H
|
||||
#define LMP_PAIR_YLZ_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairYLZ : public Pair {
|
||||
public:
|
||||
PairYLZ(LAMMPS *lmp);
|
||||
virtual ~PairYLZ();
|
||||
virtual void compute(int, int);
|
||||
virtual void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
virtual void init_style();
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
void write_data(FILE *);
|
||||
void write_data_all(FILE *);
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
double **epsilon, **sigma, **cut, **zeta, **mu, **beta;
|
||||
|
||||
class AtomVecEllipsoid *avec;
|
||||
|
||||
void allocate();
|
||||
double ylz_analytic(const int i, const int j, double a1[3][3], double a2[3][3], double *r12,
|
||||
const double rsq, double *fforce, double *ttor, double *rtor);
|
||||
};
|
||||
} // namespace LAMMPS_NS
|
||||
#endif
|
||||
#endif
|
||||
@ -30,7 +30,8 @@ namespace MathConst {
|
||||
static constexpr double MY_ISPI4 = 1.12837916709551257389; // 1/sqrt(pi/4)
|
||||
static constexpr double MY_SQRT2 = 1.41421356237309504880; // sqrt(2)
|
||||
static constexpr double MY_ISQRT2 = 0.707106781186547524401; // 1/sqrt(2)
|
||||
static constexpr double MY_CUBEROOT2 = 1.25992104989487316476; // 2*(1/3)
|
||||
static constexpr double MY_CUBEROOT2 = 1.25992104989487316476; // 2^(1/3)
|
||||
static constexpr double MY_TWOBYSIXTH = 1.12246204830937298142; // 2^(1/6) //
|
||||
static constexpr double DEG2RAD = MY_PI / 180.0; // degree to radians
|
||||
static constexpr double RAD2DEG = 180.0 / MY_PI; // radians to degree
|
||||
} // namespace MathConst
|
||||
|
||||
@ -49,7 +49,7 @@ else()
|
||||
target_compile_definitions(style_tests PRIVATE TEST_INPUT_FOLDER=${TEST_INPUT_FOLDER} YAML_DECLARE_STATIC)
|
||||
endif()
|
||||
target_include_directories(style_tests PRIVATE ${LAMMPS_SOURCE_DIR})
|
||||
target_link_libraries(style_tests PUBLIC gmock Yaml::Yaml lammps)
|
||||
target_link_libraries(style_tests PUBLIC GTest::GMock Yaml::Yaml lammps)
|
||||
|
||||
# propagate sanitizer options to test tools
|
||||
if(ENABLE_SANITIZER AND (NOT (ENABLE_SANITIZER STREQUAL "none")))
|
||||
@ -62,7 +62,7 @@ endif()
|
||||
# unit test for error stats class
|
||||
add_executable(test_error_stats test_error_stats.cpp)
|
||||
target_include_directories(test_error_stats PRIVATE ${CMAKE_CURRENT_SOURCE_DIR} ${LAMMPS_SOURCE_DIR})
|
||||
target_link_libraries(test_error_stats PRIVATE gtest_main)
|
||||
target_link_libraries(test_error_stats PRIVATE GTest::GMockMain)
|
||||
add_test(NAME ErrorStats COMMAND test_error_stats)
|
||||
|
||||
# pair style tester
|
||||
|
||||
Reference in New Issue
Block a user