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Merge remote-tracking branch 'github/develop' into collected-small-changes

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This commit is contained in:
Axel Kohlmeyer
2024-06-19 14:46:04 -04:00
parent 80556214e4 629a9cbe3d
commit 778d11c79e
33 changed files with 3706 additions and 22 deletions
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2
.github/CODEOWNERS vendored
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@ -73,6 +73,8 @@ src/MC/fix_sgcmc.* @athomps
src/REAXFF/compute_reaxff_atom.* @rbberger src/REAXFF/compute_reaxff_atom.* @rbberger
src/KOKKOS/compute_reaxff_atom_kokkos.* @rbberger src/KOKKOS/compute_reaxff_atom_kokkos.* @rbberger
src/REPLICA/fix_pimd_langevin.* @Yi-FanLi src/REPLICA/fix_pimd_langevin.* @Yi-FanLi
src/DPD-BASIC/pair_dpd_coul_slater_long.* @Eddy-Barraud
src/GPU/pair_dpd_coul_slater_long.* @Eddy-Barraud
# core LAMMPS classes # core LAMMPS classes
src/lammps.* @sjplimp src/lammps.* @sjplimp

2
cmake/CMakeLists.txt
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@ -690,7 +690,7 @@ endif()
# packages which selectively include variants based on enabled styles # packages which selectively include variants based on enabled styles
# e.g. accelerator packages # e.g. accelerator packages
###################################################################### ######################################################################
foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU) foreach(PKG_WITH_INCL CORESHELL DPD-BASIC DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
if(PKG_${PKG_WITH_INCL}) if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL}) include(Packages/${PKG_WITH_INCL})
endif() endif()

9
cmake/Modules/Packages/DPD-BASIC.cmake Normal file
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@ -0,0 +1,9 @@
# pair style dpd/coul/slater/long may only be installed if also KSPACE is installed
if(NOT PKG_KSPACE)
get_property(LAMMPS_PAIR_HEADERS GLOBAL PROPERTY PAIR)
list(REMOVE_ITEM LAMMPS_PAIR_HEADERS ${LAMMPS_SOURCE_DIR}/DPD-BASIC/pair_dpd_coul_slater_long.h)
set_property(GLOBAL PROPERTY PAIR "${LAMMPS_PAIR_HEADERS}")
get_target_property(LAMMPS_SOURCES lammps SOURCES)
list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/DPD-BASIC/pair_dpd_coul_slater_long.cpp)
set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
endif()

14
cmake/Modules/Packages/PLUMED.cmake
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@ -1,5 +1,9 @@
# Plumed2 support for PLUMED package # Plumed2 support for PLUMED package
# for supporting multiple concurrent plumed2 installations for debugging and testing
set(PLUMED_SUFFIX "" CACHE STRING "Suffix for Plumed2 library")
mark_as_advanced(PLUMED_SUFFIX)
if(BUILD_MPI) if(BUILD_MPI)
set(PLUMED_CONFIG_MPI "--enable-mpi") set(PLUMED_CONFIG_MPI "--enable-mpi")
set(PLUMED_CONFIG_CC ${CMAKE_MPI_C_COMPILER}) set(PLUMED_CONFIG_CC ${CMAKE_MPI_C_COMPILER})
@ -153,15 +157,15 @@ else()
file(MAKE_DIRECTORY ${INSTALL_DIR}/include) file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
else() else()
find_package(PkgConfig REQUIRED) find_package(PkgConfig REQUIRED)
pkg_check_modules(PLUMED REQUIRED plumed) pkg_check_modules(PLUMED REQUIRED plumed${PLUMED_SUFFIX})
add_library(LAMMPS::PLUMED INTERFACE IMPORTED) add_library(LAMMPS::PLUMED INTERFACE IMPORTED)
if(PLUMED_MODE STREQUAL "STATIC") if(PLUMED_MODE STREQUAL "STATIC")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static) include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.static)
elseif(PLUMED_MODE STREQUAL "SHARED") elseif(PLUMED_MODE STREQUAL "SHARED")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared) include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.shared)
elseif(PLUMED_MODE STREQUAL "RUNTIME") elseif(PLUMED_MODE STREQUAL "RUNTIME")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}") set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${PLUMED_SUFFIX}Kernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime) include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.runtime)
endif() endif()
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}") set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}") set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}")

3
doc/src/Commands_pair.rst
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@ -94,9 +94,10 @@ OPT.
* :doc:`coul/wolf (ko) <pair_coul>` * :doc:`coul/wolf (ko) <pair_coul>`
* :doc:`coul/wolf/cs <pair_cs>` * :doc:`coul/wolf/cs <pair_cs>`
* :doc:`dpd (giko) <pair_dpd>` * :doc:`dpd (giko) <pair_dpd>`
* :doc:`dpd/fdt <pair_dpd_fdt>` * :doc:`dpd/coul/slater/long (g) <pair_dpd_coul_slater_long>`
* :doc:`dpd/ext (ko) <pair_dpd_ext>` * :doc:`dpd/ext (ko) <pair_dpd_ext>`
* :doc:`dpd/ext/tstat (ko) <pair_dpd_ext>` * :doc:`dpd/ext/tstat (ko) <pair_dpd_ext>`
* :doc:`dpd/fdt <pair_dpd_fdt>`
* :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>` * :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
* :doc:`dpd/tstat (gko) <pair_dpd>` * :doc:`dpd/tstat (gko) <pair_dpd>`
* :doc:`dsmc <pair_dsmc>` * :doc:`dsmc <pair_dsmc>`

8
doc/src/Packages_details.rst
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@ -677,7 +677,12 @@ DPD-BASIC package
Pair styles for the basic dissipative particle dynamics (DPD) method Pair styles for the basic dissipative particle dynamics (DPD) method
and DPD thermostatting. and DPD thermostatting.
**Author:** Kurt Smith (U Pittsburgh), Martin Svoboda, Martin Lisal (ICPF and UJEP) Pair style :doc:`dpd/coul/slater/long <pair_dpd_coul_slater_long>` also
includes smeared charges for coulomb interactions and thus requires the
:ref:`KSPACE <PKG-KSPACE>` package to be installed to handle the long-range
Coulomb part of the interactions.
**Authors:** Kurt Smith (U Pittsburgh), Martin Svoboda, Martin Lisal (ICPF and UJEP), Eddy Barraud (IFPEN)
**Supporting info:** **Supporting info:**
@ -686,6 +691,7 @@ and DPD thermostatting.
* :doc:`pair_style dpd/tstat <pair_dpd>` * :doc:`pair_style dpd/tstat <pair_dpd>`
* :doc:`pair_style dpd/ext <pair_dpd_ext>` * :doc:`pair_style dpd/ext <pair_dpd_ext>`
* :doc:`pair_style dpd/ext/tstat <pair_dpd_ext>` * :doc:`pair_style dpd/ext/tstat <pair_dpd_ext>`
* :doc:`pair_style dpd/coul/slater/long <pair_dpd_coul_slater_long>`
* examples/PACKAGES/dpd-basic * examples/PACKAGES/dpd-basic
---------- ----------

177
doc/src/pair_dpd_coul_slater_long.rst Normal file
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@ -0,0 +1,177 @@
.. index:: pair_style dpd/coul/slater/long
.. index:: pair_style dpd/coul/slater/long/gpu
pair_style dpd/coul/slater/long command
=======================================
Accelerator Variants: *dpd/coul/slater/long/gpu*
Syntax
""""""
.. code-block:: LAMMPS
pair_style dpd/coul/slater/long T cutoff_DPD seed lambda cutoff_coul
pair_coeff I J a_IJ Gamma is_charged
* T = temperature (temperature units) (dpd only)
* cutoff_DPD = global cutoff for DPD interactions (distance units)
* seed = random # seed (positive integer)
* lambda = decay length of the charge (distance units)
* cutoff_coul = real part cutoff for Coulombic interactions (distance units)
* I,J = numeric atom types, or type labels
* Gamma = DPD Gamma coefficient
* is_charged (boolean) set to yes if I and J are charged beads
Examples
""""""""
.. code-block:: LAMMPS
pair_style dpd/coul/slater/long 1.0 2.5 34387 0.25 3.0
pair_coeff 1 1 78.0 4.5 # not charged by default
pair_coeff 2 2 78.0 4.5 yes
Description
"""""""""""
Style *dpd/coul/slater/long* computes a force field for dissipative particle dynamics
(DPD) following the exposition in :ref:`(Groot) <Groot5>` with the addition of
electrostatic interactions. The coulombic forces in mesoscopic models
employ potentials without explicit excluded-volume interactions.
The goal is to prevent artificial ionic pair formation by including a charge
distribution in the Coulomb potential, following the formulation of
:ref:`(Melchor) <Melchor>`:
The force on bead I due to bead J is given as a sum
of 4 terms
.. math::
\vec{f} = & (F^C + F^D + F^R + F^E) \hat{r_{ij}} \\
F^C = & A w(r) \qquad \qquad \qquad \qquad \qquad r < r_c \\
F^D = & - \gamma w^2(r) (\hat{r_{ij}} \bullet \vec{v}_{ij}) \qquad \qquad r < r_c \\
F^R = & \sigma w(r) \alpha (\Delta t)^{-1/2} \qquad \qquad \qquad r < r_c \\
w(r) = & 1 - \frac{r}{r_c} \\
F^E = & \frac{Cq_iq_j}{\epsilon r^2} \left( 1- exp\left( \frac{2r_{ij}}{\lambda} \right) \left( 1 + \frac{2r_{ij}}{\lambda} \left( 1 + \frac{r_{ij}}{\lambda} \right)\right) \right)
where :math:`F^C` is a conservative force, :math:`F^D` is a dissipative
force, :math:`F^R` is a random force, and :math:`F^E` is an electrostatic force.
:math:`\hat{r_{ij}}` is a unit vector in the direction
:math:`r_i - r_j`, :math:`\vec{v}_{ij}` is
the vector difference in velocities of the two atoms :math:`\vec{v}_i -
\vec{v}_j`, :math:`\alpha` is a Gaussian random number with zero mean
and unit variance, *dt* is the timestep size, and :math:`w(r)` is a
weighting factor that varies between 0 and 1. :math:`r_c` is the
pairwise cutoff. :math:`\sigma` is set equal to :math:`\sqrt{2 k_B T
\gamma}`, where :math:`k_B` is the Boltzmann constant and *T* is the
temperature parameter in the pair_style command.
C is the same Coulomb conversion factor as in the pair_styles
coul/cut and coul/long. In this way the Coulomb
interaction between ions is corrected at small distances r, and
the long-range interactions are computed either by the Ewald or the PPPM technique.
The following parameters 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:
* A (force units)
* :math:`\gamma` (force/velocity units)
* is_charged (boolean)
.. note::
This style is the combination of :doc:`pair_style dpd <pair_dpd>` and :doc:`pair_style coul/slater/long <pair_coul_slater>`.
----------
.. include:: accel_styles.rst
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This pair style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
This pair style does not support the :doc:`pair_modify <pair_modify>`
shift option for the energy of the pair interaction.
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. Note that the
user-specified random number seed is stored in the restart file, so when
a simulation is restarted, each processor will re-initialize its random
number generator the same way it did initially. This means the random
forces will be random, but will not be the same as they would have been
if the original simulation had continued past the restart time.
This pair style can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. They do not support the
*inner*, *middle*, *outer* keywords.
----------
Restrictions
""""""""""""
This style is part of the DPD-BASIC package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
The default frequency for rebuilding neighbor lists is every 10 steps
(see the :doc:`neigh_modify <neigh_modify>` command). This may be too
infrequent since particles move rapidly and
can overlap by large amounts. If this setting yields a non-zero number
of "dangerous" reneighborings (printed at the end of a simulation), you
should experiment with forcing reneighboring more often and see if
system energies/trajectories change.
This pair style requires you to use the :doc:`comm_modify vel yes
<comm_modify>` command so that velocities are stored by ghost atoms.
This pair style also requires the long-range solvers included in the KSPACE package.
This pair style will not restart exactly when using the
:doc:`read_restart <read_restart>` command, though they should provide
statistically similar results. This is because the forces they compute
depend on atom velocities. See the :doc:`read_restart <read_restart>`
command for more details.
Related commands
""""""""""""""""
:doc:`pair_style dpd <pair_dpd>`, :doc:`pair_style coul/slater/long <pair_coul_slater>`,
:doc:`pair_coeff <pair_coeff>`, :doc:`fix nvt <fix_nh>`, :doc:`fix langevin <fix_langevin>`,
:doc:`pair_style srp <pair_srp>`, :doc:`fix mvv/dpd <fix_mvv_dpd>`.
Default
"""""""
is_charged = no
----------
.. _Groot5:
**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
.. _Melchor:
**(Melchor)** Gonzalez-Melchor, Mayoral, Velazquez, and Alejandre, J Chem Phys, 125, 224107 (2006).

1
doc/src/pair_style.rst
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@ -172,6 +172,7 @@ accelerated styles exist.
* :doc:`coul/wolf <pair_coul>` - Coulomb via Wolf potential * :doc:`coul/wolf <pair_coul>` - Coulomb via Wolf potential
* :doc:`coul/wolf/cs <pair_cs>` - Coulomb via Wolf potential with core/shell adjustments * :doc:`coul/wolf/cs <pair_cs>` - Coulomb via Wolf potential with core/shell adjustments
* :doc:`dpd <pair_dpd>` - dissipative particle dynamics (DPD) * :doc:`dpd <pair_dpd>` - dissipative particle dynamics (DPD)
* :doc:`dpd/coul/slater/long <pair_dpd_coul_slater_long>` - dissipative particle dynamics (DPD) with electrostatic interactions
* :doc:`dpd/ext <pair_dpd_ext>` - generalized force field for DPD * :doc:`dpd/ext <pair_dpd_ext>` - generalized force field for DPD
* :doc:`dpd/ext/tstat <pair_dpd_ext>` - pairwise DPD thermostatting with generalized force field * :doc:`dpd/ext/tstat <pair_dpd_ext>` - pairwise DPD thermostatting with generalized force field
* :doc:`dpd/fdt <pair_dpd_fdt>` - DPD for constant temperature and pressure * :doc:`dpd/fdt <pair_dpd_fdt>` - DPD for constant temperature and pressure

2
examples/PACKAGES/dpd-basic/README
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@ -14,3 +14,5 @@ pair styles from the DPD-BASIC package.
4) 'dpdext_tstat' - coarse-grained SPC/E water example for 'dpd/ext/tstat' pair style 4) 'dpdext_tstat' - coarse-grained SPC/E water example for 'dpd/ext/tstat' pair style
(in.dpdext_tstat), an initial configuration (dpdext.data) and tabulated potential (in.dpdext_tstat), an initial configuration (dpdext.data) and tabulated potential
(cg_spce_table.pot) obtained by bottom-up coarse-graining of the atomistic SPC/E water. (cg_spce_table.pot) obtained by bottom-up coarse-graining of the atomistic SPC/E water.
5) 'dpd_coul_slater_long' - simple example (DPD ionic fluid) for 'dpd/coul/slater/long' pair style (in.dpd_coul_slater_long).

779
examples/PACKAGES/dpd-basic/dpd_coul_slater_long/data.dpd_coul_slater_long Normal file
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@ -0,0 +1,779 @@
LAMMPS data file via write_data, version 17 Apr 2024, timestep = 1394, units = lj
375 atoms
3 atom types
0 5 xlo xhi
0 5 ylo yhi
0 5 zlo zhi
Masses
1 1
2 1
3 1
PairIJ Coeffs # dpd/coul/slater/long
1 1 78 4.5 yes 1
1 2 78 4.5 yes 1
1 3 78 4.5 yes 1
2 2 78 4.5 no 1
2 3 78 4.5 no 1
3 3 78 4.5 no 1
Atoms # full
189 0 1 0 0.8621554018960034 1.5213257556560191 0.4064444607843129 0 1 0
107 0 1 0 2.040249318291146 0.3862591116608294 1.8661957131854634 0 0 0
253 0 1 0 3.511834308089607 0.7338273870464224 0.801173549802059 0 1 1
163 0 1 0 2.303289649738226 0.6809493239075631 0.7383435796468727 0 1 0
26 0 1 0 0.03534770106704549 1.4889933012536283 1.4815498922617432 0 0 0
27 0 1 0 4.170525658289272 1.8438490221677797 2.1918634082517614 -1 0 0
56 0 1 0 2.9501314702448633 2.322938987390429 0.6158870411938201 0 0 0
167 0 1 0 1.948558457807243 0.1261294591496785 0.039492485708843984 0 1 0
364 0 3 -1 4.538825953029656 0.2655458359259118 2.131668601530241 0 1 0
61 0 1 0 4.645784299395809 0.3574274125207269 1.7056474795918568 -1 0 0
222 0 1 0 4.41481966340897 2.262979887349817 1.1679075968940398 0 0 0
332 0 2 1 3.853874714249102 0.1758912358513287 0.8799773810713412 0 1 0
1 0 1 0 4.608301143657016 1.4090100132224024 1.218887039455649 -1 0 0
319 0 2 1 3.732213186171727 0.981827023519373 2.3857377768158727 -1 0 0
53 0 1 0 2.380311878254328 0.953677113042391 1.8268738776443192 0 0 0
68 0 1 0 0.33279009298924916 1.0106375746131884 0.7038515854567269 0 0 0
220 0 1 0 1.1094848303775686 2.378414106514282 1.4793246435196352 1 0 0
44 0 1 0 0.12449238274832848 1.7475396894040345 0.5495194876290164 0 0 0
55 0 1 0 0.1451415441609303 2.337329820574407 0.940744164662616 0 0 0
362 0 3 -1 1.2987762452744613 1.8352325797868587 1.1809674941775483 0 0 0
165 0 1 0 0.6610209400465688 2.22554349560855 1.971912177574677 0 0 0
60 0 1 0 1.8643313870571518 0.6352678895179578 1.4416996493100478 0 0 0
202 0 1 0 0.007896731087640774 1.5385720917803027 0.18965671583085075 0 1 0
85 0 1 0 1.5630176980330266 1.1482985441214197 2.019916217302335 1 0 0
73 0 1 0 0.5556133646182337 1.6170466333456652 2.101792903006452 0 0 0
96 0 1 0 1.6611967219346682 0.07688637034882238 0.46572063062814617 0 0 1
30 0 1 0 0.46644353751713447 1.8254820637852556 1.2380479793915407 1 0 0
67 0 1 0 3.4270812515248483 2.350996339385886 1.77527952461483 0 0 0
349 0 3 -1 1.7935506583370944 1.7235931740659332 0.4478371869612185 1 0 0
132 0 1 0 4.951074988035153 1.5039089286454406 2.4219801232797398 -1 0 0
328 0 2 1 0.8958492991096989 1.2809413147557527 1.0440931858570435 0 0 1
161 0 1 0 4.798276598985588 0.9882558902185279 2.462987088497934 0 1 0
185 0 1 0 0.6126520391294695 0.04940161418784647 0.6135262263024062 0 1 0
219 0 1 0 1.647872968759676 2.305100092833184 2.0217182617222096 0 0 0
8 0 1 0 2.8077478718165207 0.7661158156519451 1.3602857540877684 0 0 0
69 0 1 0 2.8568644931819835 0.13340029053585767 2.106212637519767 0 0 0
3 0 1 0 1.908450187819087 2.298808713848062 0.4221817812562634 0 0 0
7 0 1 0 1.8799145446976495 0.9814789886011673 0.955308672406064 0 0 0
329 0 2 1 0.9727877144189607 0.8906662949552561 1.4472553696387669 0 1 0
174 0 1 0 3.9905681672951636 0.6401683928312465 1.0284041192891435 -1 1 0
20 0 1 0 3.392515194191721 2.0774851454870427 0.8812446323305514 0 0 0
57 0 1 0 4.874212056539195 0.13899230379169403 0.7199140773346149 0 0 0
325 0 2 1 1.362093021934204 2.3422237404192465 0.6655225660551776 0 0 1
40 0 1 0 4.306473534903154 1.7047871476017826 0.8560715024613603 0 0 0
51 0 1 0 2.297377802384159 0.11499650506694176 1.4731005354419167 0 0 0
54 0 1 0 2.971300335884777 1.8792385205105047 1.3973014092900102 0 0 0
186 0 1 0 3.583414064904102 1.7542346893771112 0.35130247738019466 0 0 0
289 0 1 0 2.5651653875350906 1.4858962835620086 0.6587351599193196 0 0 1
75 0 1 0 3.132107705055228 0.19794042232605677 0.44488993973642094 0 0 1
48 0 1 0 3.4384178020381717 0.7217742755424055 1.7304812232062636 0 0 0
66 0 1 0 3.191389133037332 1.1674191637093172 1.7413707516914332 0 0 0
52 0 1 0 1.856006413772654 1.871405713016935 1.5164995404363106 0 0 0
158 0 1 0 3.725559226243618 1.2320067990055215 0.4240371305587515 -1 1 0
330 0 2 1 0.4226192821951129 0.22648053650193767 0.04025715930862768 1 1 0
359 0 3 -1 4.4476116877707925 0.8271711042623823 1.1688054720798116 0 1 0
366 0 3 -1 0.13989896192253948 0.6502137062351493 0.845841913773404 1 1 0
196 0 1 0 0.21878194805964699 2.4139077401885523 1.602735237996178 1 0 0
128 0 1 0 2.474112780481313 1.5036993910540244 1.234391076605564 0 0 1
118 0 1 0 0.1703454662324439 0.9401878407982331 0.17224714060344348 0 0 1
43 0 1 0 3.708324777814944 2.4767443359210524 0.5791362456922102 0 0 0
184 0 1 0 0.4061592126934206 0.22209165285150972 1.3598048859115588 0 1 0
360 0 3 -1 1.225690366400486 0.4472136514952278 1.0864811555493794 0 1 0
64 0 1 0 2.6116937036965266 1.793563094424563 2.091822223631947 0 0 0
285 0 1 0 0.7747031518566616 0.24118573693540882 2.1434463705260494 0 1 0
58 0 1 0 1.598997109049339 1.2355543729347458 1.1437352681100093 0 0 0
257 0 1 0 0.02882436640692898 0.8179392413775496 1.6880006059524528 1 1 0
356 0 3 -1 2.0441963785801733 1.236982129976697 2.2147135788798726 0 0 0
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240 0.705376364763962 -0.6227531276788822 1.6071635134558022

58
examples/PACKAGES/dpd-basic/dpd_coul_slater_long/in.dpd_coul_slater_long Normal file
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@ -0,0 +1,58 @@
# DPD Ionic Fluid
variable T equal 1.0
variable cut_DPD equal 1.0
variable seed equal 165412
variable lambda equal 0.25
variable cut_coul equal 2.0
#-------------------------------------------------------------------------------
# Initialize LAMMPS run for 3-d periodic
#-------------------------------------------------------------------------------
units lj
boundary p p p # periodic at all axes
atom_style full
dimension 3
bond_style none
angle_style none
dihedral_style none
improper_style none
newton on
comm_modify vel yes # store info of ghost atoms btw processors
#-------------------------------------------------------------------------------
# Box creation and configuration
#-------------------------------------------------------------------------------
# Define pair style and coefficients
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
read_data data.dpd_coul_slater_long
# Enable long range electrostatics solver
kspace_style pppm 1e-04
# Construct neighbors every steps
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
#-------------------------------------------------------------------------------
# Run the simulation
#-------------------------------------------------------------------------------
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
thermo_modify norm no
thermo 100
timestep 0.01
run_style verlet
fix 1 all nve
run 1000
unfix 1

147
examples/PACKAGES/dpd-basic/dpd_coul_slater_long/log.19Jun24.dpd_coul_slater.g++.1 Normal file
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LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-262-g0aff26705c-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# DPD Ionic Fluid
variable T equal 1.0
variable cut_DPD equal 1.0
variable seed equal 165412
variable lambda equal 0.25
variable cut_coul equal 2.0
#-------------------------------------------------------------------------------
# Initialize LAMMPS run for 3-d periodic
#-------------------------------------------------------------------------------
units lj
boundary p p p # periodic at all axes
atom_style full
dimension 3
bond_style none
angle_style none
dihedral_style none
improper_style none
newton on
comm_modify vel yes # store info of ghost atoms btw processors
#-------------------------------------------------------------------------------
# Box creation and configuration
#-------------------------------------------------------------------------------
# Define pair style and coefficients
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 0.25 2
read_data data.dpd_coul_slater_long
Reading data file ...
orthogonal box = (0 0 0) to (5 5 5)
1 by 1 by 1 MPI processor grid
reading atoms ...
375 atoms
reading velocities ...
375 velocities
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
# Enable long range electrostatics solver
kspace_style pppm 1e-04
# Construct neighbors every steps
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
#-------------------------------------------------------------------------------
# Run the simulation
#-------------------------------------------------------------------------------
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
thermo_modify norm no
thermo 100
timestep 0.01
run_style verlet
fix 1 all nve
run 1000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 1.4828454
grid = 20 20 20
stencil order = 5
estimated absolute RMS force accuracy = 7.7240141e-05
estimated relative force accuracy = 7.7240141e-05
using double precision FFTW3
3d grid and FFT values/proc = 24389 8000
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3
ghost atom cutoff = 3
binsize = 1.5, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair dpd/coul/slater/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.359 | 8.359 | 8.359 Mbytes
Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax
0 0.9849949 69.271905 125 4673.0443 0 -30.365103 4642.6792 552.58214 646.76798 65.851035
100 1.0614027 69.794624 125 4659.0139 0 -31.906319 4627.1075 595.44692 612.94396 60.338653
200 0.9422517 68.721098 125 4687.8862 0 -33.81531 4654.0709 528.6032 620.25627 62.726994
300 0.8956649 69.323482 125 4721.0824 0 -33.854275 4687.2281 502.46801 670.22699 73.087908
400 0.99584547 69.670416 125 4713.9086 0 -30.783633 4683.125 558.66931 607.65881 59.224652
500 1.0565931 69.497816 125 4701.2584 0 -26.80545 4674.4529 592.74873 646.18907 71.398122
600 1.0071523 70.26222 125 4659.2061 0 -29.98909 4629.217 565.01243 630.00244 58.264115
700 1.0507355 67.920078 125 4695.255 0 -32.649209 4662.6058 589.46259 651.80459 70.573524
800 0.98561942 68.279591 125 4745.7603 0 -28.98491 4716.7754 552.9325 627.14371 67.196483
900 0.96470105 70.742864 125 4706.3605 0 -30.271633 4676.0889 541.19729 644.43036 79.474998
1000 1.0204819 70.164419 125 4654.6077 0 -27.797433 4626.8103 572.49035 624.19728 71.825307
Loop time of 2.10153 on 1 procs for 1000 steps with 375 atoms
Performance: 411128.483 tau/day, 475.843 timesteps/s, 178.441 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1779 | 1.1779 | 1.1779 | 0.0 | 56.05
Bond | 6.507e-05 | 6.507e-05 | 6.507e-05 | 0.0 | 0.00
Kspace | 0.74636 | 0.74636 | 0.74636 | 0.0 | 35.51
Neigh | 0.12903 | 0.12903 | 0.12903 | 0.0 | 6.14
Comm | 0.039726 | 0.039726 | 0.039726 | 0.0 | 1.89
Output | 0.00027587 | 0.00027587 | 0.00027587 | 0.0 | 0.01
Modify | 0.0037596 | 0.0037596 | 0.0037596 | 0.0 | 0.18
Other | | 0.004451 | | | 0.21
Nlocal: 375 ave 375 max 375 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3613 ave 3613 max 3613 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 62354 ave 62354 max 62354 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 62354
Ave neighs/atom = 166.27733
Ave special neighs/atom = 0
Neighbor list builds = 65
Dangerous builds = 0
unfix 1
Total wall time: 0:00:02

147
examples/PACKAGES/dpd-basic/dpd_coul_slater_long/log.19Jun24.dpd_coul_slater.g++.4 Normal file
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@ -0,0 +1,147 @@
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-262-g0aff26705c-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# DPD Ionic Fluid
variable T equal 1.0
variable cut_DPD equal 1.0
variable seed equal 165412
variable lambda equal 0.25
variable cut_coul equal 2.0
#-------------------------------------------------------------------------------
# Initialize LAMMPS run for 3-d periodic
#-------------------------------------------------------------------------------
units lj
boundary p p p # periodic at all axes
atom_style full
dimension 3
bond_style none
angle_style none
dihedral_style none
improper_style none
newton on
comm_modify vel yes # store info of ghost atoms btw processors
#-------------------------------------------------------------------------------
# Box creation and configuration
#-------------------------------------------------------------------------------
# Define pair style and coefficients
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 0.25 2
read_data data.dpd_coul_slater_long
Reading data file ...
orthogonal box = (0 0 0) to (5 5 5)
1 by 2 by 2 MPI processor grid
reading atoms ...
375 atoms
reading velocities ...
375 velocities
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
# Enable long range electrostatics solver
kspace_style pppm 1e-04
# Construct neighbors every steps
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
#-------------------------------------------------------------------------------
# Run the simulation
#-------------------------------------------------------------------------------
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
thermo_modify norm no
thermo 100
timestep 0.01
run_style verlet
fix 1 all nve
run 1000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 1.4828454
grid = 20 20 20
stencil order = 5
estimated absolute RMS force accuracy = 7.7240141e-05
estimated relative force accuracy = 7.7240141e-05
using double precision FFTW3
3d grid and FFT values/proc = 10469 2000
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3
ghost atom cutoff = 3
binsize = 1.5, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair dpd/coul/slater/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.208 | 7.208 | 7.209 Mbytes
Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax
0 0.9849949 69.076433 125 4673.0443 0 -30.365103 4642.6792 552.58214 613.18374 70.700582
100 0.95374867 69.110009 125 4681.1097 0 -31.260804 4649.8489 535.053 629.95109 62.05418
200 1.0076152 69.824904 125 4670.7458 0 -28.382203 4642.3636 565.27213 656.8501 72.049813
300 1.0014752 69.666331 125 4696.454 0 -26.943577 4669.5105 561.8276 631.49861 74.737274
400 0.98863876 69.731774 125 4700.7552 0 -23.816077 4676.9391 554.62634 637.74742 68.928573
500 0.95782852 68.588075 125 4698.588 0 -29.249543 4669.3385 537.3418 646.31897 68.800569
600 0.97443232 70.864079 125 4674.8821 0 -26.415644 4648.4664 546.65653 606.50755 78.664429
700 0.98783988 68.908299 125 4692.5536 0 -28.092022 4664.4616 554.17817 638.98401 69.691814
800 0.98000145 69.83977 125 4706.6365 0 -29.648365 4676.9881 549.78082 626.84362 73.133934
900 1.0526251 69.466078 125 4671.9648 0 -30.941117 4641.0237 590.52269 618.1049 62.333546
1000 0.98340746 69.527121 125 4728.2894 0 -31.869907 4696.4195 551.69159 630.14208 61.392611
Loop time of 0.928543 on 4 procs for 1000 steps with 375 atoms
Performance: 930490.137 tau/day, 1076.956 timesteps/s, 403.859 katom-step/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.30761 | 0.34974 | 0.38864 | 4.9 | 37.67
Bond | 8.4633e-05 | 9.0539e-05 | 9.9184e-05 | 0.0 | 0.01
Kspace | 0.39038 | 0.42976 | 0.47215 | 4.4 | 46.28
Neigh | 0.033986 | 0.035576 | 0.036791 | 0.5 | 3.83
Comm | 0.10247 | 0.10324 | 0.10481 | 0.3 | 11.12
Output | 0.00024145 | 0.00027404 | 0.00036867 | 0.0 | 0.03
Modify | 0.0022402 | 0.0025068 | 0.0026343 | 0.3 | 0.27
Other | | 0.007356 | | | 0.79
Nlocal: 93.75 ave 96 max 93 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 2289.75 ave 2317 max 2271 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Neighs: 15590.2 ave 16765 max 14540 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 62361
Ave neighs/atom = 166.296
Ave special neighs/atom = 0
Neighbor list builds = 64
Dangerous builds = 0
unfix 1
Total wall time: 0:00:00

4
lib/gpu/lal_base_dpd.cpp
View File

@ -57,7 +57,7 @@ int BaseDPDT::init_atomic(const int nlocal, const int nall,
const double cell_size, const double gpu_split, const double cell_size, const double gpu_split,
FILE *_screen, const void *pair_program, FILE *_screen, const void *pair_program,
const char *k_name, const int onetype, const char *k_name, const int onetype,
const int extra_fields) { const int extra_fields, bool need_charges) {
screen=_screen; screen=_screen;
int gpu_nbor=0; int gpu_nbor=0;
@ -73,7 +73,7 @@ int BaseDPDT::init_atomic(const int nlocal, const int nall,
_threads_per_atom=device->threads_per_atom(); _threads_per_atom=device->threads_per_atom();
bool charge = false; bool charge = need_charges;
bool rot = false; bool rot = false;
bool vel = true; bool vel = true;
_extra_fields = extra_fields; _extra_fields = extra_fields;

3
lib/gpu/lal_base_dpd.h
View File

@ -53,7 +53,8 @@ class BaseDPD {
const int maxspecial, const double cell_size, const int maxspecial, const double cell_size,
const double gpu_split, FILE *screen, const double gpu_split, FILE *screen,
const void *pair_program, const char *k_name, const void *pair_program, const char *k_name,
const int onetype=0, const int extra_fields=0); const int onetype=0, const int extra_fields=0,
bool need_charges=false);
/// Estimate the overhead for GPU context changes and CPU driver /// Estimate the overhead for GPU context changes and CPU driver
void estimate_gpu_overhead(); void estimate_gpu_overhead();

238
lib/gpu/lal_dpd_coul_slater_long.cpp Normal file
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@ -0,0 +1,238 @@
/***************************************************************************
lal_dpd_coul_slater_long.cpp
-------------------
Eddy BARRAUD (IFPEN/Sorbonne)
Class for acceleration of the dpd/coul/slater/long pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : May 28, 2024
email : eddy.barraud@outlook.fr
***************************************************************************/
#if defined(USE_OPENCL)
#include "dpd_coul_slater_long_cl.h"
#elif defined(USE_CUDART)
const char *dpd_coul_slater_long=0;
#else
#include "dpd_coul_slater_long_cubin.h"
#endif
#include "lal_dpd_coul_slater_long.h"
#include <cassert>
namespace LAMMPS_AL {
#define DPDCoulSlaterLongT DPDCoulSlaterLong<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> device;
template <class numtyp, class acctyp>
DPDCoulSlaterLongT::DPDCoulSlaterLong() : BaseDPD<numtyp,acctyp>(), _allocated(false) {
}
template <class numtyp, class acctyp>
DPDCoulSlaterLongT::~DPDCoulSlaterLong() {
clear();
}
template <class numtyp, class acctyp>
int DPDCoulSlaterLongT::bytes_per_atom(const int max_nbors) const {
return this->bytes_per_atom_atomic(max_nbors);
}
template <class numtyp, class acctyp>
int DPDCoulSlaterLongT::init(const int ntypes,
double **host_cutsq, double **host_a0,
double **host_gamma, double **host_sigma,
double **host_cut_dpd, double **host_cut_dpdsq,
double **host_cut_slatersq, double *host_special_lj,
const bool tstat_only,
const int nlocal, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size,
const double gpu_split, FILE *_screen, double *host_special_coul,
const double qqrd2e, const double g_ewald, double lamda) {
const int max_shared_types=this->device->max_shared_types();
int onetype=0;
#ifdef USE_OPENCL
if (maxspecial==0)
for (int i=1; i<ntypes; i++)
for (int j=i; j<ntypes; j++)
if (host_cutsq[i][j]>0) {
if (onetype>0)
onetype=-1;
else if (onetype==0)
onetype=i*max_shared_types+j;
}
if (onetype<0) onetype=0;
#endif
int extra_fields = 4; // round up to accomodate quadruples of numtyp values
// q
int success;
bool need_charges = true;
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,
gpu_split,_screen,dpd_coul_slater_long,"k_dpd_coul_slater_long",onetype, extra_fields, need_charges);
if (success!=0)
return success;
// If atom type constants fit in shared memory use fast kernel
int lj_types=ntypes;
shared_types=false;
if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
lj_types=max_shared_types;
shared_types=true;
}
// Allocate a host write buffer for data initialization
UCL_H_Vec<numtyp> host_write_coul(lj_types*lj_types*32,*(this->ucl_device),
UCL_WRITE_ONLY);
sp_cl.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
for (int i=0; i<4; i++) {
host_write_coul[i]=host_special_coul[i];
}
ucl_copy(sp_cl,host_write_coul,4,false);
_lj_types=lj_types;
_qqrd2e=qqrd2e;
_g_ewald=g_ewald;
_lamda=lamda;
// Allocate a host write buffer for data initialization
UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
UCL_WRITE_ONLY);
for (int i=0; i<lj_types*lj_types; i++)
host_write[i]=0.0;
coeff.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,lj_types,coeff,host_write,host_a0,host_gamma,
host_sigma,host_cut_dpd);
cutsq.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,lj_types,cutsq,host_write,host_cutsq,
host_cut_dpdsq,host_cut_slatersq);
double special_sqrt[4];
special_sqrt[0] = sqrt(host_special_lj[0]);
special_sqrt[1] = sqrt(host_special_lj[1]);
special_sqrt[2] = sqrt(host_special_lj[2]);
special_sqrt[3] = sqrt(host_special_lj[3]);
UCL_H_Vec<double> dview;
sp_lj.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
dview.view(host_special_lj,4,*(this->ucl_device));
ucl_copy(sp_lj,dview,false);
sp_sqrt.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
dview.view(special_sqrt,4,*(this->ucl_device));
ucl_copy(sp_sqrt,dview,false);
_tstat_only = 0;
if (tstat_only) _tstat_only=1;
_allocated=true;
this->_max_bytes=coeff.row_bytes()+cutsq.row_bytes()+sp_lj.row_bytes()+sp_sqrt.row_bytes();
return 0;
}
template <class numtyp, class acctyp>
void DPDCoulSlaterLongT::clear() {
if (!_allocated)
return;
_allocated=false;
coeff.clear();
cutsq.clear();
sp_lj.clear();
sp_sqrt.clear();
this->clear_atomic();
}
template <class numtyp, class acctyp>
double DPDCoulSlaterLongT::host_memory_usage() const {
return this->host_memory_usage_atomic()+sizeof(DPDCoulSlaterLong<numtyp,acctyp>);
}
// ---------------------------------------------------------------------------
// Calculate energies, forces, and torques
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int DPDCoulSlaterLongT::loop(const int eflag, const int vflag) {
int nall = this->atom->nall();
// signal that we need to transfer extra data from the host
this->atom->extra_data_unavail();
numtyp4 *pextra=reinterpret_cast<numtyp4*>(&(this->atom->extra[0]));
int n = 0;
int nstride = 1;
for (int i = 0; i < nall; i++) {
int idx = n+i*nstride;
numtyp4 v;
v.x = q[i];
v.y = 0;
v.z = 0;
v.w = 0;
pextra[idx] = v;
}
this->atom->add_extra_data();
// Compute the block size and grid size to keep all cores busy
const int BX=this->block_size();
int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
(BX/this->_threads_per_atom)));
int ainum=this->ans->inum();
int nbor_pitch=this->nbor->nbor_pitch();
this->time_pair.start();
if (shared_types) {
this->k_pair_sel->set_size(GX,BX);
this->k_pair_sel->run(&this->atom->x, &this->atom->extra, &coeff, &sp_lj, &sp_cl, &sp_sqrt,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &eflag,
&vflag, &ainum, &nbor_pitch, &this->atom->v, &cutsq,
&this->_dtinvsqrt, &this->_seed, &this->_timestep,
&_qqrd2e, &_g_ewald, &_lamda,
&this->_tstat_only, &this->_threads_per_atom);
} else {
this->k_pair.set_size(GX,BX);
this->k_pair.run(&this->atom->x, &this->atom->extra, &coeff, &_lj_types, &sp_lj, &sp_cl, &sp_sqrt,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &eflag, &vflag,
&ainum, &nbor_pitch, &this->atom->v, &cutsq, &this->_dtinvsqrt,
&this->_seed, &this->_timestep,
&_qqrd2e, &_g_ewald, &_lamda,
&this->_tstat_only, &this->_threads_per_atom);
}
this->time_pair.stop();
return GX;
}
template <class numtyp, class acctyp>
void DPDCoulSlaterLongT::update_coeff(int ntypes, double **host_a0, double **host_gamma,
double **host_sigma, double **host_cut_dpd)
{
UCL_H_Vec<numtyp> host_write(_lj_types*_lj_types*32,*(this->ucl_device),
UCL_WRITE_ONLY);
this->atom->type_pack4(ntypes,_lj_types,coeff,host_write,host_a0,host_gamma,
host_sigma,host_cut_dpd);
}
// ---------------------------------------------------------------------------
// Get the extra data pointers from host
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
void DPDCoulSlaterLongT::get_extra_data(double *host_q) {
q = host_q;
}
template class DPDCoulSlaterLong<PRECISION,ACC_PRECISION>;
}

523
lib/gpu/lal_dpd_coul_slater_long.cu Normal file
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@ -0,0 +1,523 @@
// **************************************************************************
// dpd.cu
// -------------------
// Eddy BARRAUD (IFPEN/Sorbonne)
// Trung Dac Nguyen (U Chicago)
//
// Device code for acceleration of the dpd/coul/slater/long pair style
//
// __________________________________________________________________________
// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
// __________________________________________________________________________
//
// begin : May 28, 2024
// email : eddy.barraud@outlook.fr
// ***************************************************************************
#if defined(NV_KERNEL) || defined(USE_HIP)
#include "lal_aux_fun1.h"
#ifndef _DOUBLE_DOUBLE
_texture( pos_tex,float4);
_texture( vel_tex,float4);
#else
_texture_2d( pos_tex,int4);
_texture_2d( vel_tex,int4);
#endif
#else
#define pos_tex x_
#define vel_tex v_
#endif
#define EPSILON (numtyp)1.0e-10
//#define _USE_UNIFORM_SARU_LCG
//#define _USE_UNIFORM_SARU_TEA8
//#define _USE_GAUSSIAN_SARU_LCG
#if !defined(_USE_UNIFORM_SARU_LCG) && !defined(_USE_UNIFORM_SARU_TEA8) && !defined(_USE_GAUSSIAN_SARU_LCG)
#define _USE_UNIFORM_SARU_LCG
#endif
// References:
// 1. Y. Afshar, F. Schmid, A. Pishevar, S. Worley, Comput. Phys. Comm. 184 (2013), 1119–1128.
// 2. C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput. Phys. Comm. 230 (2011), 7191-7201.
// PRNG period = 3666320093*2^32 ~ 2^64 ~ 10^19
#define LCGA 0x4beb5d59 /* Full period 32 bit LCG */
#define LCGC 0x2600e1f7
#define oWeylPeriod 0xda879add /* Prime period 3666320093 */
#define oWeylOffset 0x8009d14b
#define TWO_N32 0.232830643653869628906250e-9f /* 2^-32 */
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns uniformly distributed random numbers u in [-1.0;1.0]
// using the inherent LCG, then multiply u with sqrt(3) to "match"
// with a normal random distribution.
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
// Curly brackets to make variables local to the scope.
#ifdef _USE_UNIFORM_SARU_LCG
#define SQRT3 (numtyp)1.7320508075688772935274463
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
unsigned int wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
unsigned int v = (state ^ (state>>26)) + wstate; \
unsigned int s = (signed int)((v^(v>>20))*0x6957f5a7); \
randnum = SQRT3*(s*TWO_N32*(numtyp)2.0-(numtyp)1.0); \
}
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns uniformly distributed random numbers u in [-1.0;1.0] using TEA8
// then multiply u with sqrt(3) to "match" with a normal random distribution
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
#ifdef _USE_UNIFORM_SARU_TEA8
#define SQRT3 (numtyp)1.7320508075688772935274463
#define k0 0xA341316C
#define k1 0xC8013EA4
#define k2 0xAD90777D
#define k3 0x7E95761E
#define delta 0x9e3779b9
#define rounds 8
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
unsigned int wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
unsigned int sum = 0; \
for (int i=0; i < rounds; i++) { \
sum += delta; \
state += ((wstate<<4) + k0)^(wstate + sum)^((wstate>>5) + k1); \
wstate += ((state<<4) + k2)^(state + sum)^((state>>5) + k3); \
} \
unsigned int v = (state ^ (state>>26)) + wstate; \
unsigned int s = (signed int)((v^(v>>20))*0x6957f5a7); \
randnum = SQRT3*(s*TWO_N32*(numtyp)2.0-(numtyp)1.0); \
}
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns two uniformly distributed random numbers r1 and r2 in [-1.0;1.0],
// and uses the polar method (Marsaglia's) to transform to a normal random value
// This is used to compared with CPU DPD using RandMars::gaussian()
#ifdef _USE_GAUSSIAN_SARU_LCG
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state=0x12345678; \
unsigned int wstate=12345678; \
state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
unsigned int v, s; \
numtyp r1, r2, rsq; \
while (1) { \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
v = (state ^ (state>>26)) + wstate; \
s = (signed int)((v^(v>>20))*0x6957f5a7); \
r1 = s*TWO_N32*(numtyp)2.0-(numtyp)1.0; \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
v = (state ^ (state>>26)) + wstate; \
s = (signed int)((v^(v>>20))*0x6957f5a7); \
r2 = s*TWO_N32*(numtyp)2.0-(numtyp)1.0; \
rsq = r1 * r1 + r2 * r2; \
if (rsq < (numtyp)1.0) break; \
} \
numtyp fac = ucl_sqrt((numtyp)-2.0*log(rsq)/rsq); \
randnum = r2*fac; \
}
#endif
__kernel void k_dpd_coul_slater_long(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict extra,
const __global numtyp4 *restrict coeff,
const int lj_types,
const __global numtyp *restrict sp_lj,
const __global numtyp *restrict sp_cl_in,
const __global numtyp *restrict sp_sqrt,
const __global int * dev_nbor,
const __global int * dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
const int eflag, const int vflag, const int inum,
const int nbor_pitch,
const __global numtyp4 *restrict v_,
const __global numtyp4 *restrict cutsq,
const numtyp dtinvsqrt, const int seed,
const int timestep, const numtyp qqrd2e,
const numtyp g_ewald, const numtyp lamda,
const int tstat_only,
const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
__local numtyp sp_cl[4];
///local_allocate_store_charge();
sp_cl[0]=sp_cl_in[0];
sp_cl[1]=sp_cl_in[1];
sp_cl[2]=sp_cl_in[2];
sp_cl[3]=sp_cl_in[3];
int n_stride;
local_allocate_store_pair();
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp e_coul, energy, virial[6];
if (EVFLAG) {
energy=(acctyp)0;
e_coul=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
if (ii<inum) {
int i, numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int itype=ix.w;
numtyp4 iv; fetch4(iv,i,vel_tex); //v_[i];
int itag=iv.w;
numtyp qtmp = extra[i].x; // q[i]
numtyp lamdainv = ucl_recip(lamda);
numtyp factor_dpd, factor_sqrt;
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
factor_dpd = sp_lj[sbmask(j)];
factor_sqrt = sp_sqrt[sbmask(j)];
numtyp factor_coul;
factor_coul = (numtyp)1.0-sp_cl[sbmask(j)];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype=jx.w;
numtyp4 jv; fetch4(jv,j,vel_tex); //v_[j];
int jtag=jv.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
int mtype=itype*lj_types+jtype;
// cutsq[mtype].x -> global squared cutoff
if (rsq<cutsq[mtype].x) {
numtyp r=ucl_sqrt(rsq);
numtyp force_dpd = (numtyp)0.0;
numtyp force_coul = (numtyp)0.0;
// apply DPD force if distance below DPD cutoff
// cutsq[mtype].y -> DPD squared cutoff
if (rsq < cutsq[mtype].y && r > EPSILON) {
numtyp rinv=ucl_recip(r);
numtyp delvx = iv.x - jv.x;
numtyp delvy = iv.y - jv.y;
numtyp delvz = iv.z - jv.z;
numtyp dot = delx*delvx + dely*delvy + delz*delvz;
numtyp wd = (numtyp)1.0 - r/coeff[mtype].w;
unsigned int tag1=itag, tag2=jtag;
if (tag1 > tag2) {
tag1 = jtag; tag2 = itag;
}
numtyp randnum = (numtyp)0.0;
saru(tag1, tag2, seed, timestep, randnum);
// conservative force = a0 * wd, or 0 if tstat only
// drag force = -gamma * wd^2 * (delx dot delv) / r
// random force = sigma * wd * rnd * dtinvsqrt;
if (!tstat_only) force_dpd = coeff[mtype].x*wd;
force_dpd -= coeff[mtype].y*wd*wd*dot*rinv;
force_dpd *= factor_dpd;
force_dpd += factor_sqrt*coeff[mtype].z*wd*randnum*dtinvsqrt;
force_dpd *=rinv;
if (EVFLAG && eflag) {
// unshifted eng of conservative term:
// evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]);
// eng shifted to 0.0 at cutoff
numtyp e = (numtyp)0.5*coeff[mtype].x*coeff[mtype].w * wd*wd;
energy += factor_dpd*e;
}
}// if cut_dpdsq
// apply Slater electrostatic force if distance below Slater cutoff
// and the two species have a slater coeff
// cutsq[mtype].z -> Coulombic squared cutoff
if ( cutsq[mtype].z != 0.0 && rsq < cutsq[mtype].z){
numtyp r2inv=ucl_recip(rsq);
numtyp _erfc;
numtyp grij = g_ewald * r;
numtyp expm2 = ucl_exp(-grij*grij);
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij);
_erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
numtyp prefactor = extra[j].x;
prefactor *= qqrd2e * cutsq[mtype].z * qtmp/r;
numtyp rlamdainv = r * lamdainv;
numtyp exprlmdainv = ucl_exp((numtyp)-2.0*rlamdainv);
numtyp slater_term = exprlmdainv*((numtyp)1.0 + ((numtyp)2.0*rlamdainv*((numtyp)1.0+rlamdainv)));
force_coul = prefactor*(_erfc + EWALD_F*grij*expm2-slater_term);
if (factor_coul > (numtyp)0) force_coul -= factor_coul*prefactor*((numtyp)1.0-slater_term);
force_coul *= r2inv;
if (EVFLAG && eflag) {
numtyp e_slater = ((numtyp)1.0 + rlamdainv)*exprlmdainv;
numtyp e = prefactor*(_erfc-e_slater);
if (factor_coul > (numtyp)0) e -= factor_coul*prefactor*((numtyp)1.0 - e_slater);
e_coul += e;
}
} // if cut_coulsq
numtyp force = force_coul + force_dpd;
f.x += delx*force;
f.y += dely*force;
f.z += delz*force;
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
} // if cutsq
} // for nbor
} // if ii
store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag,
ans,engv);
}
__kernel void k_dpd_coul_slater_long_fast(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict extra,
const __global numtyp4 *restrict coeff_in,
const __global numtyp *restrict sp_lj_in,
const __global numtyp *restrict sp_cl_in,
const __global numtyp *restrict sp_sqrt_in,
const __global int * dev_nbor,
const __global int * dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
const int eflag, const int vflag, const int inum,
const int nbor_pitch,
const __global numtyp4 *restrict v_,
const __global numtyp4 *restrict cutsq_in,
const numtyp dtinvsqrt, const int seed,
const int timestep, const numtyp qqrd2e,
const numtyp g_ewald, const numtyp lamda,
const int tstat_only,
const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
__local numtyp4 coeff[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp4 cutsq[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp sp_lj[4];
__local numtyp sp_sqrt[4];
/// COUL Init
__local numtyp sp_cl[4];
if (tid<4) {
sp_lj[tid]=sp_lj_in[tid];
sp_sqrt[tid]=sp_sqrt_in[tid];
sp_cl[tid]=sp_cl_in[tid];
}
if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES) {
coeff[tid]=coeff_in[tid];
cutsq[tid]=cutsq_in[tid];
}
__syncthreads();
int n_stride;
local_allocate_store_pair();
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp e_coul, energy, virial[6];
if (EVFLAG) {
energy=(acctyp)0;
e_coul=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
if (ii<inum) {
int i, numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int iw=ix.w;
int itype=fast_mul((int)MAX_SHARED_TYPES,iw);
numtyp4 iv; fetch4(iv,i,vel_tex); //v_[i];
int itag=iv.w;
numtyp qtmp = extra[i].x; // q[i]
numtyp lamdainv = ucl_recip(lamda);
numtyp factor_dpd, factor_sqrt;
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
factor_dpd = sp_lj[sbmask(j)];
factor_sqrt = sp_sqrt[sbmask(j)];
numtyp factor_coul;
factor_coul = (numtyp)1.0-sp_cl[sbmask(j)];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
numtyp4 jv; fetch4(jv,j,vel_tex); //v_[j];
int jtag=jv.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
int mtype=itype+jx.w;
/// cutsq.x = cutsq, cutsq.y = cut_dpdsq, cutsq.z = cut_slatersq
if (rsq<cutsq[mtype].x) {
numtyp r=ucl_sqrt(rsq);
numtyp force_dpd = (numtyp)0.0;
numtyp force_coul = (numtyp)0.0;
// apply DPD force if distance below DPD cutoff
// cutsq[mtype].y -> DPD squared cutoff
if (rsq < cutsq[mtype].y && r > EPSILON) {
numtyp rinv=ucl_recip(r);
numtyp delvx = iv.x - jv.x;
numtyp delvy = iv.y - jv.y;
numtyp delvz = iv.z - jv.z;
numtyp dot = delx*delvx + dely*delvy + delz*delvz;
numtyp wd = (numtyp)1.0 - r/coeff[mtype].w;
unsigned int tag1=itag, tag2=jtag;
if (tag1 > tag2) {
tag1 = jtag; tag2 = itag;
}
numtyp randnum = (numtyp)0.0;
saru(tag1, tag2, seed, timestep, randnum);
// conservative force = a0 * wd, or 0 if tstat only
// drag force = -gamma * wd^2 * (delx dot delv) / r
// random force = sigma * wd * rnd * dtinvsqrt;
/// coeff.x = a0, coeff.y = gamma, coeff.z = sigma, coeff.w = cut_dpd
if (!tstat_only) force_dpd = coeff[mtype].x*wd;
force_dpd -= coeff[mtype].y*wd*wd*dot*rinv;
force_dpd *= factor_dpd;
force_dpd += factor_sqrt*coeff[mtype].z*wd*randnum*dtinvsqrt;
force_dpd *=rinv;
if (EVFLAG && eflag) {
// unshifted eng of conservative term:
// evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]);
// eng shifted to 0.0 at cutoff
numtyp e = (numtyp)0.5*coeff[mtype].x*coeff[mtype].w * wd*wd;
energy += factor_dpd*e;
}
}// if cut_dpdsq
// apply Slater electrostatic force if distance below Slater cutoff
// and the two species have a slater coeff
// cutsq[mtype].z -> Coulombic squared cutoff
if ( cutsq[mtype].z != 0.0 && rsq < cutsq[mtype].z){
numtyp r2inv=ucl_recip(rsq);
numtyp _erfc;
numtyp grij = g_ewald * r;
numtyp expm2 = ucl_exp(-grij*grij);
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij);
_erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
numtyp prefactor = extra[j].x;
prefactor *= qqrd2e * cutsq[mtype].z * qtmp/r;
numtyp rlamdainv = r * lamdainv;
numtyp exprlmdainv = ucl_exp((numtyp)-2.0*rlamdainv);
numtyp slater_term = exprlmdainv*((numtyp)1.0 + ((numtyp)2.0*rlamdainv*((numtyp)1.0+rlamdainv)));
force_coul = prefactor*(_erfc + EWALD_F*grij*expm2-slater_term);
if (factor_coul > (numtyp)0) force_coul -= factor_coul*prefactor*((numtyp)1.0-slater_term);
force_coul *= r2inv;
if (EVFLAG && eflag) {
numtyp e_slater = ((numtyp)1.0 + rlamdainv)*exprlmdainv;
numtyp e_sf = prefactor*(_erfc-e_slater);
if (factor_coul > (numtyp)0) e_sf -= factor_coul*prefactor*((numtyp)1.0 - e_slater);
e_coul += e_sf;
}
} // if cut_coulsq
numtyp force = force_coul + force_dpd;
f.x += delx*force;
f.y += dely*force;
f.z += delz*force;
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
} // if cutsq
} // for nbor
} // if ii
store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag,
ans,engv);
}

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/***************************************************************************
lal_dpd_coul_slater_long.h
-------------------
Eddy BARRAUD (IFPEN/Sorbonne)
Class for acceleration of the dpd/coul/slater/long pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : May 28, 2024
email : eddy.barraud@outlook.fr
***************************************************************************/
#ifndef LAL_DPD_CHARGED_H
#define LAL_DPD_CHARGED_H
#include "lal_base_dpd.h"
namespace LAMMPS_AL {
template <class numtyp, class acctyp>
class DPDCoulSlaterLong : public BaseDPD<numtyp, acctyp> {
public:
DPDCoulSlaterLong();
~DPDCoulSlaterLong();
/// Clear any previous data and set up for a new LAMMPS run
/** \param max_nbors initial number of rows in the neighbor matrix
* \param cell_size cutoff + skin
* \param gpu_split fraction of particles handled by device
*
* Returns:
* - 0 if successful
* - -1 if fix gpu not found
* - -3 if there is an out of memory error
* - -4 if the GPU library was not compiled for GPU
* - -5 Double precision is not supported on card **/
int init(const int ntypes, double **host_cutsq, double **host_a0, double **host_gamma,
double **host_sigma, double **host_cut_dpd, double **host_cut_dpdsq,
double **host_cut_slatersq, double *host_special_lj, bool tstat_only, const int nlocal,
const int nall, const int max_nbors, const int maxspecial, const double cell_size,
const double gpu_split, FILE *screen, double *host_special_coul, const double qqrd2e,
const double g_ewald, const double lamda);
/// Clear all host and device data
/** \note This is called at the beginning of the init() routine **/
void clear();
/// Returns memory usage on device per atom
int bytes_per_atom(const int max_nbors) const;
/// Total host memory used by library for pair style
double host_memory_usage() const;
/// Update coeff if needed (tstat only)
void update_coeff(int ntypes, double **host_a0, double **host_gamma,
double **host_sigma, double **host_cut_dpd );
void get_extra_data(double *host_q);
// --------------------------- TYPE DATA --------------------------
/// coeff.x = a0, coeff.y = gamma, coeff.z = sigma, coeff.w = cut_dpd
UCL_D_Vec<numtyp4> coeff;
/// cutsq.x = cutsq, cutsq.y = cut_dpdsq, cutsq.w = cut_slatersq
UCL_D_Vec<numtyp4> cutsq;
/// Special LJ values
UCL_D_Vec<numtyp> sp_lj, sp_sqrt;
/// Special Coul values [0-3]
UCL_D_Vec<numtyp> sp_cl;
/// If atom type constants fit in shared memory, use fast kernels
bool shared_types;
/// Number of atom types
int _lj_types;
/// Only used for thermostat
int _tstat_only;
/// Coulombic terms
numtyp _qqrd2e, _g_ewald, _lamda;
/// pointer to host data for atom charge
double *q;
private:
bool _allocated;
int loop(const int eflag, const int vflag);
};
}
#endif

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/***************************************************************************
lal_dpd_coul_slater_long_ext.cpp
-------------------
Eddy BARRAUD (IFPEN/Sorbonne)
Functions for LAMMPS access to dpd/coul/slater/long acceleration routines.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : May 28, 2024
email : eddy.barraud@outlook.fr
***************************************************************************/
#include <iostream>
#include <cassert>
#include <cmath>
#include "lal_dpd_coul_slater_long.h"
using namespace std;
using namespace LAMMPS_AL;
static DPDCoulSlaterLong<PRECISION,ACC_PRECISION> DPDCMF;
// ---------------------------------------------------------------------------
// Allocate memory on host and device and copy constants to device
// ---------------------------------------------------------------------------
int dpd_coul_slater_long_gpu_init(const int ntypes, double **host_cutsq, double **host_a0,
double **host_gamma, double **host_sigma, double **host_cut_dpd,
double **host_cut_dpdsq, double **host_cut_slatersq,
double *special_lj, const int inum, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
double *host_special_coul, const double qqrd2e,
const double g_ewald, const double lamda) {
DPDCMF.clear();
gpu_mode=DPDCMF.device->gpu_mode();
double gpu_split=DPDCMF.device->particle_split();
int first_gpu=DPDCMF.device->first_device();
int last_gpu=DPDCMF.device->last_device();
int world_me=DPDCMF.device->world_me();
int gpu_rank=DPDCMF.device->gpu_rank();
int procs_per_gpu=DPDCMF.device->procs_per_gpu();
DPDCMF.device->init_message(screen,"dpd",first_gpu,last_gpu);
bool message=false;
if (DPDCMF.device->replica_me()==0 && screen)
message=true;
if (message) {
fprintf(screen,"Initializing Device and compiling on process 0...");
fflush(screen);
}
int init_ok=0;
if (world_me==0)
init_ok=DPDCMF.init(ntypes, host_cutsq, host_a0, host_gamma, host_sigma, host_cut_dpd,
host_cut_dpdsq, host_cut_slatersq, special_lj, false, inum, nall,
max_nbors, maxspecial, cell_size, gpu_split, screen, host_special_coul,
qqrd2e, g_ewald, lamda);
DPDCMF.device->world_barrier();
if (message)
fprintf(screen,"Done.\n");
for (int i=0; i<procs_per_gpu; i++) {
if (message) {
if (last_gpu-first_gpu==0)
fprintf(screen,"Initializing Device %d on core %d...",first_gpu,i);
else
fprintf(screen,"Initializing Devices %d-%d on core %d...",first_gpu,
last_gpu,i);
fflush(screen);
}
if (gpu_rank==i && world_me!=0)
init_ok=DPDCMF.init(ntypes, host_cutsq, host_a0, host_gamma, host_sigma, host_cut_dpd,
host_cut_dpdsq, host_cut_slatersq, special_lj, false, inum, nall,
max_nbors, maxspecial, cell_size, gpu_split, screen, host_special_coul,
qqrd2e, g_ewald, lamda);
DPDCMF.device->serialize_init();
if (message)
fprintf(screen,"Done.\n");
}
if (message)
fprintf(screen,"\n");
if (init_ok==0)
DPDCMF.estimate_gpu_overhead();
return init_ok;
}
void dpd_coul_slater_long_gpu_clear() {
DPDCMF.clear();
}
int ** dpd_coul_slater_long_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time, bool &success,
double **host_v, const double dtinvsqrt,
const int seed, const int timestep,
double *boxlo, double *prd) {
return DPDCMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
subhi, tag, nspecial, special, eflag, vflag, eatom,
vatom, host_start, ilist, jnum, cpu_time, success,
host_v, dtinvsqrt, seed, timestep, boxlo, prd);
}
void dpd_coul_slater_long_gpu_compute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, tagint *tag,
double **host_v, const double dtinvsqrt,
const int seed, const int timestep,
const int nlocal, double *boxlo, double *prd) {
DPDCMF.compute(ago, inum_full, nall, host_x, host_type, ilist, numj,
firstneigh, eflag, vflag, eatom, vatom, host_start, cpu_time, success,
tag, host_v, dtinvsqrt, seed, timestep, nlocal, boxlo, prd);
}
void dpd_coul_slater_long_gpu_update_coeff(int ntypes, double **host_a0, double **host_gamma,
double **host_sigma, double **host_cut_dpd)
{
DPDCMF.update_coeff(ntypes,host_a0,host_gamma,host_sigma, host_cut_dpd);
}
void dpd_coul_slater_long_gpu_get_extra_data(double *host_q) {
DPDCMF.get_extra_data(host_q);
}
double dpd_coul_slater_long_gpu_bytes() {
return DPDCMF.host_memory_usage();
}

2
python/lammps/core.py
View File

@ -891,7 +891,7 @@ class lammps(object):
# set length of vector for items that are not a scalar # set length of vector for items that are not a scalar
vec_dict = { 'boxlo':3, 'boxhi':3, 'sublo':3, 'subhi':3, vec_dict = { 'boxlo':3, 'boxhi':3, 'sublo':3, 'subhi':3,
'sublo_lambda':3, 'subhi_lambda':3, 'periodicity':3, 'sublo_lambda':3, 'subhi_lambda':3, 'periodicity':3,
'special_lj':4, 'special_coul':4 } 'special_lj':4, 'special_coul':4, 'procgrid':3 }
if name in vec_dict: if name in vec_dict:
veclen = vec_dict[name] veclen = vec_dict[name]
elif name == 'respa_dt': elif name == 'respa_dt':

14
python/lammps/pylammps.py
View File

@ -796,18 +796,16 @@ class PyLammps(object):
comm = {} comm = {}
comm['nprocs'] = self.lmp.extract_setting("world_size") comm['nprocs'] = self.lmp.extract_setting("world_size")
comm['nthreads'] = self.lmp.extract_setting("nthreads") comm['nthreads'] = self.lmp.extract_setting("nthreads")
comm['proc_grid'] = comm['procgrid'] = self.lmp.extract_global("procgrid")
idx = self.lmp.extract_setting("comm_style")
comm['comm_style'] = ('brick', 'tiled')[idx]
idx = self.lmp.extract_setting("comm_style")
comm['comm_layout'] = ('uniform', 'nonuniform', 'irregular')[idx]
comm['ghost_velocity'] = self.lmp.extract_setting("ghost_velocity") == 1
for line in output: for line in output:
if line.startswith("MPI library"): if line.startswith("MPI library"):
comm['mpi_version'] = line.split(':')[1].strip() comm['mpi_version'] = line.split(':')[1].strip()
elif line.startswith("Comm style"):
parts = self._split_values(line)
comm['comm_style'] = self._get_pair(parts[0])[1]
comm['comm_layout'] = self._get_pair(parts[1])[1]
elif line.startswith("Processor grid"):
comm['proc_grid'] = [int(x) for x in self._get_pair(line)[1].split('x')]
elif line.startswith("Communicate velocities for ghost atoms"):
comm['ghost_velocity'] = (self._get_pair(line)[1] == "yes")
return comm return comm
def _parse_element_list(self, output): def _parse_element_list(self, output):

2
src/.gitignore vendored
View File

@ -1715,6 +1715,8 @@
/pair_dpd.h /pair_dpd.h
/pair_dpd_tstat.cpp /pair_dpd_tstat.cpp
/pair_dpd_tstat.h /pair_dpd_tstat.h
/pair_dpd_coul_slater_long.cpp
/pair_dpd_coul_slater_long.h
/pair_dpd_ext.cpp /pair_dpd_ext.cpp
/pair_dpd_ext.h /pair_dpd_ext.h
/pair_dpd_ext_tstat.cpp /pair_dpd_ext_tstat.cpp

39
src/DPD-BASIC/Install.sh Executable file
View File

@ -0,0 +1,39 @@
# Install/unInstall package files in LAMMPS
# mode = 0/1/2 for uninstall/install/update
mode=$1
# enforce using portable C locale
LC_ALL=C
export LC_ALL
# arg1 = file, arg2 = file it depends on
action () {
if (test $mode = 0) then
rm -f ../$1
elif (! cmp -s $1 ../$1) then
if (test -z "$2" || test -e ../$2) then
cp $1 ..
if (test $mode = 2) then
echo " updating src/$1"
fi
fi
elif (test -n "$2") then
if (test ! -e ../$2) then
rm -f ../$1
fi
fi
}
# list of files with optional dependcies
action pair_dpd_coul_slater_long.cpp pppm.cpp
action pair_dpd_coul_slater_long.h pppm.h
action pair_dpd.cpp
action pair_dpd_ext.cpp
action pair_dpd_ext.h
action pair_dpd_ext_tstat.cpp
action pair_dpd_ext_tstat.h
action pair_dpd.h
action pair_dpd_tstat.cpp
action pair_dpd_tstat.h

544
src/DPD-BASIC/pair_dpd_coul_slater_long.cpp Normal file
View File

@ -0,0 +1,544 @@
// clang-format off
/* ----------------------------------------------------------------------
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: Eddy BARRAUD (IFPEN/Sorbonne)
------------------------------------------------------------------------- */
#include "pair_dpd_coul_slater_long.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "random_mars.h"
#include "update.h"
#include "ewald_const.h"
#include "kspace.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace EwaldConst;
static constexpr double EPSILON = 1.0e-10;
/* ---------------------------------------------------------------------- */
PairDPDCoulSlaterLong::PairDPDCoulSlaterLong(LAMMPS *lmp) :
Pair(lmp), cut_dpd(nullptr), cut_dpdsq(nullptr), cut_slatersq(nullptr),
a0(nullptr), gamma(nullptr), sigma(nullptr), random(nullptr)
{
writedata = 1;
ewaldflag = pppmflag = 1;
respa_enable = 0;
}
/* ---------------------------------------------------------------------- */
PairDPDCoulSlaterLong::~PairDPDCoulSlaterLong()
{
if (copymode) return;
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut_dpd);
memory->destroy(cut_dpdsq);
memory->destroy(cut_slatersq);
memory->destroy(cut);
memory->destroy(a0);
memory->destroy(gamma);
memory->destroy(sigma);
}
if (random) delete random;
}
/* ---------------------------------------------------------------------- */
void PairDPDCoulSlaterLong::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double vxtmp,vytmp,vztmp,delvx,delvy,delvz;
double r2inv,forcedpd,forcecoul,factor_coul;
double grij,expm2,prefactor,t,erfc;
double rsq,r,rinv,dot,wd,randnum,factor_dpd,factor_sqrt;
int *ilist,*jlist,*numneigh,**firstneigh;
double slater_term;
evdwl = ecoul = 0.0;
ev_init(eflag,vflag);
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double dtinvsqrt = 1.0/sqrt(update->dt);
double *q = atom->q;
double *special_coul = force->special_coul;
double qqrd2e = force->qqrd2e;
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];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
vxtmp = v[i][0];
vytmp = v[i][1];
vztmp = v[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_dpd = special_lj[sbmask(j)];
factor_sqrt = special_sqrt[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
// forces if below maximum cutoff
if (rsq < cutsq[itype][jtype]) {
r = sqrt(rsq);
if (evflag) evdwl = ecoul = 0.0;
// apply DPD force if distance below DPD cutoff
if (rsq < cut_dpdsq[itype][jtype] && r > EPSILON) {
rinv = 1.0/r;
delvx = vxtmp - v[j][0];
delvy = vytmp - v[j][1];
delvz = vztmp - v[j][2];
dot = delx*delvx + dely*delvy + delz*delvz;
wd = 1.0 - r/cut_dpd[itype][jtype];
randnum = random->gaussian();
// conservative force = a0 * wd
// drag force = -gamma * wd^2 * (delx dot delv) / r
// random force = sigma * wd * rnd * dtinvsqrt;
// random force must be scaled by sqrt(factor_dpd)
forcedpd = a0[itype][jtype]*wd;
forcedpd -= gamma[itype][jtype]*wd*wd*dot*rinv;
forcedpd *= factor_dpd;
forcedpd += factor_sqrt*sigma[itype][jtype]*wd*randnum*dtinvsqrt;
forcedpd *= rinv;
if (eflag) {
// eng shifted to 0.0 at cutoff
evdwl = 0.5*a0[itype][jtype]*cut_dpd[itype][jtype] * wd*wd;
evdwl *= factor_dpd;
}
} else forcedpd = 0.0;
// apply Slater electrostatic force if distance below Slater cutoff
// and the two species are charged
if (rsq < cut_slatersq[itype][jtype]){
r2inv = 1.0/rsq;
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
slater_term = exp(-2*r/lamda)*(1 + (2*r/lamda*(1+r/lamda)));
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - slater_term);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor*(1-slater_term);
forcecoul *= r2inv;
if (eflag) {
ecoul = prefactor*(erfc - (1 + r/lamda)*exp(-2*r/lamda));
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor*(1.0-(1 + r/lamda)*exp(-2*r/lamda));
}
} else forcecoul = 0.0;
fpair = forcedpd + forcecoul;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairDPDCoulSlaterLong::allocate()
{
int i,j;
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (i = 1; i <= n; i++)
for (j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cut,n+1,n+1,"pair:cut");
memory->create(cut_dpd,n+1,n+1,"pair:cut_dpd");
memory->create(cut_dpdsq,n+1,n+1,"pair:cut_dpdsq");
memory->create(cut_slatersq,n+1,n+1,"pair:cut_slatersq");
memory->create(a0,n+1,n+1,"pair:a0");
memory->create(gamma,n+1,n+1,"pair:gamma");
memory->create(sigma,n+1,n+1,"pair:sigma");
for (i = 0; i <= atom->ntypes; i++)
for (j = 0; j <= atom->ntypes; j++)
sigma[i][j] = gamma[i][j] = 0.0;
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairDPDCoulSlaterLong::settings(int narg, char **arg)
{
// params : T cut_dpd seed lambda cut_coul
if (narg != 5) error->all(FLERR,"Illegal pair_style command");
temperature = utils::numeric(FLERR,arg[0],false,lmp);
cut_global = utils::numeric(FLERR,arg[1],false,lmp);
seed = utils::inumeric(FLERR,arg[2],false,lmp);
lamda = utils::numeric(FLERR,arg[3],false,lmp);
cut_coul = utils::numeric(FLERR,arg[4],false,lmp);
// initialize Marsaglia RNG with processor-unique seed
if (seed <= 0)
error->all(FLERR,"Invalid random seed {} for pair_style dpd/coul/slater/long command", seed);
delete random;
random = new RanMars(lmp,seed + comm->me);
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++)
if (setflag[i][j]) cut_dpd[i][j] = MAX(cut_global,cut_coul);
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairDPDCoulSlaterLong::coeff(int narg, char **arg)
{
if (narg < 4 || narg > 6)
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 a0_one = utils::numeric(FLERR,arg[2],false,lmp);
double gamma_one = utils::numeric(FLERR,arg[3],false,lmp);
double cut_one = cut_global;
double cut_two = 0.0;
if (narg > 4) {
bool do_slater = utils::logical(FLERR,arg[4],false,lmp);
if (do_slater) cut_two = cut_coul;
}
if (narg > 5) cut_one = utils::numeric(FLERR,arg[5],false,lmp);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
a0[i][j] = a0_one;
gamma[i][j] = gamma_one;
cut_dpd[i][j] = cut_one;
cut_slatersq[i][j] = cut_two * cut_two;
cut[i][j] = MAX(cut_one, cut_two);
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairDPDCoulSlaterLong::init_style()
{
if (comm->ghost_velocity == 0)
error->all(FLERR,"Pair dpd requires ghost atoms store velocity");
if (!atom->q_flag)
error->all(FLERR,"Pair style coul/slater/long requires atom attribute q");
// if newton off, forces between atoms ij will be double computed
// using different random numbers
if (force->newton_pair == 0 && comm->me == 0)
error->warning(FLERR, "Pair dpd needs newton pair on for momentum conservation");
neighbor->add_request(this);
// precompute random force scaling factors
for (int i = 0; i < 4; ++i) special_sqrt[i] = sqrt(force->special_lj[i]);
// ensure use of KSpace long-range solver, set g_ewald
if (force->kspace == nullptr)
error->all(FLERR,"Pair style requires a KSpace style");
g_ewald = force->kspace->g_ewald;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
return the maximum cutoff between Slater or DPD cutoff if charged
return the DPD cutoff for uncharged
------------------------------------------------------------------------- */
double PairDPDCoulSlaterLong::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
sigma[i][j] = sqrt(2.0*force->boltz*temperature*gamma[i][j]);
cut_dpdsq[i][j] = cut_dpd[i][j] * cut_dpd[i][j];
a0[j][i] = a0[i][j];
gamma[j][i] = gamma[i][j];
sigma[j][i] = sigma[i][j];
cut_dpd[j][i] = cut_dpd[i][j];
cut[j][i] = cut[i][j];
cut_dpdsq[j][i] = cut_dpdsq[i][j];
cut_slatersq[j][i] = cut_slatersq[i][j];
return MAX(cut_dpd[i][j], sqrt(cut_slatersq[i][j]));
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairDPDCoulSlaterLong::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
for (i = 1; i <= atom->ntypes; i++) {
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&a0[i][j],sizeof(double),1,fp);
fwrite(&gamma[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
fwrite(&cut_dpd[i][j],sizeof(double),1,fp);
fwrite(&cut_slatersq[i][j],sizeof(double),1,fp);
}
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairDPDCoulSlaterLong::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++) {
for (j = i; j <= atom->ntypes; j++) {
if (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 (me == 0) {
utils::sfread(FLERR,&a0[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut_dpd[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut_slatersq[i][j],sizeof(double),1,fp,nullptr,error);
}
MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_dpd[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_slatersq[i][j],1,MPI_DOUBLE,0,world);
}
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairDPDCoulSlaterLong::write_restart_settings(FILE *fp)
{
fwrite(&temperature,sizeof(double),1,fp);
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&seed,sizeof(int),1,fp);
fwrite(&lamda,sizeof(double),1,fp);
fwrite(&cut_coul,sizeof(double),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairDPDCoulSlaterLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
utils::sfread(FLERR,&temperature,sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&seed,sizeof(int),1,fp,nullptr,error);
utils::sfread(FLERR,&lamda,sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,nullptr,error);
}
MPI_Bcast(&temperature,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&seed,1,MPI_INT,0,world);
MPI_Bcast(&lamda,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
// initialize Marsaglia RNG with processor-unique seed
// same seed that pair_style command initially specified
if (random) delete random;
random = new RanMars(lmp,seed + comm->me);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairDPDCoulSlaterLong::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g\n",i,a0[i][i],gamma[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairDPDCoulSlaterLong::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 %s %g\n",i,j,a0[i][j],gamma[i][j],
(cut_slatersq[i][j] == 0.0) ? "yes" : "no", cut_dpd[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairDPDCoulSlaterLong::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_dpd, double &fforce)
{
double r,rinv,wd,phi;
double r2inv,grij,expm2,t,erfc,prefactor;
double slater_term;
double forcecoul,phicoul;
double energy = 0.0;
fforce = 0.0;
r = sqrt(rsq);
// compute DPD force and energy
if (rsq < cut_dpdsq[itype][jtype] && r > EPSILON) {
rinv = 1.0/r;
wd = 1.0 - r/cut_dpd[itype][jtype];
fforce += a0[itype][jtype]*wd * factor_dpd*rinv;
phi = 0.5*a0[itype][jtype]*cut_dpd[itype][jtype] * wd*wd;
energy += factor_dpd*phi;
}
// compute Slater coulombic force and energy
if (atom->q[i]*atom->q[j] != 0.0 && rsq < cut_slatersq[itype][jtype]) {
r2inv = 1.0/rsq;
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
slater_term = exp(-2*r/lamda)*(1 + (2*r/lamda*(1+r/lamda)));
prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - slater_term);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
fforce += forcecoul * r2inv;
phicoul = prefactor*(erfc - (1 + r/lamda)*exp(-2*r/lamda));
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
energy += phicoul;
}
return energy;
}
void *PairDPDCoulSlaterLong::extract(const char *str, int &dim)
{
dim = 0;
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
if (strcmp(str,"lamda") == 0) return (void *) &lamda;
dim = 2;
if (strcmp(str,"a0") == 0) return (void *) a0;
if (strcmp(str,"gamma") == 0) return (void *) gamma;
return nullptr;
}

64
src/DPD-BASIC/pair_dpd_coul_slater_long.h Normal file
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@ -0,0 +1,64 @@
/* -*- 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(dpd/coul/slater/long,PairDPDCoulSlaterLong);
// clang-format on
#else
#ifndef LMP_PAIR_DPD_COUL_SLATER_LONG_H
#define LMP_PAIR_DPD_COUL_SLATER_LONG_H
#include "pair.h"
namespace LAMMPS_NS {
class PairDPDCoulSlaterLong : public Pair {
public:
PairDPDCoulSlaterLong(class LAMMPS *);
~PairDPDCoulSlaterLong() override;
void compute(int, int) override;
void settings(int, char **) override;
void coeff(int, char **) override;
void init_style() override;
double init_one(int, int) override;
void write_restart(FILE *) override;
void read_restart(FILE *) override;
void write_restart_settings(FILE *) override;
void read_restart_settings(FILE *) override;
void write_data(FILE *) override;
void write_data_all(FILE *) override;
double single(int, int, int, int, double, double, double, double &) override;
void *extract(const char *, int &) override;
protected:
double cut_global, temperature;
double special_sqrt[4];
int seed;
double **cut;
double **cut_dpd, **cut_dpdsq, **cut_slatersq;
double **a0, **gamma;
double **sigma;
class RanMars *random;
double cut_coul, qdist;
double lamda;
double g_ewald;
virtual void allocate();
};
} // namespace LAMMPS_NS
#endif
#endif

1
src/Depend.sh
View File

@ -116,6 +116,7 @@ if (test $1 = "KSPACE") then
depend CG-SPICA depend CG-SPICA
depend CORESHELL depend CORESHELL
depend DIELECTRIC depend DIELECTRIC
depend DPD-BASIC
depend GPU depend GPU
depend KOKKOS depend KOKKOS
depend OPT depend OPT

474
src/GPU/pair_dpd_coul_slater_long_gpu.cpp Normal file
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/* ----------------------------------------------------------------------
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: Eddy BARRAUD (IFPEN/Sorbonne)
------------------------------------------------------------------------- */
#include "pair_dpd_coul_slater_long_gpu.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "gpu_extra.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "suffix.h"
#include "update.h"
#include "ewald_const.h"
#include "kspace.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace EwaldConst;
// External functions from cuda library for atom decomposition
int dpd_coul_slater_long_gpu_init(const int ntypes, double **cutsq, double **host_a0,
double **host_gamma, double **host_sigma, double **host_cut_dpd,
double **host_cut_dpdsq, double **host_cut_slatersq,
double *special_lj, const int inum, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
double *host_special_coul, const double qqrd2e,
const double g_ewald, const double lamda);
void dpd_coul_slater_long_gpu_clear();
int **dpd_coul_slater_long_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, double **host_v, const double dtinvsqrt,
const int seed, const int timestep, double *boxlo,
double *prd);
void dpd_coul_slater_long_gpu_compute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, tagint *tag,
double **host_v, const double dtinvsqrt, const int seed,
const int timestep, const int nlocal, double *boxlo,
double *prd);
void dpd_coul_slater_long_gpu_get_extra_data(double *host_q);
double dpd_coul_slater_long_gpu_bytes();
static constexpr double EPSILON = 1.0e-10;
//#define _USE_UNIFORM_SARU_LCG
//#define _USE_UNIFORM_SARU_TEA8
//#define _USE_GAUSSIAN_SARU_LCG
#if !defined(_USE_UNIFORM_SARU_LCG) && !defined(_USE_UNIFORM_SARU_TEA8) && \
!defined(_USE_GAUSSIAN_SARU_LCG)
#define _USE_UNIFORM_SARU_LCG
#endif
// References:
// 1. Y. Afshar, F. Schmid, A. Pishevar, S. Worley, Comput. Phys. Comm. 184 (2013), 1119–1128.
// 2. C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput. Phys. Comm. 230 (2011), 7191-7201.
// PRNG period = 3666320093*2^32 ~ 2^64 ~ 10^19
#define LCGA 0x4beb5d59 // Full period 32 bit LCG
#define LCGC 0x2600e1f7
#define oWeylPeriod 0xda879add // Prime period 3666320093
#define oWeylOffset 0x8009d14b
#define TWO_N32 0.232830643653869628906250e-9f /* 2^-32 */
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns uniformly distributed random numbers u in [-1.0;1.0]
// using the inherent LCG, then multiply u with sqrt(3) to "match"
// with a normal random distribution.
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
// Curly brackets to make variables local to the scope.
#ifdef _USE_UNIFORM_SARU_LCG
#define numtyp double
#define SQRT3 (numtyp) 1.7320508075688772935274463
#define saru(seed1, seed2, seed, timestep, randnum) \
{ \
unsigned int seed3 = seed + timestep; \
seed3 ^= (seed1 << 7) ^ (seed2 >> 6); \
seed2 += (seed1 >> 4) ^ (seed3 >> 15); \
seed1 ^= (seed2 << 9) + (seed3 << 8); \
seed3 ^= 0xA5366B4D * ((seed2 >> 11) ^ (seed1 << 1)); \
seed2 += 0x72BE1579 * ((seed1 << 4) ^ (seed3 >> 16)); \
seed1 ^= 0x3F38A6ED * ((seed3 >> 5) ^ (((signed int) seed2) >> 22)); \
seed2 += seed1 * seed3; \
seed1 += seed3 ^ (seed2 >> 2); \
seed2 ^= ((signed int) seed2) >> 17; \
unsigned int state = 0x79dedea3 * (seed1 ^ (((signed int) seed1) >> 14)); \
unsigned int wstate = (state + seed2) ^ (((signed int) state) >> 8); \
state = state + (wstate * (wstate ^ 0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate >> 1); \
state = LCGA * state + LCGC; \
wstate = wstate + oWeylOffset + ((((signed int) wstate) >> 31) & oWeylPeriod); \
unsigned int v = (state ^ (state >> 26)) + wstate; \
unsigned int s = (signed int) ((v ^ (v >> 20)) * 0x6957f5a7); \
randnum = SQRT3 * (s * TWO_N32 * (numtyp) 2.0 - (numtyp) 1.0); \
}
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns uniformly distributed random numbers u in [-1.0;1.0] using TEA8
// then multiply u with sqrt(3) to "match" with a normal random distribution
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
#ifdef _USE_UNIFORM_SARU_TEA8
#define numtyp double
#define SQRT3 (numtyp) 1.7320508075688772935274463
#define k0 0xA341316C
#define k1 0xC8013EA4
#define k2 0xAD90777D
#define k3 0x7E95761E
#define delta 0x9e3779b9
#define rounds 8
#define saru(seed1, seed2, seed, timestep, randnum) \
{ \
unsigned int seed3 = seed + timestep; \
seed3 ^= (seed1 << 7) ^ (seed2 >> 6); \
seed2 += (seed1 >> 4) ^ (seed3 >> 15); \
seed1 ^= (seed2 << 9) + (seed3 << 8); \
seed3 ^= 0xA5366B4D * ((seed2 >> 11) ^ (seed1 << 1)); \
seed2 += 0x72BE1579 * ((seed1 << 4) ^ (seed3 >> 16)); \
seed1 ^= 0x3F38A6ED * ((seed3 >> 5) ^ (((signed int) seed2) >> 22)); \
seed2 += seed1 * seed3; \
seed1 += seed3 ^ (seed2 >> 2); \
seed2 ^= ((signed int) seed2) >> 17; \
unsigned int state = 0x79dedea3 * (seed1 ^ (((signed int) seed1) >> 14)); \
unsigned int wstate = (state + seed2) ^ (((signed int) state) >> 8); \
state = state + (wstate * (wstate ^ 0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate >> 1); \
unsigned int sum = 0; \
for (int i = 0; i < rounds; i++) { \
sum += delta; \
state += ((wstate << 4) + k0) ^ (wstate + sum) ^ ((wstate >> 5) + k1); \
wstate += ((state << 4) + k2) ^ (state + sum) ^ ((state >> 5) + k3); \
} \
unsigned int v = (state ^ (state >> 26)) + wstate; \
unsigned int s = (signed int) ((v ^ (v >> 20)) * 0x6957f5a7); \
randnum = SQRT3 * (s * TWO_N32 * (numtyp) 2.0 - (numtyp) 1.0); \
}
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns two uniformly distributed random numbers r1 and r2 in [-1.0;1.0],
// and uses the polar method (Marsaglia's) to transform to a normal random value
// This is used to compared with CPU DPD using RandMars::gaussian()
#ifdef _USE_GAUSSIAN_SARU_LCG
#define numtyp double
#define saru(seed1, seed2, seed, timestep, randnum) \
{ \
unsigned int seed3 = seed + timestep; \
seed3 ^= (seed1 << 7) ^ (seed2 >> 6); \
seed2 += (seed1 >> 4) ^ (seed3 >> 15); \
seed1 ^= (seed2 << 9) + (seed3 << 8); \
seed3 ^= 0xA5366B4D * ((seed2 >> 11) ^ (seed1 << 1)); \
seed2 += 0x72BE1579 * ((seed1 << 4) ^ (seed3 >> 16)); \
seed1 ^= 0x3F38A6ED * ((seed3 >> 5) ^ (((signed int) seed2) >> 22)); \
seed2 += seed1 * seed3; \
seed1 += seed3 ^ (seed2 >> 2); \
seed2 ^= ((signed int) seed2) >> 17; \
unsigned int state = 0x12345678; \
unsigned int wstate = 12345678; \
state = 0x79dedea3 * (seed1 ^ (((signed int) seed1) >> 14)); \
wstate = (state + seed2) ^ (((signed int) state) >> 8); \
state = state + (wstate * (wstate ^ 0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate >> 1); \
unsigned int v, s; \
numtyp r1, r2, rsq; \
while (1) { \
state = LCGA * state + LCGC; \
wstate = wstate + oWeylOffset + ((((signed int) wstate) >> 31) & oWeylPeriod); \
v = (state ^ (state >> 26)) + wstate; \
s = (signed int) ((v ^ (v >> 20)) * 0x6957f5a7); \
r1 = s * TWO_N32 * (numtyp) 2.0 - (numtyp) 1.0; \
state = LCGA * state + LCGC; \
wstate = wstate + oWeylOffset + ((((signed int) wstate) >> 31) & oWeylPeriod); \
v = (state ^ (state >> 26)) + wstate; \
s = (signed int) ((v ^ (v >> 20)) * 0x6957f5a7); \
r2 = s * TWO_N32 * (numtyp) 2.0 - (numtyp) 1.0; \
rsq = r1 * r1 + r2 * r2; \
if (rsq < (numtyp) 1.0) break; \
} \
numtyp fac = sqrt((numtyp) -2.0 * log(rsq) / rsq); \
randnum = r2 * fac; \
}
#endif
/* ---------------------------------------------------------------------- */
PairDPDCoulSlaterLongGPU::PairDPDCoulSlaterLongGPU(LAMMPS *lmp) : PairDPDCoulSlaterLong(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
suffix_flag |= Suffix::GPU;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairDPDCoulSlaterLongGPU::~PairDPDCoulSlaterLongGPU()
{
dpd_coul_slater_long_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairDPDCoulSlaterLongGPU::compute(int eflag, int vflag)
{
ev_init(eflag, vflag);
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
double dtinvsqrt = 1.0 / sqrt(update->dt);
bool success = true;
int *ilist, *numneigh, **firstneigh;
double *q = atom->q;
dpd_coul_slater_long_gpu_get_extra_data(q);
if (gpu_mode != GPU_FORCE) {
double sublo[3], subhi[3];
if (domain->triclinic == 0) {
sublo[0] = domain->sublo[0];
sublo[1] = domain->sublo[1];
sublo[2] = domain->sublo[2];
subhi[0] = domain->subhi[0];
subhi[1] = domain->subhi[1];
subhi[2] = domain->subhi[2];
} else {
domain->bbox(domain->sublo_lamda, domain->subhi_lamda, sublo, subhi);
}
inum = atom->nlocal;
firstneigh = dpd_coul_slater_long_gpu_compute_n(
neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom, vflag_atom, host_start, &ilist, &numneigh,
cpu_time, success, atom->v, dtinvsqrt, seed, update->ntimestep, domain->boxlo, domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
dpd_coul_slater_long_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh,
eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time, success, atom->tag,
atom->v, dtinvsqrt, seed, update->ntimestep, atom->nlocal, domain->boxlo,
domain->prd);
}
if (!success) error->one(FLERR, "Insufficient memory on accelerator");
if (atom->molecular != Atom::ATOMIC && neighbor->ago == 0)
neighbor->build_topology();
if (host_start < inum) {
cpu_time = platform::walltime();
cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
cpu_time = platform::walltime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairDPDCoulSlaterLongGPU::init_style()
{
if (comm->ghost_velocity == 0)
error->all(FLERR,"Pair dpd requires ghost atoms store velocity");
if (!atom->q_flag)
error->all(FLERR,"Pair style coul/slater/long requires atom attribute q");
// ensure use of KSpace long-range solver, set g_ewald
if (force->kspace == nullptr) error->all(FLERR, "Pair style requires a KSpace style");
g_ewald = force->kspace->g_ewald;
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double mcut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
mcut = init_one(i, j);
mcut *= mcut;
if (mcut > maxcut) maxcut = mcut;
cutsq[i][j] = cutsq[j][i] = mcut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial = 0;
if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success =
dpd_coul_slater_long_gpu_init(atom->ntypes + 1, cutsq, a0, gamma, sigma,
cut_dpd, cut_dpdsq, cut_slatersq, force->special_lj, atom->nlocal,
atom->nlocal + atom->nghost, mnf, maxspecial, cell_size, gpu_mode, screen,
force->special_coul, force->qqrd2e, g_ewald, lamda);
GPU_EXTRA::check_flag(success, error, world);
if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL);
}
/* ---------------------------------------------------------------------- */
double PairDPDCoulSlaterLongGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + dpd_coul_slater_long_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairDPDCoulSlaterLongGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */, int *ilist,
int *numneigh, int **firstneigh)
{
int i, j, ii, jj, jnum, itype, jtype;
double qtmp, xtmp, ytmp, ztmp, delx, dely, delz, evdwl, ecoul, fpair;
double vxtmp, vytmp, vztmp, delvx, delvy, delvz;
double r2inv,forcedpd,forcecoul,factor_coul;
double grij,expm2,prefactor,t,erfc;
double rsq,r,rinv,dot,wd,randnum,factor_dpd,factor_sqrt;
int *jlist;
double slater_term;
tagint itag, jtag;
double *q = atom->q;
double *special_coul = force->special_coul;
double qqrd2e = force->qqrd2e;
evdwl = 0.0;
ecoul = 0.0;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
int *type = atom->type;
tagint *tag = atom->tag;
double *special_lj = force->special_lj;
double dtinvsqrt = 1.0 / sqrt(update->dt);
int timestep = (int) update->ntimestep;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
vxtmp = v[i][0];
vytmp = v[i][1];
vztmp = v[i][2];
itype = type[i];
itag = tag[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_dpd = special_lj[sbmask(j)];
factor_sqrt = special_sqrt[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx * delx + dely * dely + delz * delz;
jtype = type[j];
jtag = tag[j];
// forces if below maximum cutoff
if (rsq < cutsq[itype][jtype]) {
r = sqrt(rsq);
if (evflag) evdwl = ecoul = 0.0;
// apply DPD force if distance below DPD cutoff
if (rsq < cut_dpdsq[itype][jtype] && r > EPSILON ) {
rinv = 1.0 / r;
delvx = vxtmp - v[j][0];
delvy = vytmp - v[j][1];
delvz = vztmp - v[j][2];
dot = delx * delvx + dely * delvy + delz * delvz;
wd = 1.0 - r / cut[itype][jtype];
unsigned int tag1 = itag, tag2 = jtag;
if (tag1 > tag2) {
tag1 = jtag;
tag2 = itag;
}
randnum = 0.0;
saru(tag1, tag2, seed, timestep, randnum);
// conservative force = a0 * wd
// drag force = -gamma * wd^2 * (delx dot delv) / r
// random force = sigma * wd * rnd * dtinvsqrt;
forcedpd = a0[itype][jtype]*wd;
forcedpd -= gamma[itype][jtype]*wd*wd*dot*rinv;
forcedpd *= factor_dpd;
forcedpd += factor_sqrt*sigma[itype][jtype]*wd*randnum*dtinvsqrt;
forcedpd *= rinv;
if (eflag) {
// eng shifted to 0.0 at cutoff
evdwl = 0.5*a0[itype][jtype]*cut_dpd[itype][jtype] * wd*wd;
evdwl *= factor_dpd;
}
} else forcedpd = 0.0;
// apply Slater electrostatic force if distance below Slater cutoff
// and the two species are charged
if (rsq < cut_slatersq[itype][jtype]){
r2inv = 1.0/rsq;
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
slater_term = exp(-2*r/lamda)*(1 + (2*r/lamda*(1+r/lamda)));
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - slater_term);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor*(1-slater_term);
forcecoul *= r2inv;
if (eflag) {
ecoul = prefactor*(erfc - (1 + r/lamda)*exp(-2*r/lamda));
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor*(1.0-(1 + r/lamda)*exp(-2*r/lamda));
}
} else forcecoul = 0.0;
fpair = forcedpd + forcecoul;
f[i][0] += delx * fpair;
f[i][1] += dely * fpair;
f[i][2] += delz * fpair;
if (evflag) ev_tally_full(i, evdwl, ecoul, fpair, delx, dely, delz);
}
}
}
}

45
src/GPU/pair_dpd_coul_slater_long_gpu.h Normal file
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@ -0,0 +1,45 @@
/* -*- 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(dpd/coul/slater/long/gpu,PairDPDCoulSlaterLongGPU);
// clang-format on
#else
#ifndef LMP_PAIR_DPD_COUL_SLATER_LONG_GPU_H
#define LMP_PAIR_DPD_COUL_SLATER_LONG_GPU_H
#include "pair_dpd_coul_slater_long.h"
namespace LAMMPS_NS {
class PairDPDCoulSlaterLongGPU : public PairDPDCoulSlaterLong {
public:
PairDPDCoulSlaterLongGPU(LAMMPS *lmp);
~PairDPDCoulSlaterLongGPU() override;
void cpu_compute(int, int, int, int, int *, int *, int **);
void compute(int, int) override;
void init_style() override;
double memory_usage() override;
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
private:
int gpu_mode;
double cpu_time;
};
} // namespace LAMMPS_NS
#endif
#endif

1
src/PLUMED/fix_plumed.cpp
View File

@ -205,6 +205,7 @@ FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) :
double dt=update->dt; double dt=update->dt;
p->cmd("setTimestep",&dt); p->cmd("setTimestep",&dt);
extscalar = 1;
scalar_flag = 1; scalar_flag = 1;
energy_global_flag = virial_global_flag = 1; energy_global_flag = virial_global_flag = 1;
thermo_energy = thermo_virial = 1; thermo_energy = thermo_virial = 1;

33
src/library.cpp
View File

@ -1198,14 +1198,31 @@ internally by the :doc:`Fortran interface <Fortran>` and are not likely to be us
* - triclinic * - triclinic
- 1 if the the simulation box is triclinic, 0 if orthogonal. - 1 if the the simulation box is triclinic, 0 if orthogonal.
See :doc:`change_box`. See :doc:`change_box`.
**Communication status**
.. list-table::
:header-rows: 1
:widths: auto
* - Keyword
- Description / Return value
* - universe_rank * - universe_rank
- MPI rank on LAMMPS' universe communicator (0 <= universe_rank < universe_size) - MPI rank on LAMMPS' universe communicator (0 <= universe_rank < universe_size)
* - universe_size * - universe_size
- Number of ranks on LAMMPS' universe communicator (world_size <= universe_size) - Number of ranks on LAMMPS' universe communicator (world_size <= universe_size)
* - world_rank * - world_rank
- MPI rank on LAMMPS' world communicator (0 <= world_rank < world_size) - MPI rank on LAMMPS' world communicator (0 <= world_rank < world_size, aka comm->me)
* - world_size * - world_size
- Number of ranks on LAMMPS' world communicator - Number of ranks on LAMMPS' world communicator (aka comm->nprocs)
* - comm_style
- communication style (0 = BRICK, 1 = TILED)
* - comm_layout
- communication layout (0 = LAYOUT_UNIFORM, 1 = LAYOUT_NONUNIFORM, 2 = LAYOUT_TILED)
* - comm_mode
- communication mode (0 = SINGLE, 1 = MULTI, 2 = MULTIOLD)
* - ghost_velocity
- whether velocities are communicated for ghost atoms (0 = no, 1 = yes)
.. _extract_system_sizes: .. _extract_system_sizes:
@ -1310,6 +1327,10 @@ int lammps_extract_setting(void *handle, const char *keyword)
if (strcmp(keyword,"world_rank") == 0) return lmp->comm->me; if (strcmp(keyword,"world_rank") == 0) return lmp->comm->me;
if (strcmp(keyword,"world_size") == 0) return lmp->comm->nprocs; if (strcmp(keyword,"world_size") == 0) return lmp->comm->nprocs;
if (strcmp(keyword,"nthreads") == 0) return lmp->comm->nthreads; if (strcmp(keyword,"nthreads") == 0) return lmp->comm->nthreads;
if (strcmp(keyword,"comm_style") == 0) return lmp->comm->style;
if (strcmp(keyword,"comm_layout") == 0) return lmp->comm->layout;
if (strcmp(keyword,"comm_mode") == 0) return lmp->comm->mode;
if (strcmp(keyword,"ghost_velocity") == 0) return lmp->comm->ghost_velocity;
if (strcmp(keyword,"nlocal") == 0) return lmp->atom->nlocal; if (strcmp(keyword,"nlocal") == 0) return lmp->atom->nlocal;
if (strcmp(keyword,"nghost") == 0) return lmp->atom->nghost; if (strcmp(keyword,"nghost") == 0) return lmp->atom->nghost;
@ -1386,6 +1407,7 @@ int lammps_extract_global_datatype(void * /*handle*/, const char *name)
if (strcmp(name,"xy") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"xy") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"xz") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"xz") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"yz") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"yz") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"procgrid") == 0) return LAMMPS_INT;
if (strcmp(name,"natoms") == 0) return LAMMPS_BIGINT; if (strcmp(name,"natoms") == 0) return LAMMPS_BIGINT;
if (strcmp(name,"nbonds") == 0) return LAMMPS_BIGINT; if (strcmp(name,"nbonds") == 0) return LAMMPS_BIGINT;
@ -1604,6 +1626,10 @@ report the "native" data type. The following tables are provided:
- double - double
- 1 - 1
- triclinic tilt factor. See :doc:`Howto_triclinic`. - triclinic tilt factor. See :doc:`Howto_triclinic`.
* - procgrid
- int
- 3
- processor count assigned to each dimension of 3d grid. See :doc:`processors`.
.. _extract_system_settings: .. _extract_system_settings:
@ -1861,6 +1887,9 @@ void *lammps_extract_global(void *handle, const char *name)
if (strcmp(name,"xy") == 0) return (void *) &lmp->domain->xy; if (strcmp(name,"xy") == 0) return (void *) &lmp->domain->xy;
if (strcmp(name,"xz") == 0) return (void *) &lmp->domain->xz; if (strcmp(name,"xz") == 0) return (void *) &lmp->domain->xz;
if (strcmp(name,"yz") == 0) return (void *) &lmp->domain->yz; if (strcmp(name,"yz") == 0) return (void *) &lmp->domain->yz;
if (((lmp->comm->layout == Comm::LAYOUT_UNIFORM) ||
(lmp->comm->layout == Comm::LAYOUT_NONUNIFORM)) && (strcmp(name,"procgrid") == 0))
return (void *) &lmp->comm->procgrid;
if (strcmp(name,"natoms") == 0) return (void *) &lmp->atom->natoms; if (strcmp(name,"natoms") == 0) return (void *) &lmp->atom->natoms;
if (strcmp(name,"ntypes") == 0) return (void *) &lmp->atom->ntypes; if (strcmp(name,"ntypes") == 0) return (void *) &lmp->atom->ntypes;

103
unittest/force-styles/tests/mol-pair-dpd_coul_slater_long.yaml Normal file
View File

@ -0,0 +1,103 @@
---
lammps_version: 17 Apr 2024
tags:
date_generated: Tue Jun 18 21:32:14 2024
epsilon: 5e-13
skip_tests: gpu intel kokkos_omp single
prerequisites: ! |
atom full
pair dpd/coul/slater/long
kspace ewald
pre_commands: ! |
variable newton_pair delete
variable newton_pair index on
comm_modify vel yes
post_commands: ! |
kspace_style ewald 1.0e-6
kspace_modify gewald 0.3
kspace_modify compute no
input_file: in.fourmol
pair_style: dpd/coul/slater/long 100.0 8.0 11223344 1.0 8.0
pair_coeff: ! |
* * 0.4 4.0 yes
1 1 0.4 4.0 yes
2 2 0.1 2.0 no
2 4 0.1 1.0
3 3 0.4 3.2 yes
4 4 0.3 3.1 yes
5 5 0.3 3.1 yes
extract: ! |
cut_coul 0
lamda 0
a0 2
gamma 2
natoms: 29
init_vdwl: 50.81607024833933
init_coul: 246.30486150616926
init_stress: ! |2-
3.8847917252197334e+01 6.0909421169945198e+01 1.3177337627459440e+01 -2.5125674673037557e-01 -2.6831071031318483e+01 -1.5576430133730318e+01
init_forces: ! |2
1 1.7431218673076398e+00 -3.3508607597652662e-01 -2.4777022847678101e+00
2 4.3303449895107429e+00 -4.7270196423904629e+00 8.9179383719117788e-01
3 -3.0026241136767506e-01 1.4898682537669559e+00 -2.9373470062765152e+00
4 5.2673340332969785e+00 -4.7092409943919726e+00 -1.4235077704192447e+00
5 -6.8022719083087080e-01 5.7354131392205714e+00 -3.4748110565769061e+00
6 -3.8215670358728731e+00 2.7445299161598462e+00 -2.7043379570240411e+00
7 -3.3428118289029851e+00 2.6368994495618775e-01 4.1564102694578011e+00
8 -7.7861329310896457e+00 8.2082649420572917e-01 4.8567883896169803e+00
9 3.1057899939121918e+00 -3.9223414133714560e+00 8.4873882988538636e+00
10 -4.1521241974355734e+00 2.6307631121111197e-01 3.4593985187994503e+00
11 1.8308032335061764e+00 2.2688626790466668e+00 2.1488881927591183e-01
12 -3.8361154861853802e-01 9.7381188622448867e-01 -2.9002001998530074e+00
13 3.7110360694271507e+00 -6.0293319508894081e+00 -3.2353735026836565e+00
14 -7.1298424060686427e-01 2.4558730338472174e+00 -1.4114476204389881e+00
15 6.4421713828496296e-01 2.6560445474171779e+00 4.1805189129601663e+00
16 2.4609814411173456e+00 1.0005691236622609e+00 -1.3310794681660751e+00
17 4.3419008357709892e+00 3.5242769399360668e-01 -3.0595452598808506e+00
18 -8.6307586369950978e-02 8.2040370677288337e+00 -5.3929118878835798e+00
19 6.1879926571299937e-01 2.5540397129551908e+00 1.5642703712618800e+00
20 -3.0582098014826045e+00 -4.2726657137759743e+00 3.7804333126216734e+00
21 3.4138725239637657e+00 -2.8998556794986174e+00 -3.3216284249543198e+00
22 8.3753401659388671e-01 6.0848461632864803e-01 5.5206263511303710e-01
23 1.6137939864950199e+00 -1.9075657957633927e+00 -1.1740851854919403e+00
24 -9.2620994683392499e-01 -3.2450229700911435e+00 -8.0867271168075465e+00
25 -1.3940090389654722e+00 5.2843663545938764e+00 3.5772359574449069e+00
26 3.9218467465706744e-02 1.1015801783435457e+00 1.8824821245496248e+00
27 -2.4611420161719555e+00 -1.9453626284928394e+00 -3.3205056628962853e-01
28 1.4062959703817013e+00 -1.5914533664642678e+00 2.6909036096293515e+00
29 -6.2594440581983282e+00 -3.1925547225558533e+00 2.9681802507382837e+00
run_vdwl: 50.80969849155796
run_coul: 246.30257595743123
run_stress: ! |2-
2.5169432057277767e+01 1.3291837479686518e+02 7.8314082956801457e+01 1.4188397409481186e+00 4.7717966551748061e+00 -6.3215212489343497e-01
run_forces: ! |2
1 -6.3863580151106092e-01 6.6929475226486339e+00 3.7704563748664892e+00
2 -4.3037556793948211e+00 9.5723509028532272e-02 -2.0030241717125286e+00
3 -1.2783833512172147e+00 1.7381921345191331e+00 -6.4662583653508925e+00
4 2.4827815076802873e+00 1.3730024199636431e-01 -2.0006851631917272e-01
5 4.7603332815631365e+00 -2.2528146831857900e+00 -3.4274535000597357e+00
6 -1.2817868583433294e+00 -5.9968609698691075e+00 -3.2762169423954415e+00
7 -6.6867815106826880e+00 -7.6943923258643654e-01 -2.6780134761760793e-01
8 -3.3343023480304996e+00 6.4339698400391008e+00 -6.4172530505932164e+00
9 -3.8353029345585190e+00 9.8394636146294001e+00 1.9174283216744969e+00
10 -2.7100348949081012e+00 1.4548533898989857e-01 -7.4888242419930628e-01
11 -3.5716272980494614e+00 -5.6333424874513238e-01 -1.7669409895579073e+00
12 8.7749889216756269e+00 -3.0182112894280873e+00 2.3328096163511405e+00
13 -7.1201394227081138e+00 8.5405234502858711e+00 4.5843737570467056e+00
14 -8.7413969567458588e-02 -3.7153733247848848e+00 -3.2874441379609167e+00
15 4.3120572612995609e+00 1.7256832039357071e+00 3.3428599179267393e-01
16 3.8021838909677803e+00 -1.3766365519719326e+01 2.2813835507927651e+00
17 4.9734505785815566e+00 -2.4146919042613795e+00 1.8287742974940246e+00
18 -1.7572559387593672e-03 3.8187261679342619e+00 -1.0584087358440382e+00
19 1.0838708527692988e+00 -6.6703633150528441e-01 -4.6973954164255893e-01
20 1.1923743451913014e+00 1.7419734493475330e+00 -3.6369159702300224e-01
21 2.3316248125417141e+00 -1.0849270685777668e+00 -3.2073997386907678e+00
22 2.6135216134985972e+00 -1.1025272637629011e+00 4.8873485142461329e-02
23 -1.2854577922712009e+00 -2.9253148869589518e+00 -4.6563146954583601e-01
24 -1.4021980080098731e-01 1.9672435672875048e+00 3.1379645935988041e+00
25 1.9085702323304496e+00 5.2270676739892066e+00 7.3556254244703823e+00
26 8.7357677171207004e-01 -1.1308292622526788e+00 -8.0741590972110988e-01
27 -1.1543680887940906e+00 -9.4513879574846338e-01 1.0062759048570287e+00
28 2.3730888896530073e+00 -1.9664779055036602e-01 1.0051483653476245e+00
29 -4.0524559526880868e+00 -7.5547871426945932e+00 4.6302307547994435e+00
...

38
unittest/python/python-commands.py
View File

@ -580,6 +580,37 @@ create_atoms 1 single &
"Press" : 0.0} "Press" : 0.0}
self.assertDictEqual(self.lmp.last_thermo(), ref) self.assertDictEqual(self.lmp.last_thermo(), ref)
def test_extract_setting(self):
self.assertEqual(self.lmp.extract_setting("dimension"), 3)
self.assertEqual(self.lmp.extract_setting("box_exist"), 0)
self.assertEqual(self.lmp.extract_setting("kokkos_active"), 0)
self.assertEqual(self.lmp.extract_setting("kokkos_nthreads"), 0)
self.assertEqual(self.lmp.extract_setting("kokkos_ngpus"), 0)
self.lmp.command("region box block -1 1 -2 2 -3 3")
self.lmp.command("create_box 1 box")
self.lmp.command("special_bonds lj 0.0 0.5 0.8 coul 0.1 0.5 1.0")
self.assertEqual(self.lmp.extract_setting("newton_bond"), 1)
self.assertEqual(self.lmp.extract_setting("newton_pair"), 1)
self.assertEqual(self.lmp.extract_setting("triclinic"), 0)
self.assertEqual(self.lmp.extract_setting("universe_rank"), 0)
self.assertEqual(self.lmp.extract_setting("universe_size"), 1)
self.assertEqual(self.lmp.extract_setting("world_rank"), 0)
self.assertEqual(self.lmp.extract_setting("world_size"), 1)
self.assertEqual(self.lmp.extract_setting("triclinic"), 0)
self.assertEqual(self.lmp.extract_setting("comm_style"), 0)
self.assertEqual(self.lmp.extract_setting("comm_layout"), 0)
self.assertEqual(self.lmp.extract_setting("comm_mode"), 0)
self.assertEqual(self.lmp.extract_setting("ghost_velocity"), 0)
self.lmp.command("comm_style tiled")
self.lmp.command("comm_modify vel yes")
self.lmp.command("mass 1 1.0")
self.lmp.command("run 0 post no")
self.lmp.command("balance 0.1 rcb")
self.assertEqual(self.lmp.extract_setting("comm_style"), 1)
self.assertEqual(self.lmp.extract_setting("comm_layout"), 2)
self.assertEqual(self.lmp.extract_setting("comm_mode"), 0)
self.assertEqual(self.lmp.extract_setting("ghost_velocity"), 1)
def test_extract_global(self): def test_extract_global(self):
self.lmp.command("region box block -1 1 -2 2 -3 3") self.lmp.command("region box block -1 1 -2 2 -3 3")
self.lmp.command("create_box 1 box") self.lmp.command("create_box 1 box")
@ -628,6 +659,13 @@ create_atoms 1 single &
self.assertEqual(self.lmp.extract_global("sublo_lambda"), [0.0, 0.0, 0.0]) self.assertEqual(self.lmp.extract_global("sublo_lambda"), [0.0, 0.0, 0.0])
self.assertEqual(self.lmp.extract_global("subhi_lambda"), [1.0, 1.0, 1.0]) self.assertEqual(self.lmp.extract_global("subhi_lambda"), [1.0, 1.0, 1.0])
# processor grid
self.assertEqual(self.lmp.extract_global("procgrid"), [1,1,1])
self.lmp.command("comm_style tiled")
self.lmp.command("run 0 post no")
self.lmp.command("balance 0.1 rcb")
self.assertEqual(self.lmp.extract_global("procgrid"), None)
def test_create_atoms(self): def test_create_atoms(self):
self.lmp.command("boundary f p m") self.lmp.command("boundary f p m")
self.lmp.command("region box block 0 10 0 10 0 10") self.lmp.command("region box block 0 10 0 10 0 10")

9
unittest/python/python-pylammps.py
View File

@ -119,6 +119,10 @@ class PythonPyLammps(unittest.TestCase):
self.assertEqual(self.pylmp.communication.comm_style,'brick') self.assertEqual(self.pylmp.communication.comm_style,'brick')
self.assertEqual(self.pylmp.communication.comm_layout,'uniform') self.assertEqual(self.pylmp.communication.comm_layout,'uniform')
self.assertEqual(self.pylmp.communication.nprocs,1) self.assertEqual(self.pylmp.communication.nprocs,1)
self.assertEqual(self.pylmp.communication.nthreads,1)
self.assertEqual(self.pylmp.communication.procgrid,[1,1,1])
self.assertEqual(self.pylmp.communication.proc_grid,[1,1,1])
self.assertEqual(self.pylmp.communication.ghost_velocity,0)
self.assertEqual(len(self.pylmp.computes),3) self.assertEqual(len(self.pylmp.computes),3)
self.assertEqual(self.pylmp.computes[0]['name'], 'thermo_temp') self.assertEqual(self.pylmp.computes[0]['name'], 'thermo_temp')
self.assertEqual(self.pylmp.computes[0]['style'], 'temp') self.assertEqual(self.pylmp.computes[0]['style'], 'temp')
@ -137,6 +141,11 @@ class PythonPyLammps(unittest.TestCase):
self.assertEqual(self.pylmp.fixes[0]['group'], 'all') self.assertEqual(self.pylmp.fixes[0]['group'], 'all')
self.pylmp.group('none','empty') self.pylmp.group('none','empty')
self.assertEqual(len(self.pylmp.groups),2) self.assertEqual(len(self.pylmp.groups),2)
self.pylmp.comm_style('tiled')
self.pylmp.mass('*',1.0)
self.pylmp.run('0','post','no')
self.pylmp.balance(0.1,'rcb')
self.assertEqual(self.pylmp.communication.procgrid,None)
if __name__ == "__main__": if __name__ == "__main__":
unittest.main() unittest.main()