forked from lijiext/lammps
Merge branch 'master' into lammps_gjf
This commit is contained in:
charlie sievers
commit
f0b6ca82dd
|
|
@ -589,6 +589,7 @@ if(BUILD_TOOLS)
|
|||
enable_language(Fortran)
|
||||
add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
|
||||
target_link_libraries(chain.x ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
|
||||
install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
|
||||
endif()
|
||||
|
||||
enable_language(C)
|
||||
|
|
|
|||
|
|
@ -37,6 +37,26 @@
|
|||
# KIM-API-CMAKE_Fortran_COMPILER
|
||||
#
|
||||
|
||||
function(_KIMAPI_GET_VERSION _OUT_ver _version_hdr)
|
||||
if(NOT EXISTS ${_version_hdr})
|
||||
message(FATAL_ERROR "Header file ${_version_hdr} not found (check value of KIM-API_INCLUDE_DIR)")
|
||||
endif()
|
||||
foreach(_var KIM_VERSION_MAJOR KIM_VERSION_MINOR KIM_VERSION_PATCH)
|
||||
file(STRINGS ${_version_hdr} _contents REGEX "#define ${_var}[ \t]+")
|
||||
if(_contents)
|
||||
string(REGEX REPLACE ".*#define ${_var}[ \t]+([0-9]+).*" "\\1" _${_var} "${_contents}")
|
||||
if(${_${_var}} STREQUAL "")
|
||||
message(FATAL_ERROR "Version parsing failed for ${_var} in ${_version_hdr}, got empty return!")
|
||||
elseif(NOT ${_${_var}} MATCHES "^[0-9]+$")
|
||||
message(FATAL_ERROR "Version parsing failed for ${_var} in ${_version_hdr}, excepted a number but got ${_${_var}}!")
|
||||
endif()
|
||||
else()
|
||||
message(FATAL_ERROR "No ${_var} line found in include file ${_version_hdr}")
|
||||
endif()
|
||||
endforeach()
|
||||
set(${_OUT_ver} ${_KIM_VERSION_MAJOR}.${_KIM_VERSION_MINOR}.${_KIM_VERSION_PATCH} PARENT_SCOPE)
|
||||
endfunction()
|
||||
|
||||
if(KIM-API_FIND_QUIETLY)
|
||||
set(REQ_OR_QUI "QUIET")
|
||||
else()
|
||||
|
|
@ -54,6 +74,12 @@ if(KIM-API_FOUND)
|
|||
pkg_get_variable(KIM-API_CMAKE_Fortran_COMPILER libkim-api CMAKE_Fortran_COMPILER)
|
||||
endif()
|
||||
|
||||
if(KIM-API_INCLUDEDIR)
|
||||
_KIMAPI_GET_VERSION(KIM-API_VERSION ${KIM-API_INCLUDEDIR}/KIM_Version.h)
|
||||
else()
|
||||
set(KIM-API_VERSION 0)
|
||||
endif()
|
||||
|
||||
# handle the QUIETLY and REQUIRED arguments and set KIM-API_FOUND to TRUE
|
||||
# if all listed variables are TRUE
|
||||
find_package_handle_standard_args(KIM-API REQUIRED_VARS KIM-API_LIBRARIES)
|
||||
find_package_handle_standard_args(KIM-API REQUIRED_VARS KIM-API_LIBRARIES VERSION_VAR KIM-API_VERSION)
|
||||
|
|
|
|||
|
|
@ -1,4 +1,5 @@
|
|||
if(PKG_KIM)
|
||||
set(KIM-API_MIN_VERSION 2.1)
|
||||
find_package(CURL)
|
||||
if(CURL_FOUND)
|
||||
include_directories(${CURL_INCLUDE_DIRS})
|
||||
|
|
@ -7,10 +8,17 @@ if(PKG_KIM)
|
|||
endif()
|
||||
find_package(KIM-API QUIET)
|
||||
if(KIM-API_FOUND)
|
||||
set(DOWNLOAD_KIM_DEFAULT OFF)
|
||||
if (KIM-API_VERSION VERSION_LESS ${KIM-API_MIN_VERSION})
|
||||
if ("${DOWNLOAD_KIM}" STREQUAL "")
|
||||
message(WARNING "Unsuitable KIM-API version \"${KIM-API_VERSION}\" found, but required is at least \"${KIM-API_MIN_VERSION}\". Default behavior set to download and build our own.")
|
||||
endif()
|
||||
set(DOWNLOAD_KIM_DEFAULT ON)
|
||||
else()
|
||||
set(DOWNLOAD_KIM_DEFAULT OFF)
|
||||
endif()
|
||||
else()
|
||||
if (NOT DOWNLOAD_KIM)
|
||||
message(WARNING "KIM-API package not found. We will download and build our own")
|
||||
if ("${DOWNLOAD_KIM}" STREQUAL "")
|
||||
message(WARNING "KIM-API package not found. Default behavior set to download and build our own")
|
||||
endif()
|
||||
set(DOWNLOAD_KIM_DEFAULT ON)
|
||||
endif()
|
||||
|
|
@ -28,8 +36,8 @@ if(PKG_KIM)
|
|||
message(FATAL_ERROR "Compiling the KIM-API library requires a Fortran compiler")
|
||||
endif()
|
||||
ExternalProject_Add(kim_build
|
||||
URL https://s3.openkim.org/kim-api/kim-api-2.1.2.txz
|
||||
URL_MD5 6ac52e14ef52967fc7858220b208cba5
|
||||
URL https://s3.openkim.org/kim-api/kim-api-2.1.3.txz
|
||||
URL_MD5 6ee829a1bbba5f8b9874c88c4c4ebff8
|
||||
BINARY_DIR build
|
||||
CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
|
||||
-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
|
||||
|
|
@ -42,7 +50,7 @@ if(PKG_KIM)
|
|||
set(KIM-API_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX})
|
||||
list(APPEND LAMMPS_DEPS kim_build)
|
||||
else()
|
||||
find_package(KIM-API REQUIRED)
|
||||
find_package(KIM-API ${KIM-API_MIN_VERSION} REQUIRED)
|
||||
endif()
|
||||
list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}")
|
||||
include_directories(${KIM-API_INCLUDE_DIRS})
|
||||
|
|
|
|||
|
|
@ -23,6 +23,7 @@ if(PKG_KOKKOS)
|
|||
${KOKKOS_PKG_SOURCES_DIR}/fix_nh_kokkos.cpp
|
||||
${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.cpp
|
||||
${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.cpp
|
||||
${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.cpp
|
||||
${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
|
||||
${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
|
||||
|
||||
|
|
@ -38,6 +39,7 @@ if(PKG_KOKKOS)
|
|||
# register kokkos-only styles
|
||||
RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h)
|
||||
RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h)
|
||||
RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.h)
|
||||
|
||||
if(PKG_USER-DPD)
|
||||
get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
|
||||
|
|
|
|||
|
|
@ -232,6 +232,7 @@ OPT.
|
|||
"wall/lj1043"_fix_wall.html,
|
||||
"wall/lj126"_fix_wall.html,
|
||||
"wall/lj93 (k)"_fix_wall.html,
|
||||
"wall/morse"_fix_wall.html,
|
||||
"wall/piston"_fix_wall_piston.html,
|
||||
"wall/reflect (k)"_fix_wall_reflect.html,
|
||||
"wall/region"_fix_wall_region.html,
|
||||
|
|
|
|||
|
|
@ -65,6 +65,7 @@ OPT.
|
|||
"colloid (go)"_pair_colloid.html,
|
||||
"comb (o)"_pair_comb.html,
|
||||
"comb3"_pair_comb.html,
|
||||
"cosine/squared"_pair_cosine_squared.html,
|
||||
"coul/cut (gko)"_pair_coul.html,
|
||||
"coul/cut/soft (o)"_pair_fep_soft.html,
|
||||
"coul/debye (gko)"_pair_coul.html,
|
||||
|
|
|
|||
Binary file not shown.
|
After Width: | Height: | Size: 8.7 KiB |
|
|
@ -0,0 +1,16 @@
|
|||
\documentclass[12pt]{article}
|
||||
|
||||
\usepackage{amsmath}
|
||||
|
||||
\begin{document}
|
||||
|
||||
\begin{align*}
|
||||
E =
|
||||
\begin{cases}
|
||||
-\epsilon& \quad r < \sigma \\
|
||||
-\epsilon\cos\left(\frac{\pi\left(r - \sigma\right)}{2\left(r_c - \sigma\right)}\right)&\quad \sigma \leq r < r_c \\
|
||||
0& \quad r \geq r_c
|
||||
\end{cases}
|
||||
\end{align*}
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 6.6 KiB |
|
|
@ -0,0 +1,11 @@
|
|||
\documentstyle[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
|
||||
2\left(\frac{\sigma}{r}\right)^6 + 1\right]
|
||||
, \quad r < \sigma
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
|
|
@ -136,7 +136,9 @@ The "compute chunk/spread/atom"_compute_chunk_spread_atom.html command
|
|||
spreads per-chunk values to each atom in the chunk, producing per-atom
|
||||
values as its output. This can be useful for outputting per-chunk
|
||||
values to a per-atom "dump file"_dump.html. Or for using an atom's
|
||||
associated chunk value in an "atom-style variable"_variable.html.
|
||||
associated chunk value in an "atom-style variable"_variable.html. Or
|
||||
as input to the "fix ave/chunk"_fix_ave_chunk.html command to
|
||||
spatially average per-chunk values calculated by a per-chunk compute.
|
||||
|
||||
The "compute reduce/chunk"_compute_reduce_chunk.html command reduces a
|
||||
peratom value across the atoms in each chunk to produce a value per
|
||||
|
|
@ -184,12 +186,20 @@ compute cc1 all chunk/atom c_cluster compress yes
|
|||
compute size all property/chunk cc1 count
|
||||
fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre
|
||||
|
||||
(6) An example of using a per-chunk value to apply per-atom forces to
|
||||
(6) An example for using a per-chunk value to apply per-atom forces to
|
||||
compress individual polymer chains (molecules) in a mixture, is
|
||||
explained on the "compute
|
||||
chunk/spread/atom"_compute_chunk_spread_atom.html command doc page.
|
||||
|
||||
(7) An example of using one set of per-chunk values for molecule
|
||||
(7) An example for using one set of per-chunk values for molecule
|
||||
chunks, to create a 2nd set of micelle-scale chunks (clustered
|
||||
molecules, due to hydrophobicity), is explained on the "compute
|
||||
chunk/reduce"_compute_reduce_chunk.html command doc page.
|
||||
|
||||
(8) An example for using one set of per-chunk values (dipole moment
|
||||
vectors) for molecule chunks, spreading the values to each atom in
|
||||
each chunk, then defining a second set of chunks as spatial bins, and
|
||||
using the "fix ave/chunk"_fix_ave_chunk.html command to calculate an
|
||||
average dipole moment vector for each bin. This example is explained
|
||||
on the "compute chunk/spread/atom"_compute_chunk_spread_atom.html
|
||||
command doc page.
|
||||
|
|
|
|||
|
|
@ -59,14 +59,15 @@ granular particles; all the other commands create smooth walls.
|
|||
"fix wall/lj126"_fix_wall.html - flat walls, with Lennard-Jones 12/6 potential
|
||||
"fix wall/colloid"_fix_wall.html - flat walls, with "pair_style colloid"_pair_colloid.html potential
|
||||
"fix wall/harmonic"_fix_wall.html - flat walls, with repulsive harmonic spring potential
|
||||
"fix wall/morse"_fix_wall.html - flat walls, with Morse potential
|
||||
"fix wall/region"_fix_wall_region.html - use region surface as wall
|
||||
"fix wall/gran"_fix_wall_gran.html - flat or curved walls with "pair_style granular"_pair_gran.html potential :ul
|
||||
|
||||
The {lj93}, {lj126}, {colloid}, and {harmonic} styles all allow the
|
||||
flat walls to move with a constant velocity, or oscillate in time.
|
||||
The "fix wall/region"_fix_wall_region.html command offers the most
|
||||
generality, since the region surface is treated as a wall, and the
|
||||
geometry of the region can be a simple primitive volume (e.g. a
|
||||
The {lj93}, {lj126}, {colloid}, {harmonic}, and {morse} styles all
|
||||
allow the flat walls to move with a constant velocity, or oscillate in
|
||||
time. The "fix wall/region"_fix_wall_region.html command offers the
|
||||
most generality, since the region surface is treated as a wall, and
|
||||
the geometry of the region can be a simple primitive volume (e.g. a
|
||||
sphere, or cube, or plane), or a complex volume made from the union
|
||||
and intersection of primitive volumes. "Regions"_region.html can also
|
||||
specify a volume "interior" or "exterior" to the specified primitive
|
||||
|
|
|
|||
Binary file not shown.
|
After Width: | Height: | Size: 29 KiB |
|
|
@ -217,6 +217,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
|
|||
"heat/flux"_compute_heat_flux.html - heat flux through a group of atoms
|
||||
"heat/flux/tally"_compute_tally.html -
|
||||
"hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6
|
||||
"hma"_compute_hma.html - harmonically mapped averaging for atomic crystals
|
||||
"improper"_compute_improper.html - energy of each improper sub-style
|
||||
"improper/local"_compute_improper_local.html - angle of each improper
|
||||
"inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk
|
||||
|
|
|
|||
|
|
@ -30,11 +30,18 @@ compute 1 all chunk/spread/atom mychunk c_com[*] c_gyration :pre
|
|||
[Description:]
|
||||
|
||||
Define a calculation that "spreads" one or more per-chunk values to
|
||||
each atom in the chunk. This can be useful for creating a "dump
|
||||
file"_dump.html where each atom lists info about the chunk it is in,
|
||||
e.g. for post-processing purposes. It can also be used in "atom-style
|
||||
variables"_variable.html that need info about the chunk each atom is
|
||||
in. Examples are given below.
|
||||
each atom in the chunk. This can be useful in several scenarios:
|
||||
|
||||
For creating a "dump file"_dump.html where each atom lists info about
|
||||
the chunk it is in, e.g. for post-processing purposes. :ulb,l
|
||||
|
||||
To access chunk value in "atom-style variables"_variable.html that
|
||||
need info about the chunk each atom is in. :l
|
||||
|
||||
To use the "fix ave/chunk"_fix_ave_chunk.html command to spatially
|
||||
average per-chunk values calculated by a per-chunk compute. :l,ule
|
||||
|
||||
Examples are given below.
|
||||
|
||||
In LAMMPS, chunks are collections of atoms defined by a "compute
|
||||
chunk/atom"_compute_chunk_atom.html command, which assigns each atom
|
||||
|
|
@ -148,6 +155,28 @@ thermo_style custom step etotal press v_ave :pre
|
|||
|
||||
:line
|
||||
|
||||
Here is an example for using one set of chunks, defined for molecules,
|
||||
to compute the dipole moment vector for each chunk. E.g. for water
|
||||
molecules. Then spreading those values to each atom in each chunk.
|
||||
Then defining a second set of chunks based on spatial bins. And
|
||||
finally, using the "fix ave/chunk"_fix_ave_chunk.html command to
|
||||
calculate an average dipole moment vector per spatial bin.
|
||||
|
||||
compute cmol all chunk/atom molecule
|
||||
compute dipole all dipole/chunk cmol
|
||||
compute spread all chunk/spread/atom cmol c_dipole\[1\] c_dipole\[2\] c_dipole\[3\]
|
||||
compute cspatial all chunk/atom bin/1d z lower 0.1 units reduced
|
||||
fix ave all ave/chunk 100 10 1000 cspatial c_spread\[*\] :pre
|
||||
|
||||
Note that the "fix ave/chunk"_fix_ave_chunk.html command requires
|
||||
per-atom values as input. That is why the compute chunk/spread/atom
|
||||
command is used to assign per-chunk values to each atom in the chunk.
|
||||
If a molecule straddles bin boundaries, each of its atoms contributes
|
||||
in a weighted manner to the average dipole moment of the spatial bin
|
||||
it is in.
|
||||
|
||||
:line
|
||||
|
||||
[Output info:]
|
||||
|
||||
This compute calculates a per-atom vector or array, which can be
|
||||
|
|
|
|||
|
|
@ -0,0 +1,184 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
compute hma command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID hma temp-ID keyword ... :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command :l
|
||||
hma = style name of this compute command :l
|
||||
temp-ID = ID of fix that specifies the set temperature during canonical simulation :l
|
||||
keyword = {anharmonic} {u} {p Pharm} {cv} :l
|
||||
{anharmonic} = compute will return anharmonic property values
|
||||
{u} = compute will return potential energy
|
||||
{p} = compute will return pressure. the following keyword must be the difference between the harmonic pressure and lattice pressure as described below
|
||||
{cv} = compute will return the heat capacity :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 2 all hma 1 u
|
||||
compute 2 all hma 1 anharmonic u p 0.9
|
||||
compute 2 all hma 1 u cv :pre
|
||||
|
||||
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates the properties of a solid (potential
|
||||
energy, pressure or heat capacity), using the harmonically-mapped averaging
|
||||
(HMA) method.
|
||||
This command yields much higher precision than the equivalent compute commands
|
||||
("compute pe"_compute_pe.html, "compute pressure"_compute_pressure.html, etc.)
|
||||
commands during a canonical simulation of an atomic crystal. Specifically,
|
||||
near melting HMA can yield averages of a given precision an order of magnitude
|
||||
faster than conventional methods, and this only improves as the temperatures is
|
||||
lowered. This is particularly important for evaluating the free energy by
|
||||
thermodynamic integration, where the low-temperature contributions are the
|
||||
greatest source of statistical uncertainty. Moreover, HMA has other
|
||||
advantages, including smaller potential-truncation effects, finite-size
|
||||
effects, smaller timestep inaccuracy, faster equilibration and shorter
|
||||
decorrelation time.
|
||||
|
||||
HMA should not be used if atoms are expected to diffuse. It is also
|
||||
restricted to simulations in the NVT ensemble. While this compute may be
|
||||
used with any potential in LAMMPS, it will provide inaccurate results
|
||||
for potentials that do not go to 0 at the truncation distance;
|
||||
"pair_lj_smooth_linear"_pair_lj_smooth_linear.html and Ewald summation should
|
||||
work fine, while "pair_lj"_pair_lj.html will perform poorly unless
|
||||
the potential is shifted (via "pair_modify"_pair_modify.html shift) or the cutoff is large. Furthermore, computation of the heat capacity with
|
||||
this compute is restricted to those that implement the single_hessian method
|
||||
in Pair. Implementing single_hessian in additional pair styles is simple.
|
||||
Please contact Andrew Schultz (ajs42 at buffalo.edu) and David Kofke (kofke at
|
||||
buffalo.edu) if your desired pair style does not have this method. This is
|
||||
the list of pair styles that currently implement pair_hessian:
|
||||
|
||||
"lj_smooth_linear"_pair_lj_smooth_linear.html :l
|
||||
:ule
|
||||
|
||||
In this method, the analytically known harmonic behavior of a crystal is removed from the traditional ensemble
|
||||
averages, which leads to an accurate and precise measurement of the anharmonic contributions without contamination
|
||||
by noise produced by the already-known harmonic behavior.
|
||||
A detailed description of this method can be found in ("Moustafa"_#hma-Moustafa). The potential energy is computed by the formula:
|
||||
|
||||
\begin\{equation\}
|
||||
\left< U\right>_\{HMA\} = \frac\{d\}\{2\} (N-1) k_B T + \left< U + \frac\{1\}\{2\} F\bullet\Delta r \right>
|
||||
\end\{equation\}
|
||||
|
||||
where \(N\) is the number of atoms in the system, \(k_B\) is Boltzmann's
|
||||
constant, \(T\) is the temperature, \(d\) is the
|
||||
dimensionality of the system (2 or 3 for 2d/3d), \(F\bullet\Delta r\) is the sum of dot products of the
|
||||
atomic force vectors and displacement (from lattice sites) vectors, and \(U\) is the sum of
|
||||
pair, bond, angle, dihedral, improper, kspace (long-range), and fix energies.
|
||||
|
||||
The pressure is computed by the formula:
|
||||
|
||||
\begin\{equation\}
|
||||
\left< P\right>_\{HMA\} = \Delta \hat P + \left< P_\{vir\} + \frac\{\beta \Delta \hat P - \rho\}\{d(N-1)\} F\bullet\Delta r \right>
|
||||
\end\{equation\}
|
||||
|
||||
where \(\rho\) is the number density of the system, \(\Delta \hat P\) is the
|
||||
difference between the harmonic and lattice pressure, \(P_\{vir\}\) is
|
||||
the virial pressure computed as the sum of pair, bond, angle, dihedral,
|
||||
improper, kspace (long-range), and fix contributions to the force on each
|
||||
atom, and \(k_B=1/k_B T\). Although the method will work for any value of \(\Delta \hat P\)
|
||||
specified (use pressure "units"_units.html), the precision of the resultant
|
||||
pressure is sensitive to \(\Delta \hat P\); the precision tends to be
|
||||
best when \(\Delta \hat P\) is the actual the difference between the lattice
|
||||
pressure and harmonic pressure.
|
||||
|
||||
\begin\{equation\}
|
||||
\left<C_V \right>_\{HMA\} = \frac\{d\}\{2\} (N-1) k_B + \frac\{1\}\{k_B T^2\} \left( \left<
|
||||
U_\{HMA\}^2 \right> - \left<U_\{HMA\}\right>^2 \right) + \frac\{1\}\{4 T\}
|
||||
\left< F\bullet\Delta r + \Delta r \bullet \Phi \bullet \Delta r \right>
|
||||
\end\{equation\}
|
||||
|
||||
where \(\Phi\) is the Hessian matrix. The compute hma command
|
||||
computes the full expression for \(C_V\) except for the
|
||||
\(\left<U_\{HMA\}^2\right>^2\) in the variance term, which can be obtained by
|
||||
passing the {u} keyword; you must add this extra contribution to the \(C_V\)
|
||||
value reported by this compute. The variance term can cause significant
|
||||
round-off error when computing \(C_V\). To address this, the {anharmonic}
|
||||
keyword can be passed and/or the output format can be specified with more
|
||||
digits.
|
||||
|
||||
thermo_modify format float '%22.15e' :pre
|
||||
|
||||
The {anharmonic} keyword will instruct the compute to return anharmonic
|
||||
properties rather than the full properties, which include lattice, harmonic
|
||||
and anharmonic contributions.
|
||||
When using this keyword, the compute must be first active (it must be included
|
||||
via a "thermo_style custom"_thermo_style.html command) while the atoms are
|
||||
still at their lattice sites (before equilibration).
|
||||
|
||||
The temp-ID specified with compute hma command should be same as the fix-ID of Nose-Hoover ("fix nvt"_fix_nh.html) or
|
||||
Berendsen ("fix temp/berendsen"_fix_temp_berendsen.html) thermostat used for the simulation. While using this command, Langevin thermostat
|
||||
("fix langevin"_fix_langevin.html)
|
||||
should be avoided as its extra forces interfere with the HMA implementation.
|
||||
|
||||
|
||||
|
||||
NOTE: Compute hma command should be used right after the energy minimization, when the atoms are at their lattice sites.
|
||||
The simulation should not be started before this command has been used in the input script.
|
||||
|
||||
|
||||
The following example illustrates the placement of this command in the input script:
|
||||
|
||||
|
||||
min_style cg
|
||||
minimize 1e-35 1e-15 50000 500000
|
||||
compute 1 all hma thermostatid u
|
||||
fix thermostatid all nvt temp 600.0 600.0 100.0 :pre
|
||||
|
||||
|
||||
|
||||
NOTE: Compute hma should be used when the atoms of the solid do not diffuse. Diffusion will reduce the precision in the potential energy computation.
|
||||
|
||||
|
||||
NOTE: The "fix_modify energy yes"_fix_modify.html command must also be specified if a fix is to contribute potential energy to this command.
|
||||
|
||||
An example input script that uses this compute is included in
|
||||
examples/USER/hma/ along with corresponding LAMMPS output showing that the HMA
|
||||
properties fluctuate less than the corresponding conventional properties.
|
||||
|
||||
[Output info:]
|
||||
|
||||
This compute calculates a global vector that includes the n properties
|
||||
requested as arguments to the command (the potential energy, pressure and/or heat
|
||||
capacity). The elements of the vector can be accessed by indices 1-n by any
|
||||
command that uses global vector values as input. See the "Howto
|
||||
output"_Howto_output.html doc page for an overview of LAMMPS output options.
|
||||
|
||||
The vector values calculated by this compute are "extensive". The
|
||||
scalar value will be in energy "units"_units.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This compute is part of the USER-MISC package. It is enabled only
|
||||
if LAMMPS was built with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
Usage restricted to canonical (NVT) ensemble simulation only.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"compute pe"_compute_pe.html, "compute pressure"_compute_pressure.html
|
||||
|
||||
"dynamical matrix"_dynamical_matrix.html provides a finite difference
|
||||
formulation of the hessian provided by Pair's single_hessian, which is used by
|
||||
this compute.
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(hma-Moustafa)
|
||||
[(Moustafa)] Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, {Very fast averaging of thermal properties of crystals by molecular simulation},
|
||||
"Phys. Rev. E \[92\], 043303 (2015)"_https://link.aps.org/doi/10.1103/PhysRevE.92.043303
|
||||
|
|
@ -47,6 +47,7 @@ Computes :h1
|
|||
compute_gyration_shape
|
||||
compute_heat_flux
|
||||
compute_hexorder_atom
|
||||
compute_hma
|
||||
compute_improper
|
||||
compute_improper_local
|
||||
compute_inertia_chunk
|
||||
|
|
|
|||
|
|
@ -47,6 +47,9 @@ package"_Build_package.html doc page for more info.
|
|||
|
||||
"fix phonon"_fix_phonon.html
|
||||
|
||||
"compute hma"_compute_hma.html uses an analytic formulation of the hessian
|
||||
provided by Pair's single_hessian.
|
||||
|
||||
[Default:]
|
||||
|
||||
The default settings are file = "dynmat.dyn", binary = no
|
||||
|
|
|
|||
|
|
@ -244,7 +244,7 @@ accelerated styles exist.
|
|||
"mscg"_fix_mscg.html - apply MSCG method for force-matching to generate coarse grain models
|
||||
"msst"_fix_msst.html - multi-scale shock technique (MSST) integration
|
||||
"mvv/dpd"_fix_mvv_dpd.html - DPD using the modified velocity-Verlet integration algorithm
|
||||
"mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algrithm
|
||||
"mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algorithm
|
||||
"mvv/tdpd"_fix_mvv_dpd.html - constant temperature DPD using the modified velocity-Verlet algorithm
|
||||
"neb"_fix_neb.html - nudged elastic band (NEB) spring forces
|
||||
"nph"_fix_nh.html - constant NPH time integration via Nose/Hoover
|
||||
|
|
@ -371,6 +371,7 @@ accelerated styles exist.
|
|||
"wall/lj1043"_fix_wall.html - Lennard-Jones 10-4-3 wall
|
||||
"wall/lj126"_fix_wall.html - Lennard-Jones 12-6 wall
|
||||
"wall/lj93"_fix_wall.html - Lennard-Jones 9-3 wall
|
||||
"wall/morse"_fix_wall.html - Morse potential wall
|
||||
"wall/piston"_fix_wall_piston.html - moving reflective piston wall
|
||||
"wall/reflect"_fix_wall_reflect.html - reflecting wall(s)
|
||||
"wall/region"_fix_wall_region.html - use region surface as wall
|
||||
|
|
|
|||
|
|
@ -12,16 +12,18 @@ fix wall/lj126 command :h3
|
|||
fix wall/lj1043 command :h3
|
||||
fix wall/colloid command :h3
|
||||
fix wall/harmonic command :h3
|
||||
fix wall/morse command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID style face args ... keyword value ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
style = {wall/lj93} or {wall/lj126} or {wall/lj1043} or {wall/colloid} or {wall/harmonic} :l
|
||||
style = {wall/lj93} or {wall/lj126} or {wall/lj1043} or {wall/colloid} or {wall/harmonic} or {wall/morse} :l
|
||||
one or more face/arg pairs may be appended :l
|
||||
face = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l
|
||||
args = coord epsilon sigma cutoff
|
||||
args for styles {lj93} or {lj126} or {lj1043} or {colloid} or {harmonic} :l
|
||||
args = coord epsilon sigma cutoff
|
||||
coord = position of wall = EDGE or constant or variable
|
||||
EDGE = current lo or hi edge of simulation box
|
||||
constant = number like 0.0 or -30.0 (distance units)
|
||||
|
|
@ -31,6 +33,19 @@ face = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l
|
|||
sigma = size factor for wall-particle interaction (distance units)
|
||||
sigma can be a variable (see below)
|
||||
cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre
|
||||
args for style {morse} :l
|
||||
args = coord D_0 alpha r_0 cutoff
|
||||
coord = position of wall = EDGE or constant or variable
|
||||
EDGE = current lo or hi edge of simulation box
|
||||
constant = number like 0.0 or -30.0 (distance units)
|
||||
variable = "equal-style variable"_variable.html like v_x or v_wiggle
|
||||
D_0 = depth of the potential (energy units)
|
||||
D_0 can be a variable (see below)
|
||||
alpha = width factor for wall-particle interaction (1/distance units)
|
||||
alpha can be a variable (see below)
|
||||
r_0 = distance of the potential minimum from the face of region (distance units)
|
||||
r_0 can be a variable (see below)
|
||||
cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {units} or {fld} :l
|
||||
{units} value = {lattice} or {box}
|
||||
|
|
@ -48,6 +63,7 @@ keyword = {units} or {fld} :l
|
|||
|
||||
fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box
|
||||
fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5
|
||||
fix wallhi all wall/morse xhi EDGE 1.0 1.0 1.0 2.5 units box
|
||||
fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5
|
||||
fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858 :pre
|
||||
|
||||
|
|
@ -80,6 +96,10 @@ potential:
|
|||
|
||||
:c,image(Eqs/fix_wall_harmonic.jpg)
|
||||
|
||||
For style {wall/morse}, the energy E is given by a Morse potential:
|
||||
|
||||
:c,image(Eqs/pair_morse.jpg)
|
||||
|
||||
In all cases, {r} is the distance from the particle to the wall at
|
||||
position {coord}, and Rc is the {cutoff} distance at which the
|
||||
particle and wall no longer interact. The energy of the wall
|
||||
|
|
@ -147,7 +167,13 @@ constant K, and has units (energy/distance^2). The input parameter
|
|||
spring is at the {cutoff}. This is a repulsive-only spring since the
|
||||
interaction is truncated at the {cutoff}
|
||||
|
||||
For any wall, the {epsilon} and/or {sigma} parameter can be specified
|
||||
For the {wall/morse} style, the three parameters are in this order:
|
||||
{D_0} the depth of the potential, {alpha} the width parameter, and
|
||||
{r_0} the location of the minimum. {D_0} has energy units, {alpha}
|
||||
inverse distance units, and {r_0} distance units.
|
||||
|
||||
For any wall, the {epsilon} and/or {sigma} and/or {alpha} parameter can
|
||||
be specified
|
||||
as an "equal-style variable"_variable.html, in which case it should be
|
||||
specified as v_name, where name is the variable name. As with a
|
||||
variable wall position, the variable is evaluated each timestep and
|
||||
|
|
|
|||
|
|
@ -10,19 +10,27 @@ fix wall/region command :h3
|
|||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID wall/region region-ID style epsilon sigma cutoff :pre
|
||||
fix ID group-ID wall/region region-ID style args ... cutoff :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command
|
||||
wall/region = style name of this fix command
|
||||
region-ID = region whose boundary will act as wall
|
||||
style = {lj93} or {lj126} or {lj1043} or {colloid} or {harmonic}
|
||||
epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
|
||||
sigma = size factor for wall-particle interaction (distance units)
|
||||
cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :ul
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
wall/region = style name of this fix command :l
|
||||
region-ID = region whose boundary will act as wall :l
|
||||
style = {lj93} or {lj126} or {lj1043} or {colloid} or {harmonic} or {morse} :l
|
||||
args for styles {lj93} or {lj126} or {lj1043} or {colloid} or {harmonic} = :l
|
||||
epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
|
||||
sigma = size factor for wall-particle interaction (distance units) :pre
|
||||
args for style {morse} = :l
|
||||
D_0 = depth of the potential (energy units)
|
||||
alpha = width parameter (1/distance units)
|
||||
r_0 = distance of the potential minimum from wall position (distance units) :pre
|
||||
cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :l
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix wall all wall/region mySphere lj93 1.0 1.0 2.5 :pre
|
||||
fix wall all wall/region mySphere lj93 1.0 1.0 2.5
|
||||
fix wall all wall/region mySphere harmonic 1.0 0.0 2.5
|
||||
fix wall all wall/region box_top morse 1.0 1.0 1.5 3.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
|
@ -122,15 +130,22 @@ the "pair_style colloid"_pair_colloid.html potential:
|
|||
:c,image(Eqs/fix_wall_colloid.jpg)
|
||||
|
||||
For style {wall/harmonic}, the energy E is given by a harmonic spring
|
||||
potential:
|
||||
potential (the distance parameter is ignored):
|
||||
|
||||
:c,image(Eqs/fix_wall_harmonic.jpg)
|
||||
|
||||
For style {wall/morse}, the energy E is given by the Morse potential:
|
||||
|
||||
:c,image(Eqs/pair_morse.jpg)
|
||||
|
||||
Unlike other styles, this requires three parameters ({D_0}, {alpha}, {r_0}
|
||||
in this order) instead of two like for the other wall styles.
|
||||
|
||||
In all cases, {r} is the distance from the particle to the region
|
||||
surface, and Rc is the {cutoff} distance at which the particle and
|
||||
surface no longer interact. The energy of the wall potential is
|
||||
shifted so that the wall-particle interaction energy is 0.0 at the
|
||||
cutoff distance.
|
||||
surface no longer interact. The cutoff is always the last argument.
|
||||
The energy of the wall potential is shifted so that the wall-particle
|
||||
interaction energy is 0.0 at the cutoff distance.
|
||||
|
||||
For a full description of these wall styles, see fix_style
|
||||
"wall"_fix_wall.html
|
||||
|
|
@ -179,7 +194,9 @@ option for this fix.
|
|||
|
||||
"fix wall/lj93"_fix_wall.html,
|
||||
"fix wall/lj126"_fix_wall.html,
|
||||
"fix wall/lj1043"_fix_wall.html,
|
||||
"fix wall/colloid"_fix_wall.html,
|
||||
"fix wall/harmonic"_fix_wall.html,
|
||||
"fix wall/gran"_fix_wall_gran.html
|
||||
|
||||
[Default:] none
|
||||
|
|
|
|||
|
|
@ -569,6 +569,7 @@ pair_charmm.html
|
|||
pair_class2.html
|
||||
pair_colloid.html
|
||||
pair_comb.html
|
||||
pair_cosine_squared.html
|
||||
pair_coul.html
|
||||
pair_coul_diel.html
|
||||
pair_coul_shield.html
|
||||
|
|
|
|||
|
|
@ -0,0 +1,108 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
pair_style cosine/squared command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style cosine/squared cutoff :pre
|
||||
|
||||
cutoff = global cutoff for cosine-squared interactions (distance units) :ul
|
||||
|
||||
pair_coeff i j eps sigma
|
||||
pair_coeff i j eps sigma cutoff
|
||||
pair_coeff i j eps sigma wca
|
||||
pair_coeff i j eps sigma cutoff wca :pre
|
||||
|
||||
i,j = a particle type
|
||||
eps = interaction strength, i.e. the depth of the potential minimum (energy units)
|
||||
sigma = distance of the potential minimum from 0
|
||||
cutoff = the cutoff distance for this pair type, if different from global (distance units)
|
||||
wca = if specified a Weeks-Chandler-Andersen potential (with eps strength and minimum at sigma) is added, otherwise not :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style cosine/squared 3.0
|
||||
pair_coeff * * 1.0 1.3
|
||||
pair_coeff 1 3 1.0 1.3 2.0
|
||||
pair_coeff 1 3 1.0 1.3 wca
|
||||
pair_coeff 1 3 1.0 1.3 2.0 wca :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {cosine/squared} computes a potential of the form
|
||||
|
||||
:c,image(Eqs/pair_cosine_squared.jpg)
|
||||
|
||||
between two point particles, where (sigma, -epsilon) is the location of
|
||||
the (rightmost) minimum of the potential, as explained in the syntax
|
||||
section above.
|
||||
|
||||
This potential was first used in (Cooke)_#CKD for a coarse-grained lipid
|
||||
membrane model. It is generally very useful as a non-specific
|
||||
interaction potential because it is fully adjustable in depth and width
|
||||
while joining the minimum at (sigma, -epsilon) and zero at (cutoff, 0)
|
||||
smoothly, requiring no shifting and causing no related artifacts, tail
|
||||
energy calculations etc. This evidently requires {cutoff} to be larger
|
||||
than {sigma}.
|
||||
|
||||
If the {wca} option is used then a Weeks-Chandler-Andersen potential
|
||||
(Weeks)_#WCA is added to the above specified cosine-squared potential,
|
||||
specifically the following:
|
||||
|
||||
:c,image(Eqs/pair_cosine_squared_wca.jpg)
|
||||
|
||||
In this case, and this case only, the {sigma} parameter can be equal to
|
||||
{cutoff} (sigma = cutoff) which will result in ONLY the WCA potential
|
||||
being used (and print a warning), so the minimum will be attained at
|
||||
(sigma, 0). This is a convenience feature that enables a purely
|
||||
repulsive potential to be used without a need to define an additional
|
||||
pair style and use the hybrid styles.
|
||||
|
||||
The energy and force of this pair style for parameters epsilon = 1.0,
|
||||
sigma = 1.0, cutoff = 2.5, with and without the WCA potential, are shown
|
||||
in the graphs below:
|
||||
|
||||
:c,image(JPG/pair_cosine_squared_graphs.jpg)
|
||||
|
||||
:line
|
||||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
Mixing is not supported for this style.
|
||||
|
||||
The {shift}, {table} and {tail} options are not relevant for this style.
|
||||
|
||||
This pair style writes its information to "binary restart
|
||||
files"_restart.html, so pair_style and pair_coeff commands do not need
|
||||
to be specified in an input script that reads a restart file.
|
||||
|
||||
These pair styles can only be used via the {pair} keyword of the
|
||||
"run_style respa"_run_style.html command. They do not support the
|
||||
{inner}, {middle}, {outer} keywords.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The {cosine/squared} style is part of the "USER-MISC" package. It is only
|
||||
enabled if LAMMPS is build with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html,
|
||||
"pair_style lj/cut"_pair_lj.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:link(CKD)
|
||||
[(Cooke)] "Cooke, Kremer and Deserno, Phys. Rev. E, 72, 011506 (2005)"
|
||||
|
||||
:link(WCA)
|
||||
[(Weeks)] "Weeks, Chandler and Andersen, J. Chem. Phys., 54, 5237 (1971)"
|
||||
|
|
@ -129,6 +129,7 @@ accelerated styles exist.
|
|||
"colloid"_pair_colloid.html - integrated colloidal potential
|
||||
"comb"_pair_comb.html - charge-optimized many-body (COMB) potential
|
||||
"comb3"_pair_comb.html - charge-optimized many-body (COMB3) potential
|
||||
"cosine/squared"_pair_cosine_squared.html - Cooke-Kremer-Deserno membrane model potential
|
||||
"coul/cut"_pair_coul.html - cutoff Coulombic potential
|
||||
"coul/cut/soft"_pair_fep_soft.html - Coulombic potential with a soft core
|
||||
"coul/debye"_pair_coul.html - cutoff Coulombic potential with Debye screening
|
||||
|
|
|
|||
|
|
@ -24,6 +24,7 @@ Pair Styles :h1
|
|||
pair_class2
|
||||
pair_colloid
|
||||
pair_comb
|
||||
pair_cosine_squared
|
||||
pair_coul
|
||||
pair_coul_diel
|
||||
pair_coul_shield
|
||||
|
|
|
|||
|
|
@ -45,6 +45,7 @@ Aidan
|
|||
aij
|
||||
airebo
|
||||
Aj
|
||||
ajs
|
||||
ajaramil
|
||||
akohlmey
|
||||
Aktulga
|
||||
|
|
@ -99,6 +100,7 @@ antisymmetry
|
|||
anton
|
||||
Antonelli
|
||||
api
|
||||
Apoorva
|
||||
Appl
|
||||
Apu
|
||||
arccos
|
||||
|
|
@ -356,6 +358,7 @@ Cii
|
|||
Cij
|
||||
cis
|
||||
civ
|
||||
CKD
|
||||
Clang
|
||||
clearstore
|
||||
Cleary
|
||||
|
|
@ -421,6 +424,7 @@ coreshell
|
|||
cornflowerblue
|
||||
cornsilk
|
||||
corotate
|
||||
corotation
|
||||
corotational
|
||||
correlator
|
||||
cosineshifted
|
||||
|
|
@ -521,6 +525,7 @@ Dcut
|
|||
de
|
||||
dE
|
||||
De
|
||||
decorrelation
|
||||
debye
|
||||
Debye
|
||||
Decius
|
||||
|
|
@ -1073,6 +1078,7 @@ Hilger
|
|||
histo
|
||||
histogrammed
|
||||
histogramming
|
||||
hma
|
||||
hmaktulga
|
||||
hoc
|
||||
Hochbruck
|
||||
|
|
@ -1329,6 +1335,8 @@ kmax
|
|||
Kmax
|
||||
Knizhnik
|
||||
knl
|
||||
Kofke
|
||||
kofke
|
||||
Kohlmeyer
|
||||
Kohn
|
||||
kokkos
|
||||
|
|
@ -1716,6 +1724,7 @@ Morteza
|
|||
Mosayebi
|
||||
Moseler
|
||||
Moskalev
|
||||
Moustafa
|
||||
mov
|
||||
mpi
|
||||
MPI
|
||||
|
|
@ -2215,6 +2224,7 @@ PTM
|
|||
ptr
|
||||
pu
|
||||
purdue
|
||||
Purohit
|
||||
pushstore
|
||||
pvar
|
||||
pw
|
||||
|
|
@ -2432,6 +2442,7 @@ Ryckaert
|
|||
Rycroft
|
||||
Rydbergs
|
||||
Rz
|
||||
Sabry
|
||||
saddlebrown
|
||||
Sadigh
|
||||
saed
|
||||
|
|
@ -2991,6 +3002,7 @@ Waltham
|
|||
wavepacket
|
||||
wB
|
||||
Wbody
|
||||
wca
|
||||
webpage
|
||||
Weckner
|
||||
WeinanE
|
||||
|
|
|
|||
|
|
@ -0,0 +1,36 @@
|
|||
# this example requires the LAMMPS Python package (lammps.py) to be installed
|
||||
# and LAMMPS to be loadable as shared library in LD_LIBRARY_PATH
|
||||
|
||||
import lammps
|
||||
|
||||
def callback(caller, ntimestep, nlocal, tag, x, fext):
|
||||
"""
|
||||
This callback receives a caller object that was setup when registering the callback
|
||||
|
||||
In addition to timestep and number of local atoms, the tag and x arrays are passed as
|
||||
NumPy arrays. The fext array is a force array allocated for fix external, which
|
||||
can be used to apply forces to all atoms. Simply update the value in the array,
|
||||
it will be directly written into the LAMMPS C arrays
|
||||
"""
|
||||
print("Data passed by caller (optional)", caller)
|
||||
print("Timestep:", ntimestep)
|
||||
print("Number of Atoms:", nlocal)
|
||||
print("Atom Tags:", tag)
|
||||
print("Atom Positions:", x)
|
||||
print("Force Additions:", fext)
|
||||
fext.fill(1.0)
|
||||
print("Force additions after update:", fext)
|
||||
print("="*40)
|
||||
|
||||
L = lammps.lammps()
|
||||
L.file("in.fix_external")
|
||||
|
||||
# you can pass an arbitrary Python object to the callback every time it is called
|
||||
# this can be useful if you need more state information such as the LAMMPS ptr to
|
||||
# make additional library calls
|
||||
custom_object = ["Some data", L]
|
||||
|
||||
L.set_fix_external_callback("2", callback, custom_object)
|
||||
L.command("run 100")
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,23 @@
|
|||
# LAMMPS input for coupling LAMMPS with Python via fix external
|
||||
|
||||
units metal
|
||||
dimension 3
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
lattice diamond 5.43
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 28.08
|
||||
|
||||
velocity all create 300.0 87293 loop geom
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all external pf/callback 1 1
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
thermo 1
|
||||
|
|
@ -0,0 +1,22 @@
|
|||
The example input script sets up a simple FCC crystal using the Lennard-Jones
|
||||
potential. The script sets up the HMA compute to calculate the energy, pressure
|
||||
and heat capacity. The output columns are:
|
||||
|
||||
1: timestep
|
||||
2: measured temperature
|
||||
3: potential energy
|
||||
4: HMA potential energy
|
||||
5: pressure
|
||||
6: HMA pressure
|
||||
7: HMA heat capacity contribution
|
||||
|
||||
Averages of the potential energy (#3 and #4) agree although #4 (HMA) is more precise.
|
||||
|
||||
Averages of the pressure (#5 and #6) agree once the ideal gas
|
||||
contribution is included; #6 (HMA) is more precise.
|
||||
|
||||
The heat capacity can be computed from colume #3 (convential) as
|
||||
Cv = Var(#3)/(k T^2)
|
||||
|
||||
With HMA, the heat capacity can be computed from column #4 and #7 as
|
||||
Cv = #7 + Var(#4)/(k T^2)
|
||||
|
|
@ -0,0 +1,36 @@
|
|||
# Harmonically mapped average example
|
||||
|
||||
units lj
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
# ---------- Create Atoms ----------------------------
|
||||
lattice fcc 1.0
|
||||
region box block 0 4 0 4 0 4 units lattice
|
||||
create_box 1 box
|
||||
lattice fcc 1.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
|
||||
create_atoms 1 region box
|
||||
# ---------- Define Interatomic Potential ---------------------
|
||||
pair_style lj/smooth/linear 3
|
||||
pair_coeff * * 1.0 1.0
|
||||
mass 1 1.0
|
||||
|
||||
atom_modify sort 0 1
|
||||
velocity all create 0.1 45678 dist gaussian
|
||||
|
||||
compute u all pe
|
||||
|
||||
compute p all pressure NULL pair
|
||||
|
||||
compute hma all hma settemp u p 9.579586686264458 cv
|
||||
|
||||
timestep 0.005
|
||||
|
||||
fix settemp all nvt temp 1.0 1.0 0.5
|
||||
thermo_style custom elapsed temp c_u c_hma[1] c_p c_hma[2] c_hma[3]
|
||||
thermo_modify format float '%22.15e'
|
||||
thermo 500
|
||||
run 20000
|
||||
thermo 20
|
||||
run 200000
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,107 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the example models provided with
|
||||
# the kim-api package are installed. see the ./lib/kim/README or
|
||||
# ./lib/kim/Install.py files for details on how to install these
|
||||
# example models.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
kim_init LennardJones_Ar real
|
||||
#=== BEGIN kim-init ==========================================
|
||||
units real
|
||||
#=== END kim-init ============================================
|
||||
|
||||
|
||||
lattice fcc 4.4300
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.004321 secs
|
||||
|
||||
kim_interactions Ar
|
||||
#=== BEGIN kim_interactions ==================================
|
||||
pair_style kim LennardJones_Ar
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
|
||||
pair_coeff * * Ar
|
||||
#=== END kim_interactions ====================================
|
||||
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 8.45
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 145069.63 0 164146.22 128015.94
|
||||
100 95.179703 154939.42 0 164017.94 131602.75
|
||||
Loop time of 3.48256 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 2.481 ns/day, 9.674 hours/ns, 28.715 timesteps/s
|
||||
98.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.0502 | 3.0502 | 3.0502 | 0.0 | 87.59
|
||||
Neigh | 0.3646 | 0.3646 | 0.3646 | 0.0 | 10.47
|
||||
Comm | 0.01783 | 0.01783 | 0.01783 | 0.0 | 0.51
|
||||
Output | 6.8e-05 | 6.8e-05 | 6.8e-05 | 0.0 | 0.00
|
||||
Modify | 0.034349 | 0.034349 | 0.034349 | 0.0 | 0.99
|
||||
Other | | 0.01547 | | | 0.44
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19911 ave 19911 max 19911 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 4253750
|
||||
Ave neighs/atom = 132.93
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
|
|
@ -0,0 +1,113 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the example models provided with
|
||||
# the kim-api package are installed. see the ./lib/kim/README or
|
||||
# ./lib/kim/Install.py files for details on how to install these
|
||||
# example models.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
kim_init LennardJones_Ar real
|
||||
#=== BEGIN kim-init ==========================================
|
||||
units real
|
||||
#=== END kim-init ============================================
|
||||
|
||||
|
||||
lattice fcc 4.4300
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.000989 secs
|
||||
|
||||
kim_interactions Ar
|
||||
#=== BEGIN kim_interactions ==================================
|
||||
pair_style kim LennardJones_Ar
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
|
||||
pair_coeff * * Ar
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
|
||||
#=== END kim_interactions ====================================
|
||||
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 8.45
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.791 | 9.791 | 9.791 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 145069.63 0 164146.22 128015.94
|
||||
100 95.179703 154939.42 0 164017.94 131602.75
|
||||
Loop time of 0.924494 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 9.346 ns/day, 2.568 hours/ns, 108.167 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.76434 | 0.76847 | 0.77207 | 0.3 | 83.12
|
||||
Neigh | 0.09089 | 0.094446 | 0.099911 | 1.1 | 10.22
|
||||
Comm | 0.038599 | 0.044759 | 0.051381 | 2.1 | 4.84
|
||||
Output | 3.5e-05 | 4e-05 | 4.9e-05 | 0.0 | 0.00
|
||||
Modify | 0.009396 | 0.009685 | 0.009941 | 0.2 | 1.05
|
||||
Other | | 0.00709 | | | 0.77
|
||||
|
||||
Nlocal: 8000 ave 8018 max 7967 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 9131 ave 9164 max 9113 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
|
||||
Total # of neighbors = 4253750
|
||||
Ave neighs/atom = 132.93
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,124 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the KIM Portable Model (PM)
|
||||
# SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# is installed. This can be done with the command
|
||||
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# If this command does not work, you may need to setup your PATH to find the utility.
|
||||
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS build directory)
|
||||
# source ./kim_build-prefix/bin/kim-api-activate
|
||||
# If you installed the kim-api using the LAMMPS Make build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS src directory)
|
||||
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
|
||||
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
|
||||
#
|
||||
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
|
||||
#=== BEGIN kim-init ==========================================
|
||||
units real
|
||||
#=== END kim-init ============================================
|
||||
|
||||
kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
|
||||
#=== BEGIN kim-query =========================================
|
||||
variable a0 string 4.146581932902336
|
||||
#=== END kim-query ===========================================
|
||||
|
||||
|
||||
lattice fcc ${a0}
|
||||
lattice fcc 4.146581932902336
|
||||
Lattice spacing in x,y,z = 4.14658 4.14658 4.14658
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (82.9316 82.9316 82.9316)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.005415 secs
|
||||
|
||||
kim_interactions Si
|
||||
#=== BEGIN kim_interactions ==================================
|
||||
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
pair_coeff * * Si
|
||||
#=== END kim_interactions ====================================
|
||||
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.07118
|
||||
ghost atom cutoff = 4.07118
|
||||
binsize = 2.03559, bins = 41 41 41
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 4.07118
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.36 | 10.36 | 10.36 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 -126084.25 0 -107007.66 1528.8768
|
||||
100 94.450495 -116016.03 0 -107007.07 2282.2685
|
||||
Loop time of 74.6055 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 0.116 ns/day, 207.238 hours/ns, 1.340 timesteps/s
|
||||
98.6% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 74.446 | 74.446 | 74.446 | 0.0 | 99.79
|
||||
Neigh | 0.096611 | 0.096611 | 0.096611 | 0.0 | 0.13
|
||||
Comm | 0.014594 | 0.014594 | 0.014594 | 0.0 | 0.02
|
||||
Output | 7.9e-05 | 7.9e-05 | 7.9e-05 | 0.0 | 0.00
|
||||
Modify | 0.03454 | 0.03454 | 0.03454 | 0.0 | 0.05
|
||||
Other | | 0.01396 | | | 0.02
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 9667 ave 9667 max 9667 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 450192 ave 450192 max 450192 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 450192
|
||||
Ave neighs/atom = 14.0685
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:01:16
|
||||
|
|
@ -0,0 +1,124 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the KIM Portable Model (PM)
|
||||
# SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# is installed. This can be done with the command
|
||||
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# If this command does not work, you may need to setup your PATH to find the utility.
|
||||
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS build directory)
|
||||
# source ./kim_build-prefix/bin/kim-api-activate
|
||||
# If you installed the kim-api using the LAMMPS Make build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS src directory)
|
||||
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
|
||||
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
|
||||
#
|
||||
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
|
||||
#=== BEGIN kim-init ==========================================
|
||||
units real
|
||||
#=== END kim-init ============================================
|
||||
|
||||
kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
|
||||
#=== BEGIN kim-query =========================================
|
||||
variable a0 string 4.146581932902336
|
||||
#=== END kim-query ===========================================
|
||||
|
||||
|
||||
lattice fcc ${a0}
|
||||
lattice fcc 4.146581932902336
|
||||
Lattice spacing in x,y,z = 4.14658 4.14658 4.14658
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (82.9316 82.9316 82.9316)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.000946 secs
|
||||
|
||||
kim_interactions Si
|
||||
#=== BEGIN kim_interactions ==================================
|
||||
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
pair_coeff * * Si
|
||||
#=== END kim_interactions ====================================
|
||||
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.07118
|
||||
ghost atom cutoff = 4.07118
|
||||
binsize = 2.03559, bins = 41 41 41
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 4.07118
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.489 | 3.489 | 3.489 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 -126084.25 0 -107007.66 1528.8768
|
||||
100 94.450495 -116016.03 0 -107007.07 2282.2685
|
||||
Loop time of 19.0792 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 0.453 ns/day, 52.998 hours/ns, 5.241 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 18.78 | 18.855 | 18.937 | 1.5 | 98.83
|
||||
Neigh | 0.026047 | 0.026274 | 0.0266 | 0.1 | 0.14
|
||||
Comm | 0.09039 | 0.17196 | 0.24675 | 15.9 | 0.90
|
||||
Output | 3.9e-05 | 4.975e-05 | 6.1e-05 | 0.0 | 0.00
|
||||
Modify | 0.015667 | 0.015819 | 0.016008 | 0.1 | 0.08
|
||||
Other | | 0.01008 | | | 0.05
|
||||
|
||||
Nlocal: 8000 ave 8029 max 7968 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Nghost: 4259 ave 4303 max 4202 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 112548 ave 113091 max 111995 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 450192
|
||||
Ave neighs/atom = 14.0685
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:20
|
||||
|
|
@ -0,0 +1,118 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the KIM Portable Model (PM)
|
||||
# SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# is installed. This can be done with the command
|
||||
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# If this command does not work, you may need to setup your PATH to find the utility.
|
||||
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS build directory)
|
||||
# source ./kim_build-prefix/bin/kim-api-activate
|
||||
# If you installed the kim-api using the LAMMPS Make build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS src directory)
|
||||
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
|
||||
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
|
||||
#
|
||||
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
|
||||
#=== BEGIN kim-init ==========================================
|
||||
units real
|
||||
#=== END kim-init ============================================
|
||||
|
||||
|
||||
lattice fcc 4.4300
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.003591 secs
|
||||
|
||||
kim_interactions Si
|
||||
#=== BEGIN kim_interactions ==================================
|
||||
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
pair_coeff * * Si
|
||||
#=== END kim_interactions ====================================
|
||||
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.07118
|
||||
ghost atom cutoff = 4.07118
|
||||
binsize = 2.03559, bins = 44 44 44
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 4.07118
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.44 | 10.44 | 10.44 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 -85249.847 0 -66173.259 -33302.387
|
||||
100 253.43357 -90346.68 0 -66173.441 -14888.698
|
||||
Loop time of 74.248 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 0.116 ns/day, 206.244 hours/ns, 1.347 timesteps/s
|
||||
98.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 74.118 | 74.118 | 74.118 | 0.0 | 99.83
|
||||
Neigh | 0.069623 | 0.069623 | 0.069623 | 0.0 | 0.09
|
||||
Comm | 0.0137 | 0.0137 | 0.0137 | 0.0 | 0.02
|
||||
Output | 7.6e-05 | 7.6e-05 | 7.6e-05 | 0.0 | 0.00
|
||||
Modify | 0.031883 | 0.031883 | 0.031883 | 0.0 | 0.04
|
||||
Other | | 0.01433 | | | 0.02
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7760 ave 7760 max 7760 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 402352 ave 402352 max 402352 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 402352
|
||||
Ave neighs/atom = 12.5735
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:01:14
|
||||
|
|
@ -0,0 +1,118 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the KIM Portable Model (PM)
|
||||
# SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# is installed. This can be done with the command
|
||||
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# If this command does not work, you may need to setup your PATH to find the utility.
|
||||
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS build directory)
|
||||
# source ./kim_build-prefix/bin/kim-api-activate
|
||||
# If you installed the kim-api using the LAMMPS Make build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS src directory)
|
||||
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
|
||||
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
|
||||
#
|
||||
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
|
||||
#=== BEGIN kim-init ==========================================
|
||||
units real
|
||||
#=== END kim-init ============================================
|
||||
|
||||
|
||||
lattice fcc 4.4300
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.000997 secs
|
||||
|
||||
kim_interactions Si
|
||||
#=== BEGIN kim_interactions ==================================
|
||||
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
pair_coeff * * Si
|
||||
#=== END kim_interactions ====================================
|
||||
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.07118
|
||||
ghost atom cutoff = 4.07118
|
||||
binsize = 2.03559, bins = 44 44 44
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 4.07118
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.517 | 3.517 | 3.517 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 -85249.847 0 -66173.259 -33302.387
|
||||
100 253.43357 -90346.68 0 -66173.441 -14888.698
|
||||
Loop time of 19.0287 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 0.454 ns/day, 52.857 hours/ns, 5.255 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 18.81 | 18.838 | 18.883 | 0.6 | 99.00
|
||||
Neigh | 0.018598 | 0.01914 | 0.020732 | 0.7 | 0.10
|
||||
Comm | 0.10341 | 0.1475 | 0.17393 | 7.1 | 0.78
|
||||
Output | 6e-05 | 6.225e-05 | 6.7e-05 | 0.0 | 0.00
|
||||
Modify | 0.014839 | 0.014925 | 0.015047 | 0.1 | 0.08
|
||||
Other | | 0.008997 | | | 0.05
|
||||
|
||||
Nlocal: 8000 ave 8014 max 7988 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Nghost: 3374.75 ave 3389 max 3361 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 100588 ave 100856 max 100392 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 402352
|
||||
Ave neighs/atom = 12.5735
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:19
|
||||
|
|
@ -0,0 +1,71 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the KIM Simulator Model (PM)
|
||||
# Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
|
||||
# is installed. This can be done with the command
|
||||
# kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
|
||||
# If this command does not work, you may need to setup your PATH to find the utility.
|
||||
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS build directory)
|
||||
# source ./kim_build-prefix/bin/kim-api-activate
|
||||
# If you installed the kim-api using the LAMMPS Make build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS src directory)
|
||||
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
|
||||
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
|
||||
#
|
||||
# See https://openkim.org/doc/obtaining-models for alternative options.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
|
||||
#=== BEGIN kim-init ==========================================
|
||||
# Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
|
||||
# For Simulator : LAMMPS 28 Feb 2019
|
||||
# Running on : LAMMPS 7 Aug 2019
|
||||
#
|
||||
units real
|
||||
atom_style charge
|
||||
neigh_modify one 4000
|
||||
#=== END kim-init ============================================
|
||||
|
||||
|
||||
lattice fcc 4.4300
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.003447 secs
|
||||
|
||||
kim_interactions O
|
||||
#=== BEGIN kim_interactions ==================================
|
||||
pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6Acs1QDbXgBx/lmp_control safezone 2.0 mincap 100
|
||||
ERROR: Unrecognized pair style 'reax/c' is part of the USER-REAXC package which is not enabled in this LAMMPS binary. (../force.cpp:262)
|
||||
Last command: pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6Acs1QDbXgBx/lmp_control safezone 2.0 mincap 100
|
||||
--------------------------------------------------------------------------
|
||||
Primary job terminated normally, but 1 process returned
|
||||
a non-zero exit code. Per user-direction, the job has been aborted.
|
||||
--------------------------------------------------------------------------
|
||||
--------------------------------------------------------------------------
|
||||
mpirun detected that one or more processes exited with non-zero status, thus causing
|
||||
the job to be terminated. The first process to do so was:
|
||||
|
||||
Process name: [[33054,1],0]
|
||||
Exit code: 1
|
||||
--------------------------------------------------------------------------
|
||||
|
|
@ -0,0 +1,60 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the KIM Simulator Model (PM)
|
||||
# Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
|
||||
# is installed. This can be done with the command
|
||||
# kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
|
||||
# If this command does not work, you may need to setup your PATH to find the utility.
|
||||
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS build directory)
|
||||
# source ./kim_build-prefix/bin/kim-api-activate
|
||||
# If you installed the kim-api using the LAMMPS Make build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS src directory)
|
||||
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
|
||||
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
|
||||
#
|
||||
# See https://openkim.org/doc/obtaining-models for alternative options.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
|
||||
#=== BEGIN kim-init ==========================================
|
||||
# Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
|
||||
# For Simulator : LAMMPS 28 Feb 2019
|
||||
# Running on : LAMMPS 7 Aug 2019
|
||||
#
|
||||
units real
|
||||
atom_style charge
|
||||
neigh_modify one 4000
|
||||
#=== END kim-init ============================================
|
||||
|
||||
|
||||
lattice fcc 4.4300
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.001307 secs
|
||||
|
||||
kim_interactions O
|
||||
#=== BEGIN kim_interactions ==================================
|
||||
pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6tmKtZEXzhgv/lmp_control safezone 2.0 mincap 100
|
||||
ERROR: Unrecognized pair style 'reax/c' is part of the USER-REAXC package which is not enabled in this LAMMPS binary. (../force.cpp:262)
|
||||
Last command: pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6tmKtZEXzhgv/lmp_control safezone 2.0 mincap 100
|
||||
|
|
@ -0,0 +1,92 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
units real
|
||||
|
||||
lattice fcc 4.4300
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.003037 secs
|
||||
|
||||
pair_style lj/cut 8.1500
|
||||
pair_coeff 1 1 0.0104 3.4000
|
||||
|
||||
#pair_style kim LennardJones_Ar
|
||||
#pair_coeff * * Ar
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.23 | 19.23 | 19.23 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 6290.8194 0 25367.408 6750.7421
|
||||
100 98.747096 15900.676 0 25319.465 10184.453
|
||||
Loop time of 2.43768 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 3.544 ns/day, 6.771 hours/ns, 41.023 timesteps/s
|
||||
97.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.1895 | 2.1895 | 2.1895 | 0.0 | 89.82
|
||||
Neigh | 0.17546 | 0.17546 | 0.17546 | 0.0 | 7.20
|
||||
Comm | 0.021001 | 0.021001 | 0.021001 | 0.0 | 0.86
|
||||
Output | 7.9e-05 | 7.9e-05 | 7.9e-05 | 0.0 | 0.00
|
||||
Modify | 0.034253 | 0.034253 | 0.034253 | 0.0 | 1.41
|
||||
Other | | 0.01735 | | | 0.71
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19911 ave 19911 max 19911 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.96027e+06 ave 1.96027e+06 max 1.96027e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1960266
|
||||
Ave neighs/atom = 61.2583
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
|
|
@ -0,0 +1,92 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
units real
|
||||
|
||||
lattice fcc 4.4300
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.001194 secs
|
||||
|
||||
pair_style lj/cut 8.1500
|
||||
pair_coeff 1 1 0.0104 3.4000
|
||||
|
||||
#pair_style kim LennardJones_Ar
|
||||
#pair_coeff * * Ar
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.633 | 7.633 | 7.633 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 6290.8194 0 25367.408 6750.7421
|
||||
100 98.747096 15900.676 0 25319.465 10184.453
|
||||
Loop time of 0.726239 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 11.897 ns/day, 2.017 hours/ns, 137.696 timesteps/s
|
||||
98.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.57617 | 0.5835 | 0.59084 | 0.9 | 80.34
|
||||
Neigh | 0.046682 | 0.047783 | 0.048641 | 0.3 | 6.58
|
||||
Comm | 0.065469 | 0.071509 | 0.07899 | 2.3 | 9.85
|
||||
Output | 3.9e-05 | 4.6e-05 | 6.1e-05 | 0.0 | 0.01
|
||||
Modify | 0.013205 | 0.01363 | 0.014044 | 0.3 | 1.88
|
||||
Other | | 0.009775 | | | 1.35
|
||||
|
||||
Nlocal: 8000 ave 8012 max 7989 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
Nghost: 9131 ave 9142 max 9119 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 490066 ave 491443 max 489273 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1960266
|
||||
Ave neighs/atom = 61.2583
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -10,7 +10,7 @@ import sys, os, subprocess, shutil
|
|||
from argparse import ArgumentParser
|
||||
|
||||
sys.path.append('..')
|
||||
from install_helpers import fullpath, geturl
|
||||
from install_helpers import fullpath, geturl, checkmd5sum
|
||||
|
||||
parser = ArgumentParser(prog='Install.py',
|
||||
description="LAMMPS library build wrapper script")
|
||||
|
|
@ -18,7 +18,15 @@ parser = ArgumentParser(prog='Install.py',
|
|||
# settings
|
||||
|
||||
thisdir = fullpath('.')
|
||||
version = "kim-api-2.1.2"
|
||||
version = "2.1.3"
|
||||
|
||||
# known checksums for different KIM-API versions. used to validate the download.
|
||||
checksums = { \
|
||||
'2.1.2' : '6ac52e14ef52967fc7858220b208cba5', \
|
||||
'2.1.3' : '6ee829a1bbba5f8b9874c88c4c4ebff8', \
|
||||
}
|
||||
|
||||
|
||||
|
||||
# help message
|
||||
|
||||
|
|
@ -50,7 +58,7 @@ pgroup.add_argument("-n", "--nobuild", action="store_true",
|
|||
help="use the previously downloaded and compiled base KIM API.")
|
||||
pgroup.add_argument("-p", "--path",
|
||||
help="specify location of existing KIM API installation.")
|
||||
parser.add_argument("-v", "--version", default=version,
|
||||
parser.add_argument("-v", "--version", default=version, choices=checksums.keys(),
|
||||
help="set version of KIM API library to download and build (default: %s)" % version)
|
||||
parser.add_argument("-a", "--add",
|
||||
help="add single KIM model or model driver. If adding 'everything', then all available OpenKIM models are added (may take a long time)")
|
||||
|
|
@ -73,6 +81,7 @@ if addflag and addmodelname == "everything":
|
|||
everythingflag = True
|
||||
buildflag = True
|
||||
verboseflag = args.verbose
|
||||
version = args.version
|
||||
|
||||
if pathflag:
|
||||
buildflag = False
|
||||
|
|
@ -81,7 +90,7 @@ if pathflag:
|
|||
sys.exit("KIM API path %s does not exist" % kimdir)
|
||||
kimdir = fullpath(kimdir)
|
||||
|
||||
url = "https://s3.openkim.org/kim-api/%s.txz" % version
|
||||
url = "https://s3.openkim.org/kim-api/kim-api-%s.txz" % version
|
||||
|
||||
# set KIM API directory
|
||||
|
||||
|
|
@ -115,21 +124,28 @@ if buildflag:
|
|||
# download entire kim-api tarball
|
||||
|
||||
print("Downloading kim-api tarball ...")
|
||||
geturl(url, "%s/%s.txz" % (thisdir, version))
|
||||
filename = "kim-api-%s.txz" % version
|
||||
geturl(url, "%s/%s" % (thisdir, filename))
|
||||
|
||||
# verify downloaded archive integrity via md5 checksum, if known.
|
||||
if version in checksums:
|
||||
if not checkmd5sum(checksums[version], filename):
|
||||
sys.exit("Checksum for KIM-API library does not match")
|
||||
|
||||
print("Unpacking kim-api tarball ...")
|
||||
cmd = 'cd "%s"; rm -rf "%s"; tar -xJvf %s.txz' % (thisdir, version, version)
|
||||
cmd = 'cd "%s"; rm -rf "kim-api-%s"; tar -xJvf %s' % (thisdir, version, filename)
|
||||
subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
|
||||
|
||||
# configure kim-api
|
||||
|
||||
print("Configuring kim-api ...")
|
||||
cmd = 'cd "%s/%s" && mkdir build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX="%s" -DCMAKE_BUILD_TYPE=Release' % (thisdir,version,kimdir)
|
||||
cmd = 'cd "%s/kim-api-%s" && mkdir build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX="%s" -DCMAKE_BUILD_TYPE=Release' % (thisdir,version,kimdir)
|
||||
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
|
||||
if verboseflag: print(txt.decode("UTF-8"))
|
||||
|
||||
# build kim-api
|
||||
print("Building kim-api ...")
|
||||
cmd = 'cd "%s/%s/build" && make -j2' % (thisdir, version)
|
||||
cmd = 'cd "%s/kim-api-%s/build" && make -j2' % (thisdir, version)
|
||||
txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
|
||||
if verboseflag:
|
||||
print(txt.decode("UTF-8"))
|
||||
|
|
@ -137,7 +153,7 @@ if buildflag:
|
|||
# install kim-api
|
||||
|
||||
print("Installing kim-api ...")
|
||||
cmd = 'cd "%s/%s/build" && make -j2 install' % (thisdir, version)
|
||||
cmd = 'cd "%s/kim-api-%s/build" && make -j2 install' % (thisdir, version)
|
||||
txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
|
||||
if verboseflag:
|
||||
print(txt.decode("UTF-8"))
|
||||
|
|
@ -145,7 +161,7 @@ if buildflag:
|
|||
# remove source files
|
||||
|
||||
print("Removing kim-api source and build files ...")
|
||||
cmd = 'cd "%s"; rm -rf %s; rm -rf %s.txz' % (thisdir, version, version)
|
||||
cmd = 'cd "%s"; rm -rf kim-api-%s; rm -rf kim-api-%s.txz' % (thisdir, version, version)
|
||||
subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
|
||||
|
||||
# add all OpenKIM models, if desired
|
||||
|
|
|
|||
|
|
@ -219,6 +219,12 @@ class lammps(object):
|
|||
self.c_imageint = get_ctypes_int(self.extract_setting("imageint"))
|
||||
self._installed_packages = None
|
||||
|
||||
# add way to insert Python callback for fix external
|
||||
self.callback = {}
|
||||
self.FIX_EXTERNAL_CALLBACK_FUNC = CFUNCTYPE(None, c_void_p, self.c_bigint, c_int, POINTER(self.c_tagint), POINTER(POINTER(c_double)), POINTER(POINTER(c_double)))
|
||||
self.lib.lammps_set_fix_external_callback.argtypes = [c_void_p, c_char_p, self.FIX_EXTERNAL_CALLBACK_FUNC, c_void_p]
|
||||
self.lib.lammps_set_fix_external_callback.restype = None
|
||||
|
||||
# shut-down LAMMPS instance
|
||||
|
||||
def __del__(self):
|
||||
|
|
@ -602,6 +608,42 @@ class lammps(object):
|
|||
self._installed_packages.append(sb.value.decode())
|
||||
return self._installed_packages
|
||||
|
||||
def set_fix_external_callback(self, fix_name, callback, caller=None):
|
||||
import numpy as np
|
||||
def _ctype_to_numpy_int(ctype_int):
|
||||
if ctype_int == c_int32:
|
||||
return np.int32
|
||||
elif ctype_int == c_int64:
|
||||
return np.int64
|
||||
return np.intc
|
||||
|
||||
def callback_wrapper(caller_ptr, ntimestep, nlocal, tag_ptr, x_ptr, fext_ptr):
|
||||
if cast(caller_ptr,POINTER(py_object)).contents:
|
||||
pyCallerObj = cast(caller_ptr,POINTER(py_object)).contents.value
|
||||
else:
|
||||
pyCallerObj = None
|
||||
|
||||
tptr = cast(tag_ptr, POINTER(self.c_tagint * nlocal))
|
||||
tag = np.frombuffer(tptr.contents, dtype=_ctype_to_numpy_int(self.c_tagint))
|
||||
tag.shape = (nlocal)
|
||||
|
||||
xptr = cast(x_ptr[0], POINTER(c_double * nlocal * 3))
|
||||
x = np.frombuffer(xptr.contents)
|
||||
x.shape = (nlocal, 3)
|
||||
|
||||
fptr = cast(fext_ptr[0], POINTER(c_double * nlocal * 3))
|
||||
f = np.frombuffer(fptr.contents)
|
||||
f.shape = (nlocal, 3)
|
||||
|
||||
callback(pyCallerObj, ntimestep, nlocal, tag, x, f)
|
||||
|
||||
cFunc = self.FIX_EXTERNAL_CALLBACK_FUNC(callback_wrapper)
|
||||
cCaller = cast(pointer(py_object(caller)), c_void_p)
|
||||
|
||||
self.callback[fix_name] = { 'function': cFunc, 'caller': caller }
|
||||
|
||||
self.lib.lammps_set_fix_external_callback(self.lmp, fix_name.encode(), cFunc, cCaller)
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
# -------------------------------------------------------------------------
|
||||
# -------------------------------------------------------------------------
|
||||
|
|
@ -872,8 +914,8 @@ class PyLammps(object):
|
|||
output = self.__getattr__('run')(*args, **kwargs)
|
||||
|
||||
if(lammps.has_mpi4py):
|
||||
output = self.lmp.comm.bcast(output, root=0)
|
||||
|
||||
output = self.lmp.comm.bcast(output, root=0)
|
||||
|
||||
self.runs += get_thermo_data(output)
|
||||
return output
|
||||
|
||||
|
|
|
|||
|
|
@ -801,6 +801,8 @@
|
|||
/pair_comb3.h
|
||||
/pair_colloid.cpp
|
||||
/pair_colloid.h
|
||||
/pair_cosine_squared.cpp
|
||||
/pair_cosine_squared.h
|
||||
/pair_coul_diel.cpp
|
||||
/pair_coul_diel.h
|
||||
/pair_coul_long.cpp
|
||||
|
|
|
|||
|
|
@ -1147,11 +1147,11 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz,
|
|||
else{
|
||||
knfac = E; //Hooke
|
||||
a = sqrt(dR);
|
||||
Fne = knfac*delta;
|
||||
if (normal_model != HOOKE) {
|
||||
Fne *= a;
|
||||
knfac *= a;
|
||||
}
|
||||
Fne = knfac*delta;
|
||||
if (normal_model == DMT)
|
||||
Fne -= 4*MY_PI*normal_coeffs[3]*Reff;
|
||||
}
|
||||
|
|
@ -1292,10 +1292,12 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz,
|
|||
// rolling resistance
|
||||
//****************************************
|
||||
|
||||
if (roll_model != ROLL_NONE) {
|
||||
if (roll_model != ROLL_NONE || twist_model != NONE) {
|
||||
relrot1 = omega[0];
|
||||
relrot2 = omega[1];
|
||||
relrot3 = omega[2];
|
||||
}
|
||||
if (roll_model != ROLL_NONE){
|
||||
|
||||
// rolling velocity, see eq. 31 of Wang et al, Particuology v 23, p 49 (2015)
|
||||
// This is different from the Marshall papers,
|
||||
|
|
|
|||
|
|
@ -64,6 +64,8 @@
|
|||
#include "input.h"
|
||||
#include "modify.h"
|
||||
#include "variable.h"
|
||||
#include "version.h"
|
||||
#include "info.h"
|
||||
#include "fix_store_kim.h"
|
||||
|
||||
#if defined(LMP_KIM_CURL)
|
||||
|
|
@ -242,6 +244,10 @@ char *do_query(char *qfunction, char * model_name, int narg, char **arg,
|
|||
curl_easy_setopt(handle, CURLOPT_SSL_VERIFYPEER, 0L);
|
||||
curl_easy_setopt(handle, CURLOPT_SSL_VERIFYHOST, 0L);
|
||||
#endif
|
||||
std::string user_agent = std::string("kim_query--LAMMPS/")
|
||||
+ LAMMPS_VERSION
|
||||
+ " (" + Info::get_os_info() + ")";
|
||||
curl_easy_setopt(handle, CURLOPT_USERAGENT, user_agent.c_str());
|
||||
|
||||
curl_easy_setopt(handle, CURLOPT_URL, url.c_str());
|
||||
curl_easy_setopt(handle, CURLOPT_FOLLOWLOCATION, 1L);
|
||||
|
|
|
|||
|
|
@ -0,0 +1,119 @@
|
|||
# astra_arm - ThunderX2 ARM/OpenMPI Based, use Arm-PL for FFTW
|
||||
|
||||
# need to load the following modules:
|
||||
# 1) arm-based developer pack
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# compiler/linker settings
|
||||
# specify flags and libraries needed for your compiler
|
||||
|
||||
CC = mpicxx
|
||||
CCFLAGS = -O3 -funroll-loops -fopenmp -mcpu=thunderx2t99 -mtune=thunderx2t99
|
||||
DEPFLAGS = -M
|
||||
LINK = mpicxx
|
||||
LINKFLAGS = -O3 -fopenmp -mcpu=thunderx2t99 -mtune=thunderx2t99
|
||||
LIB = -lstdc++
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rcsv
|
||||
SIZE = size
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings, all OPTIONAL
|
||||
# specify settings for LAMMPS features you will use
|
||||
# if you change any -D setting, do full re-compile after "make clean"
|
||||
|
||||
# LAMMPS ifdef settings
|
||||
# see possible settings in Section 2.2 (step 4) of manual
|
||||
|
||||
LMP_INC = -DLAMMPS_GZIP
|
||||
|
||||
# MPI library
|
||||
# see discussion in Section 2.2 (step 5) of manual
|
||||
# MPI wrapper compiler/linker can provide this info
|
||||
# can point to dummy MPI library in src/STUBS as in Makefile.serial
|
||||
# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts
|
||||
# INC = path for mpi.h, MPI compiler settings
|
||||
# PATH = path for MPI library
|
||||
# LIB = name of MPI library
|
||||
|
||||
MPI_INC =
|
||||
MPI_PATH =
|
||||
MPI_LIB =
|
||||
|
||||
# FFT library
|
||||
# see discussion in Section 2.2 (step 6) of manaul
|
||||
# can be left blank to use provided KISS FFT library
|
||||
# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
|
||||
# PATH = path for FFT library
|
||||
# LIB = name of FFT library
|
||||
|
||||
FFT_INC = -DFFT_FFTW2 -armpl
|
||||
FFT_PATH =
|
||||
FFT_LIB =
|
||||
|
||||
# JPEG and/or PNG library
|
||||
# see discussion in Section 2.2 (step 7) of manual
|
||||
# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
|
||||
# INC = path(s) for jpeglib.h and/or png.h
|
||||
# PATH = path(s) for JPEG library and/or PNG library
|
||||
# LIB = name(s) of JPEG library and/or PNG library
|
||||
|
||||
JPG_INC =
|
||||
JPG_PATH =
|
||||
JPG_LIB =
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# build rules and dependencies
|
||||
# do not edit this section
|
||||
|
||||
include Makefile.package.settings
|
||||
include Makefile.package
|
||||
|
||||
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
|
||||
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
|
||||
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
|
||||
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
|
||||
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)
|
||||
|
||||
# Path to src files
|
||||
|
||||
vpath %.cpp ..
|
||||
vpath %.h ..
|
||||
|
||||
# Link target
|
||||
|
||||
$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp $(EXTRA_CPP_DEPENDS)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp $(EXTRA_CPP_DEPENDS)
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
%.o:%.cu $(EXTRA_CPP_DEPENDS)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
# Individual dependencies
|
||||
|
||||
depend : fastdep.exe $(SRC)
|
||||
@./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1
|
||||
|
||||
fastdep.exe: ../DEPEND/fastdep.c
|
||||
cc -O -o $@ $<
|
||||
|
||||
sinclude .depend
|
||||
|
|
@ -0,0 +1,119 @@
|
|||
# astra-gcc - ThunderX2 GCC/OpenMPI Based, FFTW
|
||||
|
||||
# need to load the following modules:
|
||||
# 1) arm-based developer pack
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# compiler/linker settings
|
||||
# specify flags and libraries needed for your compiler
|
||||
|
||||
CC = mpicxx
|
||||
CCFLAGS = -O3 -funroll-loops -fopenmp -mcpu=thunderx2t99 -mtune=thunderx2t99
|
||||
DEPFLAGS = -M
|
||||
LINK = mpicxx
|
||||
LINKFLAGS = -O3 -fopenmp -mcpu=thunderx2t99 -mtune=thunderx2t99
|
||||
LIB = -lstdc++
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rcsv
|
||||
SIZE = size
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings, all OPTIONAL
|
||||
# specify settings for LAMMPS features you will use
|
||||
# if you change any -D setting, do full re-compile after "make clean"
|
||||
|
||||
# LAMMPS ifdef settings
|
||||
# see possible settings in Section 2.2 (step 4) of manual
|
||||
|
||||
LMP_INC = -DLAMMPS_GZIP
|
||||
|
||||
# MPI library
|
||||
# see discussion in Section 2.2 (step 5) of manual
|
||||
# MPI wrapper compiler/linker can provide this info
|
||||
# can point to dummy MPI library in src/STUBS as in Makefile.serial
|
||||
# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts
|
||||
# INC = path for mpi.h, MPI compiler settings
|
||||
# PATH = path for MPI library
|
||||
# LIB = name of MPI library
|
||||
|
||||
MPI_INC =
|
||||
MPI_PATH =
|
||||
MPI_LIB =
|
||||
|
||||
# FFT library
|
||||
# see discussion in Section 2.2 (step 6) of manaul
|
||||
# can be left blank to use provided KISS FFT library
|
||||
# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
|
||||
# PATH = path for FFT library
|
||||
# LIB = name of FFT library
|
||||
|
||||
FFT_INC = -DFFT_FFTW2 -I${FFTW_INC}
|
||||
FFT_PATH = -I${FFTW_INC}
|
||||
FFT_LIB = -L${FFTW_LIB} -lfftw3
|
||||
|
||||
# JPEG and/or PNG library
|
||||
# see discussion in Section 2.2 (step 7) of manual
|
||||
# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
|
||||
# INC = path(s) for jpeglib.h and/or png.h
|
||||
# PATH = path(s) for JPEG library and/or PNG library
|
||||
# LIB = name(s) of JPEG library and/or PNG library
|
||||
|
||||
JPG_INC =
|
||||
JPG_PATH =
|
||||
JPG_LIB =
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# build rules and dependencies
|
||||
# do not edit this section
|
||||
|
||||
include Makefile.package.settings
|
||||
include Makefile.package
|
||||
|
||||
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
|
||||
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
|
||||
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
|
||||
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
|
||||
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)
|
||||
|
||||
# Path to src files
|
||||
|
||||
vpath %.cpp ..
|
||||
vpath %.h ..
|
||||
|
||||
# Link target
|
||||
|
||||
$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp $(EXTRA_CPP_DEPENDS)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp $(EXTRA_CPP_DEPENDS)
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
%.o:%.cu $(EXTRA_CPP_DEPENDS)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
# Individual dependencies
|
||||
|
||||
depend : fastdep.exe $(SRC)
|
||||
@./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1
|
||||
|
||||
fastdep.exe: ../DEPEND/fastdep.c
|
||||
cc -O -o $@ $<
|
||||
|
||||
sinclude .depend
|
||||
|
|
@ -1,7 +1,5 @@
|
|||
# knl = Flags for Knights Landing Xeon Phi Processor,Intel Compiler/MPI,MKL FFT
|
||||
# module load perftools-base perftools
|
||||
# theta = Flags for Knights Landing Xeon Phi Processor, Intel Compiler, Cray MPI, MKL FFT
|
||||
# make theta -j 8
|
||||
# pat_build -g mpi -u ./lmp_theta
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
|
|
@ -10,24 +8,16 @@ SHELL = /bin/sh
|
|||
# specify flags and libraries needed for your compiler
|
||||
|
||||
CC = CC -mkl
|
||||
#OPTFLAGS = -O0
|
||||
OPTFLAGS = -xMIC-AVX512 -O3 -fp-model fast=2 -no-prec-div -qoverride-limits
|
||||
OPTFLAGS = -xMIC-AVX512 -O3 -fp-model fast=2 -no-prec-div -qoverride-limits
|
||||
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -qno-offload \
|
||||
-fno-alias -ansi-alias -restrict $(OPTFLAGS)
|
||||
#CCFLAGS += -DLMP_INTEL_NO_TBB
|
||||
#CCFLAGS += -DLAMMPS_BIGBIG
|
||||
#CCFLAGS += -D_USE_PAPI
|
||||
#CCFLAGS += -D_USE_CRAYPAT_API
|
||||
CCFLAGS += -std=c++11
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = $(CC)
|
||||
LINKFLAGS = -g -qopenmp $(OPTFLAGS)
|
||||
LINKFLAGS += -dynamic
|
||||
LIB =
|
||||
#LIB += -L${TBBROOT}/lib/intel64/gcc4.7 -ltbbmalloc
|
||||
LIB += -ltbbmalloc
|
||||
#LIB += /soft/debuggers/forge-7.0-2017-02-16/lib/64/libdmallocthcxx.a -zmuldefs
|
||||
LINKFLAGS = -g -qopenmp $(OPTFLAGS) -dynamic
|
||||
LIB = -ltbbmalloc
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
|
|
@ -99,35 +89,35 @@ vpath %.h ..
|
|||
# Link target
|
||||
|
||||
$(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
%.o:%.cu
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
# Individual dependencies
|
||||
|
||||
depend : fastdep.exe $(SRC)
|
||||
@./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1
|
||||
@./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1
|
||||
|
||||
fastdep.exe: ../DEPEND/fastdep.c
|
||||
icc -O -o $@ $<
|
||||
icc -O -o $@ $<
|
||||
|
||||
sinclude .depend
|
||||
|
|
|
|||
|
|
@ -10,7 +10,8 @@ CC = mpiicpc
|
|||
OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \
|
||||
-qopt-zmm-usage=high
|
||||
CCFLAGS = -qopenmp -qno-offload -fno-alias -ansi-alias -restrict \
|
||||
-DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS)
|
||||
-DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \
|
||||
-I$(MKLROOT)/include
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
|
|
|
|||
|
|
@ -10,7 +10,8 @@ CC = mpiicpc
|
|||
OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \
|
||||
-qopt-zmm-usage=high
|
||||
CCFLAGS = -qopenmp -qno-offload -fno-alias -ansi-alias -restrict \
|
||||
-DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS)
|
||||
-DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \
|
||||
-I$(MKLROOT)/include
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
|
|
|
|||
|
|
@ -10,7 +10,8 @@ CC = mpicxx -cxx=icc
|
|||
OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \
|
||||
-qopt-zmm-usage=high
|
||||
CCFLAGS = -qopenmp -qno-offload -fno-alias -ansi-alias -restrict \
|
||||
-DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS)
|
||||
-DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \
|
||||
-I$(MKLROOT)/include
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
|
|
|
|||
|
|
@ -11,7 +11,8 @@ CC = mpicxx
|
|||
OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \
|
||||
-qopt-zmm-usage=high
|
||||
CCFLAGS = -qopenmp -qno-offload -fno-alias -ansi-alias -restrict \
|
||||
-DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS)
|
||||
-DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \
|
||||
-I$(MKLROOT)/include
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
|
|
|
|||
|
|
@ -9,7 +9,8 @@ SHELL = /bin/sh
|
|||
CC = mpiicpc
|
||||
OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
|
||||
CCFLAGS = -qopenmp -qno-offload -fno-alias -ansi-alias -restrict \
|
||||
-DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS)
|
||||
-DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \
|
||||
-I$(MKLROOT)/include
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
|
|
|
|||
|
|
@ -30,9 +30,11 @@
|
|||
#include "error.h"
|
||||
|
||||
#include "math_const.h"
|
||||
#include "math_special.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
using namespace MathSpecial;
|
||||
|
||||
#define MAXLINE 1024
|
||||
#define DELTA 4
|
||||
|
|
@ -604,7 +606,7 @@ double PairTersoff::zeta(Param *param, double rsqij, double rsqik,
|
|||
costheta = (delrij[0]*delrik[0] + delrij[1]*delrik[1] +
|
||||
delrij[2]*delrik[2]) / (rij*rik);
|
||||
|
||||
if (param->powermint == 3) arg = pow(param->lam3 * (rij-rik),3.0);
|
||||
if (param->powermint == 3) arg = cube(param->lam3 * (rij-rik));
|
||||
else arg = param->lam3 * (rij-rik);
|
||||
|
||||
if (arg > 69.0776) ex_delr = 1.e30;
|
||||
|
|
@ -744,7 +746,7 @@ void PairTersoff::ters_zetaterm_d(double prefactor,
|
|||
|
||||
fc = ters_fc(rik,param);
|
||||
dfc = ters_fc_d(rik,param);
|
||||
if (param->powermint == 3) tmp = pow(param->lam3 * (rij-rik),3.0);
|
||||
if (param->powermint == 3) tmp = cube(param->lam3 * (rij-rik));
|
||||
else tmp = param->lam3 * (rij-rik);
|
||||
|
||||
if (tmp > 69.0776) ex_delr = 1.e30;
|
||||
|
|
@ -752,7 +754,7 @@ void PairTersoff::ters_zetaterm_d(double prefactor,
|
|||
else ex_delr = exp(tmp);
|
||||
|
||||
if (param->powermint == 3)
|
||||
ex_delr_d = 3.0*pow(param->lam3,3.0) * pow(rij-rik,2.0)*ex_delr;
|
||||
ex_delr_d = 3.0*cube(param->lam3) * square(rij-rik)*ex_delr;
|
||||
else ex_delr_d = param->lam3 * ex_delr;
|
||||
|
||||
cos_theta = vec3_dot(rij_hat,rik_hat);
|
||||
|
|
|
|||
|
|
@ -25,11 +25,13 @@
|
|||
#include "force.h"
|
||||
#include "comm.h"
|
||||
#include "math_const.h"
|
||||
#include "math_special.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
using namespace MathSpecial;
|
||||
|
||||
#define MAXLINE 1024
|
||||
#define DELTA 4
|
||||
|
|
@ -241,7 +243,7 @@ double PairTersoffMOD::zeta(Param *param, double rsqij, double rsqik,
|
|||
costheta = (delrij[0]*delrik[0] + delrij[1]*delrik[1] +
|
||||
delrij[2]*delrik[2]) / (rij*rik);
|
||||
|
||||
if (param->powermint == 3) arg = pow(param->lam3 * (rij-rik),3.0);
|
||||
if (param->powermint == 3) arg = cube(param->lam3 * (rij-rik));
|
||||
else arg = param->lam3 * (rij-rik);
|
||||
|
||||
if (arg > 69.0776) ex_delr = 1.e30;
|
||||
|
|
@ -314,7 +316,7 @@ void PairTersoffMOD::ters_zetaterm_d(double prefactor,
|
|||
|
||||
fc = ters_fc(rik,param);
|
||||
dfc = ters_fc_d(rik,param);
|
||||
if (param->powermint == 3) tmp = pow(param->lam3 * (rij-rik),3.0);
|
||||
if (param->powermint == 3) tmp = cube(param->lam3 * (rij-rik));
|
||||
else tmp = param->lam3 * (rij-rik);
|
||||
|
||||
if (tmp > 69.0776) ex_delr = 1.e30;
|
||||
|
|
@ -322,7 +324,7 @@ void PairTersoffMOD::ters_zetaterm_d(double prefactor,
|
|||
else ex_delr = exp(tmp);
|
||||
|
||||
if (param->powermint == 3)
|
||||
ex_delr_d = 3.0*pow(param->lam3,3.0) * pow(rij-rik,2.0)*ex_delr;
|
||||
ex_delr_d = 3.0*cube(param->lam3) * square(rij-rik)*ex_delr;
|
||||
else ex_delr_d = param->lam3 * ex_delr;
|
||||
|
||||
cos_theta = vec3_dot(rij_hat,rik_hat);
|
||||
|
|
|
|||
|
|
@ -28,9 +28,11 @@
|
|||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "math_const.h"
|
||||
#include "math_special.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
using namespace MathSpecial;
|
||||
|
||||
#define MAXLINE 1024
|
||||
#define DELTA 4
|
||||
|
|
@ -226,7 +228,7 @@ void PairTersoffZBL::repulsive(Param *param, double rsq, double &fforce,
|
|||
|
||||
// ZBL repulsive portion
|
||||
|
||||
double esq = pow(global_e,2.0);
|
||||
double esq = square(global_e);
|
||||
double a_ij = (0.8854*global_a_0) /
|
||||
(pow(param->Z_i,0.23) + pow(param->Z_j,0.23));
|
||||
double premult = (param->Z_i * param->Z_j * esq)/(4.0*MY_PI*global_epsilon_0);
|
||||
|
|
@ -286,5 +288,5 @@ double PairTersoffZBL::F_fermi(double r, Param *param)
|
|||
double PairTersoffZBL::F_fermi_d(double r, Param *param)
|
||||
{
|
||||
return param->ZBLexpscale*exp(-param->ZBLexpscale*(r-param->ZBLcut)) /
|
||||
pow(1.0 + exp(-param->ZBLexpscale*(r-param->ZBLcut)),2.0);
|
||||
square(1.0 + exp(-param->ZBLexpscale*(r-param->ZBLcut)));
|
||||
}
|
||||
|
|
|
|||
|
|
@ -40,7 +40,7 @@ export LMP_THREAD_LIST="2" # -- For 2 threads per core w/ HT enabled
|
|||
# End settings for your system
|
||||
#########################################################################
|
||||
|
||||
export WORKLOADS="lj rhodo rhodo_lrt lc sw water eam"
|
||||
export WORKLOADS="lj rhodo lc sw water eam airebo dpd tersoff"
|
||||
export LMP_ARGS="-pk intel 0 -sf intel -screen none -v d 1"
|
||||
export RLMP_ARGS="-pk intel 0 lrt yes -sf intel -screen none -v d 1"
|
||||
|
||||
|
|
@ -51,7 +51,7 @@ export LOG_DIR=$LOG_DIR_HOST"_"$LOG_DIR_HEADER"_"$DATE_STRING
|
|||
mkdir $LOG_DIR
|
||||
|
||||
export I_MPI_PIN_DOMAIN=core
|
||||
export I_MPI_FABRICS=shm
|
||||
#export I_MPI_FABRICS=shm
|
||||
export KMP_BLOCKTIME=0
|
||||
|
||||
echo -n "Creating restart file...."
|
||||
|
|
@ -59,13 +59,12 @@ $MPI -np $LMP_CORES $LMP_BIN -in in.lc_generate_restart -log none $LMP_ARGS
|
|||
echo "Done."
|
||||
for threads in $LMP_THREAD_LIST
|
||||
do
|
||||
export OMP_NUM_THREADS=$threads
|
||||
for workload in $WORKLOADS
|
||||
do
|
||||
export LOGFILE=$LOG_DIR/$workload.$LMP_CORES"c"$threads"t".log
|
||||
echo "Running $LOGFILE"
|
||||
cmd="$MPI -np $LMP_CORES $LMP_BIN -in in.intel.$workload -log $LOGFILE $LMP_ARGS";
|
||||
rthreads=$threads
|
||||
export OMP_NUM_THREADS=$threads
|
||||
unset KMP_AFFINITY
|
||||
$cmd
|
||||
|
||||
|
|
|
|||
|
|
@ -31,6 +31,7 @@ compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013
|
|||
compute cnp/atom, Paulo Branicio (USC), branicio at usc.edu, 31 May 2017
|
||||
compute entropy/atom, Pablo Piaggi (EPFL), pablo.piaggi at epfl.ch, 15 June 2018
|
||||
compute gyration/shape, Evangelos Voyiatzis, evoyiatzis at gmail.com, 25 July 2019
|
||||
compute hma, Andrew Schultz & David Kofke (UB), ajs42 at buffalo.edu & kofke at buffalo.edu, 1 Jul 2019
|
||||
compute pressure/cylinder, Cody K. Addington (NCSU), , 2 Oct 2018
|
||||
compute momentum, Rupert Nash (University of Edinburgh), r.nash at epcc.ed.ac.uk, 28 June 2019
|
||||
compute stress/mop, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18
|
||||
|
|
@ -69,6 +70,7 @@ improper_style ring, Georgios Vogiatzis, gvog at chemeng.ntua.gr, 25 May 12
|
|||
improper_style distance, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
|
||||
pair_style agni, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 16
|
||||
pair_style buck/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
|
||||
pair_style cosine/squared, Eugen Rozic, eugen.rozic.17 at ucl.ac.uk, 9 Aug 19
|
||||
pair_style coul/diel, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
|
||||
pair_style coul/shield, Wengen Ouyang (Tel Aviv University), w.g.ouyang at gmail dot com, 30 Mar 18
|
||||
pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11
|
||||
|
|
|
|||
|
|
@ -0,0 +1,516 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
This compute implements harmonically-mapped averaging for crystalline solids.
|
||||
The current implementation handles atomic crystals.
|
||||
|
||||
Computing the heat capacity relies on being able to compute the second
|
||||
derivative of the energy with respect to atom positions. This capability is
|
||||
provided by the single2 method in Pair, but is currently only implemented for
|
||||
the shifted-force LJ potential (lj/smooth/linear). Pair::single2 takes a single
|
||||
pair and (like Pair::single) returns the energy and sets the force as an out
|
||||
parameter, but also sets the elements of 6-element double array out parameter,
|
||||
which are the unique components of the atomic Hessian tensor for the pair. A
|
||||
helper method exists (Pair::pairTensor), which will compute the tensor from
|
||||
linear derivatives and the vector between the positions. HMA Heat capacity can
|
||||
be computed for other models by implementing single2 in those Pair classes.
|
||||
|
||||
More information about HMA is available in these publications:
|
||||
|
||||
A. J. Schultz, D. A. Kofke, “Comprehensive high-precision high-accuracy
|
||||
equation of state and coexistence properties for classical Lennard-Jones
|
||||
crystals and low-temperature fluid phases”, J. Chem. Phys. 149, 204508 (2018)
|
||||
https://dx.doi.org/10.1063/1.5053714
|
||||
|
||||
S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Harmonically Assisted Methods for
|
||||
Computing the Free Energy of Classical Crystals by Molecular Simulation: A
|
||||
Comparative Study”, J. Chem. Theory Comput. 13, 825-834 (2017)
|
||||
https://dx.doi.org/10.1021/acs.jctc.6b01082
|
||||
|
||||
S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Very fast averaging of thermal
|
||||
properties of crystals by molecular simulation”, Phys. Rev. E 92, 043303 (2015)
|
||||
https://dx.doi.org/10.1103/PhysRevE.92.043303
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
#include <mpi.h>
|
||||
#include "compute_hma.h"
|
||||
#include "atom.h"
|
||||
#include "update.h"
|
||||
#include "force.h"
|
||||
#include "pair.h"
|
||||
#include "bond.h"
|
||||
#include "angle.h"
|
||||
#include "dihedral.h"
|
||||
#include "improper.h"
|
||||
#include "kspace.h"
|
||||
#include "group.h"
|
||||
#include "domain.h"
|
||||
#include "modify.h"
|
||||
#include "fix.h"
|
||||
#include "fix_store.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "comm.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_request.h"
|
||||
#include "neigh_list.h"
|
||||
|
||||
#include <vector>
|
||||
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) :
|
||||
Compute(lmp, narg, arg), id_temp(NULL), deltaR(NULL)
|
||||
{
|
||||
if (narg < 4) error->all(FLERR,"Illegal compute hma command");
|
||||
if (igroup) error->all(FLERR,"Compute hma must use group all");
|
||||
if (strcmp(arg[3],"NULL") == 0) {error->all(FLERR,"fix ID specifying the set temperature of canonical simulation is required");}
|
||||
else {
|
||||
int n = strlen(arg[3]) + 1;
|
||||
id_temp = new char[n];
|
||||
strcpy(id_temp,arg[3]);
|
||||
}
|
||||
|
||||
create_attribute = 1;
|
||||
extscalar = 1;
|
||||
timeflag = 1;
|
||||
|
||||
// (from compute displace/atom) create a new fix STORE style
|
||||
// our new fix's id (id_fix)= compute-ID + COMPUTE_STORE
|
||||
// our new fix's group = same as compute group
|
||||
|
||||
int n = strlen(id) + strlen("_COMPUTE_STORE") + 1;
|
||||
id_fix = new char[n];
|
||||
strcpy(id_fix,id);
|
||||
strcat(id_fix,"_COMPUTE_STORE");
|
||||
|
||||
char **newarg = new char*[6];
|
||||
newarg[0] = id_fix;
|
||||
newarg[1] = group->names[igroup];
|
||||
newarg[2] = (char *) "STORE";
|
||||
newarg[3] = (char *) "peratom";
|
||||
newarg[4] = (char *) "1";
|
||||
newarg[5] = (char *) "3";
|
||||
modify->add_fix(6,newarg);
|
||||
fix = (FixStore *) modify->fix[modify->nfix-1];
|
||||
|
||||
delete [] newarg;
|
||||
|
||||
// calculate xu,yu,zu for fix store array
|
||||
// skip if reset from restart file
|
||||
|
||||
if (fix->restart_reset) fix->restart_reset = 0;
|
||||
else {
|
||||
double **xoriginal = fix->astore;
|
||||
double **x = atom->x;
|
||||
imageint *image = atom->image;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
domain->unmap(x[i],image[i],xoriginal[i]);
|
||||
}
|
||||
|
||||
vector_flag = 1;
|
||||
extvector = -1;
|
||||
comm_forward = 0; // 3 if 2nd derivative needed
|
||||
|
||||
computeU = computeP = computeCv = -1;
|
||||
returnAnharmonic = 0;
|
||||
size_vector = 0;
|
||||
memory->create(extlist, 3, "hma:extlist");
|
||||
for (int iarg=4; iarg<narg; iarg++) {
|
||||
if (!strcmp(arg[iarg], "u")) {
|
||||
if (computeU>-1) continue;
|
||||
computeU = size_vector;
|
||||
extlist[size_vector] = 1;
|
||||
size_vector++;
|
||||
}
|
||||
else if (!strcmp(arg[iarg], "p")) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal compute hma command");
|
||||
if (computeP>-1) continue;
|
||||
computeP = size_vector;
|
||||
deltaPcap = force->numeric(FLERR, arg[iarg+1]);
|
||||
extlist[size_vector] = 0;
|
||||
size_vector++;
|
||||
iarg++;
|
||||
}
|
||||
else if (!strcmp(arg[iarg], "cv")) {
|
||||
if (computeCv>-1) continue;
|
||||
computeCv = size_vector;
|
||||
comm_forward = 3;
|
||||
extlist[size_vector] = 1;
|
||||
size_vector++;
|
||||
}
|
||||
else if (!strcmp(arg[iarg], "anharmonic")) {
|
||||
// the first time we're called, we'll grab lattice pressure and energy
|
||||
returnAnharmonic = -1;
|
||||
}
|
||||
else {
|
||||
error->all(FLERR,"Illegal compute hma command");
|
||||
}
|
||||
}
|
||||
|
||||
if (size_vector == 0) {
|
||||
error->all(FLERR,"Illegal compute hma command");
|
||||
}
|
||||
if (size_vector<3) {
|
||||
memory->grow(extlist, size_vector, "hma:extlist");
|
||||
}
|
||||
memory->create(vector, size_vector, "hma:vector");
|
||||
|
||||
if (computeU>-1 || computeCv>-1) {
|
||||
peflag = 1;
|
||||
}
|
||||
if (computeP>-1) {
|
||||
pressflag = 1;
|
||||
}
|
||||
|
||||
nmax = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputeHMA::~ComputeHMA()
|
||||
{
|
||||
// check nfix in case all fixes have already been deleted
|
||||
if (modify->nfix) modify->delete_fix(id_fix);
|
||||
|
||||
delete [] id_fix;
|
||||
delete [] id_temp;
|
||||
memory->destroy(extlist);
|
||||
memory->destroy(vector);
|
||||
memory->destroy(deltaR);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeHMA::init() {
|
||||
if (computeCv>-1) {
|
||||
if (force->pair == NULL)
|
||||
error->all(FLERR,"No pair style is defined for compute hma cv");
|
||||
if (force->pair->single_enable == 0)
|
||||
error->all(FLERR,"Pair style does not support compute hma cv");
|
||||
}
|
||||
|
||||
int irequest = neighbor->request(this,instance_me);
|
||||
neighbor->requests[irequest]->pair = 0;
|
||||
neighbor->requests[irequest]->compute = 1;
|
||||
neighbor->requests[irequest]->occasional = 1;
|
||||
}
|
||||
|
||||
void ComputeHMA::init_list(int id, NeighList *ptr)
|
||||
{
|
||||
list = ptr;
|
||||
}
|
||||
|
||||
void ComputeHMA::setup()
|
||||
{
|
||||
int dummy=0;
|
||||
int ifix = modify->find_fix(id_temp);
|
||||
if (ifix < 0) error->all(FLERR,"Could not find compute hma temperature ID");
|
||||
double * temperat = (double *) modify->fix[ifix]->extract("t_target",dummy);
|
||||
if (temperat==NULL) error->all(FLERR,"Could not find compute hma temperature ID");
|
||||
finaltemp = * temperat;
|
||||
|
||||
// set fix which stores original atom coords
|
||||
|
||||
int ifix2 = modify->find_fix(id_fix);
|
||||
if (ifix2 < 0) error->all(FLERR,"Could not find hma store fix ID");
|
||||
fix = (FixStore *) modify->fix[ifix2];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeHMA::compute_vector()
|
||||
{
|
||||
invoked_vector = update->ntimestep;
|
||||
|
||||
// grow deltaR array if necessary
|
||||
if (comm_forward>0 && atom->nmax > nmax) {
|
||||
memory->destroy(deltaR);
|
||||
nmax = atom->nmax;
|
||||
memory->create(deltaR,nmax,3,"hma:deltaR");
|
||||
}
|
||||
|
||||
double **xoriginal = fix->astore;
|
||||
double fdr = 0.0;
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
||||
imageint *image = atom->image;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double *h = domain->h;
|
||||
double xprd = domain->xprd;
|
||||
double yprd = domain->yprd;
|
||||
double zprd = domain->zprd;
|
||||
|
||||
double u = 0.0;
|
||||
if (computeU>-1 || computeCv>-1) {
|
||||
if (force->pair) u += force->pair->eng_vdwl + force->pair->eng_coul;
|
||||
if (force->bond) u += force->bond->energy;
|
||||
if (force->angle) u += force->angle->energy;
|
||||
if (force->dihedral) u += force->dihedral->energy;
|
||||
if (force->improper) u += force->improper->energy;
|
||||
}
|
||||
|
||||
int dimension = domain->dimension;
|
||||
double p = 0, vol = 0;
|
||||
if (computeP>-1) {
|
||||
p = virial_compute(dimension);
|
||||
vol = xprd * yprd;
|
||||
if (dimension == 3) vol *= zprd;
|
||||
p *= force->nktv2p / (dimension*vol);
|
||||
if (returnAnharmonic == -1) {
|
||||
pLat = p;
|
||||
}
|
||||
}
|
||||
|
||||
if (domain->triclinic == 0) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
int xbox = (image[i] & IMGMASK) - IMGMAX;
|
||||
int ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
int zbox = (image[i] >> IMG2BITS) - IMGMAX;
|
||||
double dx = x[i][0] + xbox*xprd - xoriginal[i][0];
|
||||
double dy = x[i][1] + ybox*yprd - xoriginal[i][1];
|
||||
double dz = x[i][2] + zbox*zprd - xoriginal[i][2];
|
||||
if (comm_forward>0) {
|
||||
deltaR[i][0] = dx;
|
||||
deltaR[i][1] = dy;
|
||||
deltaR[i][2] = dz;
|
||||
}
|
||||
fdr += dx*f[i][0] + dy*f[i][1] + dz*f[i][2];
|
||||
}
|
||||
}
|
||||
else {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
int xbox = (image[i] & IMGMASK) - IMGMAX;
|
||||
int ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
int zbox = (image[i] >> IMG2BITS) - IMGMAX;
|
||||
double dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - xoriginal[i][0];
|
||||
double dy = x[i][1] + h[1]*ybox + h[3]*zbox - xoriginal[i][1];
|
||||
double dz = x[i][2] + h[2]*zbox - xoriginal[i][2];
|
||||
if (comm_forward>0) {
|
||||
deltaR[i][0] = dx;
|
||||
deltaR[i][1] = dy;
|
||||
deltaR[i][2] = dz;
|
||||
}
|
||||
fdr += ((dx*f[i][0])+(dy*f[i][1])+(dz*f[i][2]));
|
||||
}
|
||||
}
|
||||
|
||||
double phiSum = 0.0;
|
||||
if (computeCv>-1) {
|
||||
comm->forward_comm_compute(this);
|
||||
int *type = atom->type;
|
||||
double** cutsq = force->pair->cutsq;
|
||||
if (force->pair) {
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
double *special_lj = force->special_lj;
|
||||
double *special_coul = force->special_coul;
|
||||
int newton_pair = force->newton_pair;
|
||||
|
||||
if (update->firststep == update->ntimestep) neighbor->build_one(list,1);
|
||||
else neighbor->build_one(list);
|
||||
int inum = list->inum;
|
||||
int *ilist = list->ilist;
|
||||
int *numneigh = list->numneigh;
|
||||
int **firstneigh = list->firstneigh;
|
||||
|
||||
for (int ii = 0; ii < inum; ii++) {
|
||||
int i = ilist[ii];
|
||||
double fac = (newton_pair || i < nlocal) ? 1.0 : 0.5;
|
||||
double* ix = x[i];
|
||||
int itype = type[i];
|
||||
int *jlist = firstneigh[i];
|
||||
int jnum = numneigh[i];
|
||||
double *idr = deltaR[i];
|
||||
for (int jj = 0; jj < jnum; jj++) {
|
||||
int j = jlist[jj];
|
||||
if (!newton_pair && j>=nlocal) fac -= 0.5;
|
||||
double factor_lj = special_lj[sbmask(j)];
|
||||
double factor_coul = special_coul[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
double* jx = x[j];
|
||||
double delr[3];
|
||||
delr[0] = ix[0] - jx[0];
|
||||
delr[1] = ix[1] - jx[1];
|
||||
delr[2] = ix[2] - jx[2];
|
||||
double rsq = delr[0]*delr[0] + delr[1]*delr[1] + delr[2]*delr[2];
|
||||
int jtype = type[j];
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
double* jdr = deltaR[j];
|
||||
double fforce, d2u[6];
|
||||
force->pair->single_hessian(i, j, itype, jtype, rsq, delr, factor_coul, factor_lj, fforce, d2u);
|
||||
int m = 0;
|
||||
for (int k=0; k<3; k++) {
|
||||
double a = fac;
|
||||
for (int l=k; l<3; l++) {
|
||||
phiSum += a*(idr[k]*jdr[l]+jdr[k]*idr[l])*d2u[m];
|
||||
phiSum -= a*(idr[k]*idr[l]*d2u[m] + jdr[k]*jdr[l]*d2u[m]);
|
||||
m++;
|
||||
if (k==l) a *= 2;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// compute and sum up properties across processors
|
||||
|
||||
double fdrTotal;
|
||||
MPI_Allreduce(&fdr,&fdrTotal,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
double uTotal;
|
||||
if (computeU>-1 || computeCv>-1) {
|
||||
MPI_Allreduce(&u,&uTotal,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
if (returnAnharmonic == -1) {
|
||||
uLat = uTotal;
|
||||
}
|
||||
if (computeU>-1) {
|
||||
if (returnAnharmonic) {
|
||||
vector[computeU] = uTotal - uLat + 0.5*fdrTotal;
|
||||
}
|
||||
else {
|
||||
vector[computeU] = uTotal + 0.5*fdrTotal + 0.5*dimension*(atom->natoms - 1)*force->boltz*finaltemp;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (computeP>-1) {
|
||||
double fv = ((deltaPcap)-(force->boltz*finaltemp*force->nktv2p*atom->natoms/vol))/(force->boltz*finaltemp*dimension*(atom->natoms - 1));
|
||||
if (returnAnharmonic) {
|
||||
vector[computeP] = p - pLat + (fv*fdrTotal);
|
||||
}
|
||||
else {
|
||||
vector[computeP] = p + (fv*fdrTotal) + deltaPcap;
|
||||
}
|
||||
}
|
||||
|
||||
if (computeCv>-1) {
|
||||
if (computeU==-1) MPI_Allreduce(&u,&uTotal,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
double buTot;
|
||||
if (returnAnharmonic) {
|
||||
buTot = (uTotal - uLat + 0.5*fdrTotal)/finaltemp;
|
||||
}
|
||||
else {
|
||||
buTot = (uTotal + 0.5*fdrTotal)/finaltemp + 0.5*dimension*(atom->natoms - 1)*force->boltz;
|
||||
}
|
||||
double one = -0.25*(fdr + phiSum)/finaltemp;
|
||||
double Cv;
|
||||
MPI_Allreduce(&one,&Cv,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
vector[computeCv] = Cv + buTot*buTot;
|
||||
if (!returnAnharmonic) {
|
||||
vector[computeCv] += 0.5*dimension*(atom->natoms-1);
|
||||
}
|
||||
}
|
||||
if (returnAnharmonic == -1) {
|
||||
// we have our lattice properties
|
||||
returnAnharmonic = 1;
|
||||
}
|
||||
}
|
||||
|
||||
double ComputeHMA::virial_compute(int n)
|
||||
{
|
||||
double v = 0;
|
||||
|
||||
// sum contributions to virial from forces and fixes
|
||||
|
||||
if (force->pair) v += sumVirial(n, force->pair->virial);
|
||||
if (force->bond) v += sumVirial(n, force->bond->virial);
|
||||
if (force->angle) v += sumVirial(n, force->angle->virial);
|
||||
if (force->dihedral) v += sumVirial(n, force->dihedral->virial);
|
||||
if (force->improper) v += sumVirial(n, force->improper->virial);
|
||||
for (int i = 0; i < modify->nfix; i++)
|
||||
if (modify->fix[i]->thermo_virial) v += sumVirial(n, modify->fix[i]->virial);
|
||||
|
||||
// sum virial across procs
|
||||
|
||||
double virial;
|
||||
MPI_Allreduce(&v,&virial,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
// KSpace virial contribution is already summed across procs
|
||||
|
||||
if (force->kspace)
|
||||
for (int i = 0; i < n; i++) virial += force->kspace->virial[i];
|
||||
return virial;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int ComputeHMA::pack_forward_comm(int n, int *list, double *buf,
|
||||
int pbc_flag, int *pbc)
|
||||
{
|
||||
double **xoriginal = fix->astore;
|
||||
imageint *image = atom->image;
|
||||
double **x = atom->x;
|
||||
double *h = domain->h;
|
||||
double xprd = domain->xprd;
|
||||
double yprd = domain->yprd;
|
||||
double zprd = domain->zprd;
|
||||
|
||||
int m = 0;
|
||||
for (int ii = 0; ii < n; ii++) {
|
||||
int i = list[ii];
|
||||
buf[m++] = deltaR[i][0];
|
||||
buf[m++] = deltaR[i][1];
|
||||
buf[m++] = deltaR[i][2];
|
||||
}
|
||||
return m;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeHMA::unpack_forward_comm(int n, int first, double *buf)
|
||||
{
|
||||
double **xoriginal = fix->astore;
|
||||
int i,m,last;
|
||||
|
||||
m = 0;
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++) {
|
||||
deltaR[i][0] = buf[m++];
|
||||
deltaR[i][1] = buf[m++];
|
||||
deltaR[i][2] = buf[m++];
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
initialize one atom's storage values, called when atom is created
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputeHMA::set_arrays(int i)
|
||||
{
|
||||
double **xoriginal = fix->astore;
|
||||
double **x = atom->x;
|
||||
xoriginal[i][0] = x[i][0];
|
||||
xoriginal[i][1] = x[i][1];
|
||||
xoriginal[i][2] = x[i][2];
|
||||
}
|
||||
|
||||
double ComputeHMA::memory_usage()
|
||||
{
|
||||
double bytes = nmax * 3 * sizeof(double);
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,67 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef COMPUTE_CLASS
|
||||
|
||||
ComputeStyle(hma,ComputeHMA)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_COMPUTE_HMA_H
|
||||
#define LMP_COMPUTE_HMA_H
|
||||
|
||||
#include "compute.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class ComputeHMA : public Compute {
|
||||
public:
|
||||
ComputeHMA(class LAMMPS *, int, char **);
|
||||
~ComputeHMA();
|
||||
void setup();
|
||||
void init();
|
||||
void init_list(int, class NeighList *);
|
||||
void compute_vector();
|
||||
void set_arrays(int);
|
||||
int pack_forward_comm(int, int *, double *, int, int *);
|
||||
void unpack_forward_comm(int, int, double *);
|
||||
double memory_usage();
|
||||
|
||||
private:
|
||||
int nmax;
|
||||
int atomsingroup;
|
||||
char *id_fix;
|
||||
char *id_temp;
|
||||
double finaltemp;
|
||||
class FixStore *fix;
|
||||
double boltz, nktv2p, inv_volume;
|
||||
double deltaPcap;
|
||||
double virial_compute(int);
|
||||
static double sumVirial(int n, double* v) {
|
||||
double x = 0;
|
||||
for (int i=0; i<n; i++) x += v[i];
|
||||
return x;
|
||||
}
|
||||
int computeU, computeP, computeCv;
|
||||
class NeighList *list; // half neighbor list
|
||||
double **deltaR;
|
||||
int returnAnharmonic;
|
||||
double uLat, pLat;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,487 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing authors: Eugen Rozic (University College London)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "pair_cosine_squared.h"
|
||||
#include <cmath>
|
||||
#include <cstdlib>
|
||||
#include <cstring>
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neigh_request.h"
|
||||
#include "update.h"
|
||||
#include "integrate.h"
|
||||
#include "respa.h"
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairCosineSquared::PairCosineSquared(LAMMPS *lmp) : Pair(lmp)
|
||||
{
|
||||
writedata = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairCosineSquared::~PairCosineSquared()
|
||||
{
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(epsilon);
|
||||
memory->destroy(sigma);
|
||||
memory->destroy(w);
|
||||
memory->destroy(cut);
|
||||
memory->destroy(wcaflag);
|
||||
|
||||
memory->destroy(lj12_e);
|
||||
memory->destroy(lj6_e);
|
||||
memory->destroy(lj12_f);
|
||||
memory->destroy(lj6_f);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairCosineSquared::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
memory->create(setflag, n+1, n+1, "pair:setflag");
|
||||
memory->create(cutsq, n+1, n+1, "pair:cutsq");
|
||||
|
||||
memory->create(cut, n+1, n+1, "pair:cut");
|
||||
memory->create(epsilon, n+1, n+1, "pair:epsilon");
|
||||
memory->create(sigma, n+1, n+1, "pair:sigma");
|
||||
memory->create(w, n+1, n+1, "pair:w");
|
||||
memory->create(wcaflag, n+1, n+1, "pair:wcaflag");
|
||||
|
||||
memory->create(lj12_e, n+1, n+1, "pair:lj12_e");
|
||||
memory->create(lj6_e, n+1, n+1, "pair:lj6_e");
|
||||
memory->create(lj12_f, n+1, n+1, "pair:lj12_f");
|
||||
memory->create(lj6_f, n+1, n+1, "pair:lj6_f");
|
||||
|
||||
for (int i = 1; i <= n; i++) {
|
||||
for (int j = i; j <= n; j++) {
|
||||
setflag[i][j] = 0;
|
||||
wcaflag[i][j] = 0;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairCosineSquared::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 1) {
|
||||
error->all(FLERR, "Illegal pair_style command (wrong number of params)");
|
||||
}
|
||||
|
||||
cut_global = force->numeric(FLERR, arg[0]);
|
||||
|
||||
// reset cutoffs that have been explicitly set
|
||||
|
||||
if (allocated) {
|
||||
int i, j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i+1; j <= atom->ntypes; j++)
|
||||
if (setflag[i][j])
|
||||
cut[i][j] = cut_global;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairCosineSquared::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 4 || narg > 6)
|
||||
error->all(FLERR, "Incorrect args for pair coefficients (too few or too many)");
|
||||
|
||||
if (!allocated)
|
||||
allocate();
|
||||
|
||||
int ilo, ihi, jlo, jhi;
|
||||
force->bounds(FLERR, arg[0], atom->ntypes, ilo, ihi);
|
||||
force->bounds(FLERR, arg[1], atom->ntypes, jlo, jhi);
|
||||
|
||||
double epsilon_one = force->numeric(FLERR, arg[2]);
|
||||
double sigma_one = force->numeric(FLERR, arg[3]);
|
||||
|
||||
double cut_one = cut_global;
|
||||
double wca_one = 0;
|
||||
if (narg == 6) {
|
||||
cut_one = force->numeric(FLERR, arg[4]);
|
||||
if (strcmp(arg[5], "wca") == 0) {
|
||||
wca_one = 1;
|
||||
} else {
|
||||
error->all(FLERR, "Incorrect args for pair coefficients (unknown option)");
|
||||
}
|
||||
} else if (narg == 5) {
|
||||
if (strcmp(arg[4], "wca") == 0) {
|
||||
wca_one = 1;
|
||||
} else {
|
||||
cut_one = force->numeric(FLERR, arg[4]);
|
||||
}
|
||||
}
|
||||
|
||||
if (cut_one < sigma_one) {
|
||||
error->all(FLERR, "Incorrect args for pair coefficients (cutoff < sigma)");
|
||||
} else if (cut_one == sigma_one) {
|
||||
if (wca_one == 0) {
|
||||
error->all(FLERR, "Incorrect args for pair coefficients (cutoff = sigma w/o wca)");
|
||||
} else {
|
||||
error->warning(FLERR, "Cosine/squared set to WCA only (cutoff = sigma)");
|
||||
}
|
||||
}
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
epsilon[i][j] = epsilon_one;
|
||||
sigma[i][j] = sigma_one;
|
||||
cut[i][j] = cut_one;
|
||||
wcaflag[i][j] = wca_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0)
|
||||
error->all(FLERR, "Incorrect args for pair coefficients (none set)");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style (unneccesary)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/*
|
||||
void PairCosineSquared::init_style()
|
||||
{
|
||||
neighbor->request(this,instance_me);
|
||||
}
|
||||
*/
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairCosineSquared::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0)
|
||||
error->all(FLERR, "Mixing not supported in pair_style cosine/squared");
|
||||
|
||||
epsilon[j][i] = epsilon[i][j];
|
||||
sigma[j][i] = sigma[i][j];
|
||||
cut[j][i] = cut[i][j];
|
||||
wcaflag[j][i] = wcaflag[i][j];
|
||||
|
||||
w[j][i] = w[i][j] = cut[i][j] - sigma[i][j];
|
||||
|
||||
if (wcaflag[i][j]) {
|
||||
lj12_e[j][i] = lj12_e[i][j] = epsilon[i][j] * pow(sigma[i][j], 12.0);
|
||||
lj6_e[j][i] = lj6_e[i][j] = 2.0 * epsilon[i][j] * pow(sigma[i][j], 6.0);
|
||||
lj12_f[j][i] = lj12_f[i][j] = 12.0 * epsilon[i][j] * pow(sigma[i][j], 12.0);
|
||||
lj6_f[j][i] = lj6_f[i][j] = 12.0 * epsilon[i][j] * pow(sigma[i][j], 6.0);
|
||||
}
|
||||
|
||||
// Note: cutsq is set in pair.cpp
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
this is here to throw errors & warnings for given options
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairCosineSquared::modify_params(int narg, char **arg)
|
||||
{
|
||||
Pair::modify_params(narg, arg);
|
||||
|
||||
int iarg = 0;
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg], "mix") == 0) {
|
||||
error->all(FLERR, "pair_modify mix not supported for pair_style cosine/squared");
|
||||
} else if (strcmp(arg[iarg], "shift") == 0) {
|
||||
error->warning(FLERR, "pair_modify shift has no effect on pair_style cosine/squared");
|
||||
offset_flag = 0;
|
||||
} else if (strcmp(arg[iarg], "tail") == 0) {
|
||||
error->warning(FLERR, "pair_modify tail has no effect on pair_style cosine/squared");
|
||||
tail_flag = 0;
|
||||
}
|
||||
iarg++;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairCosineSquared::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(&epsilon[i][j], sizeof(double), 1, fp);
|
||||
fwrite(&sigma[i][j], sizeof(double), 1, fp);
|
||||
fwrite(&cut[i][j], sizeof(double), 1, fp);
|
||||
fwrite(&wcaflag[i][j], sizeof(int), 1, fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairCosineSquared::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)
|
||||
fread(&setflag[i][j], sizeof(int), 1, fp);
|
||||
MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
|
||||
if (setflag[i][j]) {
|
||||
if (me == 0) {
|
||||
fread(&epsilon[i][j], sizeof(double), 1, fp);
|
||||
fread(&sigma[i][j], sizeof(double), 1, fp);
|
||||
fread(&cut[i][j], sizeof(double), 1, fp);
|
||||
fread(&wcaflag[i][j], sizeof(int), 1, fp);
|
||||
}
|
||||
MPI_Bcast(&epsilon[i][j], 1, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&sigma[i][j], 1, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&wcaflag[i][j], 1, MPI_INT, 0, world);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairCosineSquared::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&cut_global, sizeof(double), 1, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairCosineSquared::read_restart_settings(FILE *fp)
|
||||
{
|
||||
int me = comm->me;
|
||||
if (me == 0) {
|
||||
fread(&cut_global, sizeof(double), 1, fp);
|
||||
}
|
||||
MPI_Bcast(&cut_global, 1, MPI_DOUBLE, 0, world);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairCosineSquared::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
fprintf(fp, "%d %g %g %g %d\n", i, epsilon[i][i], sigma[i][i],
|
||||
cut[i][i], wcaflag[i][i]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes all pairs to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairCosineSquared::write_data_all(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
for (int j = i; j <= atom->ntypes; j++)
|
||||
fprintf(fp, "%d %d %g %g %g %d\n", i, j, epsilon[i][j], sigma[i][j],
|
||||
cut[i][j], wcaflag[i][j]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairCosineSquared::compute(int eflag, int vflag)
|
||||
{
|
||||
int i, j, ii, jj, inum, jnum, itype, jtype;
|
||||
int *ilist, *jlist, *numneigh, **firstneigh;
|
||||
double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair;
|
||||
double r, rsq, r2inv, r6inv;
|
||||
double factor_lj, force_lj, force_cos, cosone;
|
||||
|
||||
evdwl = 0.0;
|
||||
if (eflag || vflag)
|
||||
ev_setup(eflag, vflag);
|
||||
else
|
||||
evflag = vflag_fdotr = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
double *special_lj = force->special_lj;
|
||||
int newton_pair = force->newton_pair;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[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];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
|
||||
/*
|
||||
This is exactly what the "single" method does, in fact it could be called
|
||||
here instead of repeating the code but here energy calculation is optional
|
||||
so a little bit of calculation is possibly saved
|
||||
*/
|
||||
|
||||
r = sqrt(rsq);
|
||||
|
||||
if (r <= sigma[itype][jtype]) {
|
||||
if (wcaflag[itype][jtype]) {
|
||||
r2inv = 1.0/rsq;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
force_lj = r6inv*(lj12_f[itype][jtype]*r6inv - lj6_f[itype][jtype]);
|
||||
fpair = factor_lj*force_lj*r2inv;
|
||||
if (eflag) {
|
||||
evdwl = factor_lj*r6inv*
|
||||
(lj12_e[itype][jtype]*r6inv - lj6_e[itype][jtype]);
|
||||
if (sigma[itype][jtype] == cut[itype][jtype]) {
|
||||
// this is the WCA-only case (it requires this shift by definition)
|
||||
evdwl += factor_lj*epsilon[itype][jtype];
|
||||
}
|
||||
}
|
||||
} else {
|
||||
fpair = 0.0;
|
||||
if (eflag) {
|
||||
evdwl = -factor_lj*epsilon[itype][jtype];
|
||||
}
|
||||
}
|
||||
} else {
|
||||
force_cos = -(MY_PI*epsilon[itype][jtype] / (2.0*w[itype][jtype])) *
|
||||
sin(MY_PI*(r-sigma[itype][jtype]) / w[itype][jtype]);
|
||||
fpair = factor_lj*force_cos / r;
|
||||
if (eflag) {
|
||||
cosone = cos(MY_PI*(r-sigma[itype][jtype]) / (2.0*w[itype][jtype]));
|
||||
evdwl = -factor_lj*epsilon[itype][jtype]*cosone*cosone;
|
||||
}
|
||||
}
|
||||
|
||||
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, 0.0, fpair, delx, dely, delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr)
|
||||
virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
This is used be pair_write;
|
||||
it is called only if rsq < cutsq[itype][jtype], no need to check that
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairCosineSquared::single(int /* i */, int /* j */, int itype, int jtype, double rsq,
|
||||
double /* factor_coul */, double factor_lj,
|
||||
double &fforce)
|
||||
{
|
||||
double r, r2inv, r6inv, cosone, force, energy;
|
||||
|
||||
r = sqrt(rsq);
|
||||
|
||||
if (r <= sigma[itype][jtype]) {
|
||||
if (wcaflag[itype][jtype]) {
|
||||
r2inv = 1.0/rsq;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
force = r6inv*(lj12_f[itype][jtype]*r6inv - lj6_f[itype][jtype])*r2inv;
|
||||
energy = r6inv*(lj12_e[itype][jtype]*r6inv - lj6_e[itype][jtype]);
|
||||
if (sigma[itype][jtype] == cut[itype][jtype]) {
|
||||
// this is the WCA-only case (it requires this shift by definition)
|
||||
energy += epsilon[itype][jtype];
|
||||
}
|
||||
} else {
|
||||
force = 0.0;
|
||||
energy = -epsilon[itype][jtype];
|
||||
}
|
||||
} else {
|
||||
cosone = cos(MY_PI*(r-sigma[itype][jtype]) / (2.0*w[itype][jtype]));
|
||||
force = -(MY_PI*epsilon[itype][jtype] / (2.0*w[itype][jtype])) *
|
||||
sin(MY_PI*(r-sigma[itype][jtype]) / w[itype][jtype]) / r;
|
||||
energy = -epsilon[itype][jtype]*cosone*cosone;
|
||||
}
|
||||
fforce = factor_lj*force;
|
||||
return factor_lj*energy;
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,100 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing authors: Eugen Rozic (University College London)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(cosine/squared, PairCosineSquared)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_COS_SQ_H
|
||||
#define LMP_PAIR_LJ_COS_SQ_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairCosineSquared : public Pair {
|
||||
public:
|
||||
PairCosineSquared(class LAMMPS *);
|
||||
virtual ~PairCosineSquared();
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
// void init_style();
|
||||
double init_one(int, int);
|
||||
void modify_params(int, char **);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
void write_data(FILE *);
|
||||
void write_data_all(FILE *);
|
||||
virtual void compute(int, int);
|
||||
double single(int, int, int, int, double, double, double, double &);
|
||||
// void *extract(const char *, int &);
|
||||
|
||||
/* RESPA stuff not implemented...
|
||||
void compute_inner();
|
||||
void compute_middle();
|
||||
void compute_outer(int, int);
|
||||
*/
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
double **epsilon, **sigma, **w, **cut;
|
||||
int **wcaflag;
|
||||
double **lj12_e, **lj6_e, **lj12_f, **lj6_f;
|
||||
|
||||
virtual void allocate();
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: Mixing not supported in pair_style cosine/squared
|
||||
|
||||
Self-explanatory. All coefficients need to be specified explicitly.
|
||||
|
||||
E: pair_modify mix not supported for pair_style cosine/squared
|
||||
|
||||
Same as above, only when calling "pair_modify" command
|
||||
|
||||
W: pair_modify shift/tail is meaningless for pair_style cosine/squared
|
||||
|
||||
This style by definition gets to zero at cutoff distance, so there is nothing
|
||||
to shift and there is no tail contribution
|
||||
|
||||
W: Cosine/squared set to WCA only (cutoff = sigma)
|
||||
|
||||
If cutoff is equal to sigma (minimum) then this pair style basically
|
||||
degenerates/reverts to only WCA. This is for convenience.
|
||||
|
||||
*/
|
||||
|
||||
|
|
@ -14,7 +14,6 @@
|
|||
#ifndef LMP_COMM_TILED_H
|
||||
#define LMP_COMM_TILED_H
|
||||
|
||||
#include <mpi.h>
|
||||
#include "comm.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
|
|
|||
|
|
@ -23,6 +23,7 @@
|
|||
#include "respa.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "utils.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
|
@ -99,6 +100,19 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) :
|
|||
estyle[nwall] = CONSTANT;
|
||||
}
|
||||
|
||||
if (utils::strmatch(style,"^wall/morse")) {
|
||||
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
|
||||
int n = strlen(&arg[iarg+3][2]) + 1;
|
||||
astr[nwall] = new char[n];
|
||||
strcpy(astr[nwall],&arg[iarg+3][2]);
|
||||
astyle[nwall] = VARIABLE;
|
||||
} else {
|
||||
alpha[nwall] = force->numeric(FLERR,arg[iarg+3]);
|
||||
astyle[nwall] = CONSTANT;
|
||||
}
|
||||
++iarg;
|
||||
}
|
||||
|
||||
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
|
||||
int n = strlen(&arg[iarg+3][2]) + 1;
|
||||
sstr[nwall] = new char[n];
|
||||
|
|
|
|||
|
|
@ -45,12 +45,12 @@ class FixWall : public Fix {
|
|||
virtual void wall_particle(int, int, double) = 0;
|
||||
|
||||
protected:
|
||||
double epsilon[6],sigma[6],cutoff[6];
|
||||
double epsilon[6],sigma[6],alpha[6],cutoff[6];
|
||||
double ewall[7],ewall_all[7];
|
||||
double xscale,yscale,zscale;
|
||||
int estyle[6],sstyle[6],wstyle[6];
|
||||
int estyle[6],sstyle[6],astyle[6],wstyle[6];
|
||||
int eindex[6],sindex[6];
|
||||
char *estr[6],*sstr[6];
|
||||
char *estr[6],*sstr[6],*astr[6];
|
||||
int varflag; // 1 if any wall position,epsilon,sigma is a var
|
||||
int eflag; // per-wall flag for energy summation
|
||||
int ilevel_respa;
|
||||
|
|
|
|||
|
|
@ -0,0 +1,87 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "fix_wall_morse.h"
|
||||
#include <cmath>
|
||||
#include "atom.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixWallMorse::FixWallMorse(LAMMPS *lmp, int narg, char **arg) :
|
||||
FixWall(lmp, narg, arg)
|
||||
{
|
||||
dynamic_group_allow = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallMorse::precompute(int m)
|
||||
{
|
||||
coeff1[m] = 2.0 * epsilon[m] * alpha[m];
|
||||
const double alpha_dr = -alpha[m] * (cutoff[m] - sigma[m]);
|
||||
offset[m] = epsilon[m] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
interaction of all particles in group with a wall
|
||||
m = index of wall coeffs
|
||||
which = xlo,xhi,ylo,yhi,zlo,zhi
|
||||
error if any particle is on or behind wall
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixWallMorse::wall_particle(int m, int which, double coord)
|
||||
{
|
||||
double delta,fwall;
|
||||
double vn;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
int dim = which / 2;
|
||||
int side = which % 2;
|
||||
if (side == 0) side = -1;
|
||||
|
||||
int onflag = 0;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
if (side < 0) delta = x[i][dim] - coord;
|
||||
else delta = coord - x[i][dim];
|
||||
if (delta >= cutoff[m]) continue;
|
||||
if (delta <= 0.0) {
|
||||
onflag = 1;
|
||||
continue;
|
||||
}
|
||||
double dr = delta - sigma[m];
|
||||
double dexp = exp(-alpha[m] * dr);
|
||||
fwall = side * coeff1[m] * (dexp*dexp - dexp) / delta;
|
||||
ewall[0] += epsilon[m] * (dexp*dexp - 2.0*dexp) - offset[m];
|
||||
f[i][dim] -= fwall;
|
||||
ewall[m+1] += fwall;
|
||||
|
||||
if (evflag) {
|
||||
if (side < 0) vn = -fwall*delta;
|
||||
else vn = fwall*delta;
|
||||
v_tally(dim, i, vn);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (onflag) error->one(FLERR,"Particle on or inside fix wall surface");
|
||||
}
|
||||
|
|
@ -0,0 +1,49 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(wall/morse,FixWallMorse)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_WALL_MORSE_H
|
||||
#define LMP_FIX_WALL_MORSE_H
|
||||
|
||||
#include "fix_wall.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixWallMorse : public FixWall {
|
||||
public:
|
||||
FixWallMorse(class LAMMPS *, int, char **);
|
||||
void precompute(int);
|
||||
void wall_particle(int, int, double);
|
||||
|
||||
private:
|
||||
double coeff1[6],offset[6];
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Particle on or inside fix wall surface
|
||||
|
||||
Particles must be "exterior" to the wall in order for energy/force to
|
||||
be calculated.
|
||||
|
||||
*/
|
||||
|
|
@ -28,7 +28,7 @@ using namespace LAMMPS_NS;
|
|||
using namespace FixConst;
|
||||
using namespace MathConst;
|
||||
|
||||
enum{LJ93,LJ126,LJ1043,COLLOID,HARMONIC};
|
||||
enum{LJ93,LJ126,LJ1043,COLLOID,HARMONIC,MORSE};
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
|
|
@ -36,7 +36,7 @@ FixWallRegion::FixWallRegion(LAMMPS *lmp, int narg, char **arg) :
|
|||
Fix(lmp, narg, arg),
|
||||
idregion(NULL)
|
||||
{
|
||||
if (narg != 8) error->all(FLERR,"Illegal fix wall/region command");
|
||||
if (narg < 8) error->all(FLERR,"Illegal fix wall/region command");
|
||||
|
||||
scalar_flag = 1;
|
||||
vector_flag = 1;
|
||||
|
|
@ -62,13 +62,28 @@ FixWallRegion::FixWallRegion(LAMMPS *lmp, int narg, char **arg) :
|
|||
else if (strcmp(arg[4],"lj1043") == 0) style = LJ1043;
|
||||
else if (strcmp(arg[4],"colloid") == 0) style = COLLOID;
|
||||
else if (strcmp(arg[4],"harmonic") == 0) style = HARMONIC;
|
||||
else if (strcmp(arg[4],"morse") == 0) style = MORSE;
|
||||
else error->all(FLERR,"Illegal fix wall/region command");
|
||||
|
||||
if (style != COLLOID) dynamic_group_allow = 1;
|
||||
|
||||
epsilon = force->numeric(FLERR,arg[5]);
|
||||
sigma = force->numeric(FLERR,arg[6]);
|
||||
cutoff = force->numeric(FLERR,arg[7]);
|
||||
if (style == MORSE) {
|
||||
if (narg != 9)
|
||||
error->all(FLERR,"Illegal fix wall/region command");
|
||||
|
||||
epsilon = force->numeric(FLERR,arg[5]);
|
||||
alpha = force->numeric(FLERR,arg[6]);
|
||||
sigma = force->numeric(FLERR,arg[7]);
|
||||
cutoff = force->numeric(FLERR,arg[8]);
|
||||
|
||||
} else {
|
||||
if (narg != 8)
|
||||
error->all(FLERR,"Illegal fix wall/region command");
|
||||
|
||||
epsilon = force->numeric(FLERR,arg[5]);
|
||||
sigma = force->numeric(FLERR,arg[6]);
|
||||
cutoff = force->numeric(FLERR,arg[7]);
|
||||
}
|
||||
|
||||
if (cutoff <= 0.0) error->all(FLERR,"Fix wall/region cutoff <= 0.0");
|
||||
|
||||
|
|
@ -154,12 +169,15 @@ void FixWallRegion::init()
|
|||
coeff5 = coeff1 * 10.0;
|
||||
coeff6 = coeff2 * 4.0;
|
||||
coeff7 = coeff3 * 3.0;
|
||||
|
||||
double rinv = 1.0/cutoff;
|
||||
double r2inv = rinv*rinv;
|
||||
double r4inv = r2inv*r2inv;
|
||||
offset = coeff1*r4inv*r4inv*r2inv - coeff2*r4inv -
|
||||
coeff3*pow(cutoff+coeff4,-3.0);
|
||||
} else if (style == MORSE) {
|
||||
coeff1 = 2 * epsilon * alpha;
|
||||
double alpha_dr = -alpha * (cutoff - sigma);
|
||||
offset = epsilon * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
|
||||
} else if (style == COLLOID) {
|
||||
coeff1 = -4.0/315.0 * epsilon * pow(sigma,6.0);
|
||||
coeff2 = -2.0/3.0 * epsilon;
|
||||
|
|
@ -250,6 +268,7 @@ void FixWallRegion::post_force(int vflag)
|
|||
if (style == LJ93) lj93(region->contact[m].r);
|
||||
else if (style == LJ126) lj126(region->contact[m].r);
|
||||
else if (style == LJ1043) lj1043(region->contact[m].r);
|
||||
else if (style == MORSE) morse(region->contact[m].r);
|
||||
else if (style == COLLOID) colloid(region->contact[m].r,radius[i]);
|
||||
else harmonic(region->contact[m].r);
|
||||
|
||||
|
|
@ -284,7 +303,7 @@ void FixWallRegion::post_force(int vflag)
|
|||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallRegion::post_force_respa(int vflag, int ilevel, int /*iloop*/)
|
||||
void FixWallRegion::post_force_respa(int vflag, int ilevel, int /* iloop */)
|
||||
{
|
||||
if (ilevel == ilevel_respa) post_force(vflag);
|
||||
}
|
||||
|
|
@ -372,6 +391,19 @@ void FixWallRegion::lj1043(double r)
|
|||
coeff3*pow(r+coeff4,-3.0) - offset;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Morse interaction for particle with wall
|
||||
compute eng and fwall = magnitude of wall force
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixWallRegion::morse(double r)
|
||||
{
|
||||
double dr = r - sigma;
|
||||
double dexp = exp(-alpha * dr);
|
||||
fwall = coeff1 * (dexp*dexp - dexp) / r;
|
||||
eng = epsilon * (dexp*dexp - 2.0*dexp) - offset;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
colloid interaction for finite-size particle of rad with wall
|
||||
compute eng and fwall = magnitude of wall force
|
||||
|
|
|
|||
|
|
@ -41,6 +41,7 @@ class FixWallRegion : public Fix {
|
|||
private:
|
||||
int style,iregion;
|
||||
double epsilon,sigma,cutoff;
|
||||
double alpha;
|
||||
int eflag;
|
||||
double ewall[4],ewall_all[4];
|
||||
int ilevel_respa;
|
||||
|
|
@ -53,6 +54,7 @@ class FixWallRegion : public Fix {
|
|||
void lj93(double);
|
||||
void lj126(double);
|
||||
void lj1043(double);
|
||||
void morse(double);
|
||||
void colloid(double, double);
|
||||
void harmonic(double);
|
||||
};
|
||||
|
|
|
|||
|
|
@ -14,7 +14,6 @@
|
|||
#ifndef LMP_IRREGULAR_H
|
||||
#define LMP_IRREGULAR_H
|
||||
|
||||
#include <mpi.h>
|
||||
#include "pointers.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
|
|
|||
|
|
@ -37,6 +37,7 @@
|
|||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "info.h"
|
||||
#include "fix_external.h"
|
||||
|
||||
#if defined(LAMMPS_EXCEPTIONS)
|
||||
#include "exceptions.h"
|
||||
|
|
@ -1595,7 +1596,7 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type,
|
|||
|
||||
if (lmp->atom->natoms != natoms_prev + n) {
|
||||
char str[128];
|
||||
sprintf(str,"Library warning in lammps_create_atoms, "
|
||||
snprintf(str, 128, "Library warning in lammps_create_atoms, "
|
||||
"invalid total atoms " BIGINT_FORMAT " " BIGINT_FORMAT,
|
||||
lmp->atom->natoms,natoms_prev+n);
|
||||
if (lmp->comm->me == 0)
|
||||
|
|
@ -1605,6 +1606,40 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type,
|
|||
END_CAPTURE
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
find fix external with given ID and set the callback function
|
||||
and caller pointer
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void lammps_set_fix_external_callback(void *ptr, char *id, FixExternalFnPtr callback_ptr, void * caller)
|
||||
{
|
||||
LAMMPS *lmp = (LAMMPS *) ptr;
|
||||
FixExternal::FnPtr callback = (FixExternal::FnPtr) callback_ptr;
|
||||
|
||||
BEGIN_CAPTURE
|
||||
{
|
||||
int ifix = lmp->modify->find_fix(id);
|
||||
if (ifix < 0) {
|
||||
char str[128];
|
||||
snprintf(str, 128, "Can not find fix with ID '%s'!", id);
|
||||
lmp->error->all(FLERR,str);
|
||||
}
|
||||
|
||||
Fix *fix = lmp->modify->fix[ifix];
|
||||
|
||||
if (strcmp("external",fix->style) != 0){
|
||||
char str[128];
|
||||
snprintf(str, 128, "Fix '%s' is not of style external!", id);
|
||||
lmp->error->all(FLERR,str);
|
||||
}
|
||||
|
||||
FixExternal * fext = (FixExternal*) fix;
|
||||
fext->set_callback(callback, caller);
|
||||
}
|
||||
END_CAPTURE
|
||||
}
|
||||
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
// library API functions for accessing LAMMPS configuration
|
||||
// ----------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -58,6 +58,14 @@ void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *);
|
|||
void lammps_scatter_atoms(void *, char *, int, int, void *);
|
||||
void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *);
|
||||
|
||||
#ifdef LAMMPS_BIGBIG
|
||||
typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **);
|
||||
void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*);
|
||||
#else
|
||||
typedef void (*FixExternalFnPtr)(void *, int, int, int *, double **, double **);
|
||||
void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*);
|
||||
#endif
|
||||
|
||||
int lammps_config_has_package(char * package_name);
|
||||
int lammps_config_package_count();
|
||||
int lammps_config_package_name(int index, char * buffer, int max_size);
|
||||
|
|
|
|||
13
src/pair.cpp
13
src/pair.cpp
|
|
@ -54,6 +54,7 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp)
|
|||
comm_forward = comm_reverse = comm_reverse_off = 0;
|
||||
|
||||
single_enable = 1;
|
||||
single_hessian_enable = 0;
|
||||
restartinfo = 1;
|
||||
respa_enable = 0;
|
||||
one_coeff = 0;
|
||||
|
|
@ -1743,6 +1744,18 @@ void Pair::init_bitmap(double inner, double outer, int ntablebits,
|
|||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void Pair::hessian_twobody(double fforce, double dfac, double delr[3], double phiTensor[6]) {
|
||||
int m = 0;
|
||||
for (int k=0; k<3; k++) {
|
||||
phiTensor[m] = fforce;
|
||||
for (int l=k; l<3; l++) {
|
||||
if (l>k) phiTensor[m] = 0;
|
||||
phiTensor[m++] += delr[k]*delr[l] * dfac;
|
||||
}
|
||||
}
|
||||
}
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double Pair::memory_usage()
|
||||
{
|
||||
double bytes = comm->nthreads*maxeatom * sizeof(double);
|
||||
|
|
|
|||
11
src/pair.h
11
src/pair.h
|
|
@ -46,6 +46,7 @@ class Pair : protected Pointers {
|
|||
int comm_reverse_off; // size of reverse comm even if newton off
|
||||
|
||||
int single_enable; // 1 if single() routine exists
|
||||
int single_hessian_enable; // 1 if single_hessian() routine exists
|
||||
int restartinfo; // 1 if pair style writes restart info
|
||||
int respa_enable; // 1 if inner/middle/outer rRESPA routines
|
||||
int one_coeff; // 1 if allows only one coeff * * call
|
||||
|
|
@ -148,6 +149,16 @@ class Pair : protected Pointers {
|
|||
return 0.0;
|
||||
}
|
||||
|
||||
void hessian_twobody(double fforce, double dfac, double delr[3], double phiTensor[6]);
|
||||
|
||||
virtual double single_hessian(int, int, int, int,
|
||||
double, double[3], double, double,
|
||||
double& fforce, double d2u[6]) {
|
||||
fforce = 0.0;
|
||||
for (int i=0; i<6; i++) d2u[i] = 0;
|
||||
return 0.0;
|
||||
}
|
||||
|
||||
virtual void settings(int, char **) = 0;
|
||||
virtual void coeff(int, char **) = 0;
|
||||
|
||||
|
|
|
|||
|
|
@ -29,7 +29,9 @@ using namespace LAMMPS_NS;
|
|||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJSmoothLinear::PairLJSmoothLinear(LAMMPS *lmp) : Pair(lmp) {}
|
||||
PairLJSmoothLinear::PairLJSmoothLinear(LAMMPS *lmp) : Pair(lmp) {
|
||||
single_hessian_enable = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
|
|
@ -345,3 +347,26 @@ double PairLJSmoothLinear::single(int /*i*/, int /*j*/, int itype, int jtype,
|
|||
|
||||
return factor_lj*philj;
|
||||
}
|
||||
|
||||
double PairLJSmoothLinear::single_hessian(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
|
||||
double delr[3], double /*factor_coul*/, double factor_lj,
|
||||
double &fforce, double d2u[6])
|
||||
{
|
||||
double r2inv,r6inv,forcelj,philj,r,rinv;
|
||||
|
||||
r2inv = 1.0/rsq;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
rinv = sqrt(r2inv);
|
||||
r = sqrt(rsq);
|
||||
forcelj = r6inv*(lj1[itype][jtype]*r6inv-lj2[itype][jtype]);
|
||||
forcelj = rinv*forcelj - dljcut[itype][jtype];
|
||||
fforce = factor_lj*forcelj*rinv;
|
||||
|
||||
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
|
||||
philj = philj - ljcut[itype][jtype]
|
||||
+ (r-cut[itype][jtype])*dljcut[itype][jtype];
|
||||
|
||||
double d2r = factor_lj * r6inv * (13.0*lj1[itype][jtype]*r6inv - 7.0*lj2[itype][jtype])/rsq;
|
||||
hessian_twobody(fforce, -(fforce + d2r) / rsq, delr, d2u);
|
||||
return factor_lj*philj;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -38,6 +38,7 @@ class PairLJSmoothLinear : public Pair {
|
|||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
double single(int, int, int, int, double, double, double, double &);
|
||||
double single_hessian(int, int, int, int, double, double[3], double, double, double&, double[6]);
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
|
|
|
|||
|
|
@ -14,7 +14,6 @@
|
|||
#ifndef LAMMPS_RCB_H
|
||||
#define LAMMPS_RCB_H
|
||||
|
||||
#include <mpi.h>
|
||||
#include "pointers.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
|
|
|||
|
|
@ -22,7 +22,6 @@ CommandStyle(read_dump,ReadDump)
|
|||
#ifndef LMP_READ_DUMP_H
|
||||
#define LMP_READ_DUMP_H
|
||||
|
||||
#include <mpi.h>
|
||||
#include "pointers.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
|
|
|||
|
|
@ -18,6 +18,7 @@
|
|||
#include <cstring>
|
||||
#include <cctype>
|
||||
#include <unistd.h>
|
||||
#include <string>
|
||||
#include "universe.h"
|
||||
#include "atom.h"
|
||||
#include "update.h"
|
||||
|
|
@ -1302,8 +1303,12 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
|
|||
if (word[0] == 'C') lowercase = 0;
|
||||
|
||||
int icompute = modify->find_compute(word+2);
|
||||
if (icompute < 0)
|
||||
print_var_error(FLERR,"Invalid compute ID in variable formula",ivar);
|
||||
if (icompute < 0) {
|
||||
std::string mesg = "Invalid compute ID '";
|
||||
mesg += (word+2);
|
||||
mesg += "' in variable formula";
|
||||
print_var_error(FLERR,mesg.c_str(),ivar);
|
||||
}
|
||||
Compute *compute = modify->compute[icompute];
|
||||
|
||||
// parse zero or one or two trailing brackets
|
||||
|
|
@ -1604,9 +1609,10 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
|
|||
|
||||
int ifix = modify->find_fix(word+2);
|
||||
if (ifix < 0) {
|
||||
char msg[128];
|
||||
snprintf(msg,128,"Invalid fix ID '%s' in variable formula",word+2);
|
||||
print_var_error(FLERR,msg,ivar);
|
||||
std::string mesg = "Invalid fix ID '";
|
||||
mesg += (word+2);
|
||||
mesg += "' in variable formula";
|
||||
print_var_error(FLERR,mesg.c_str(),ivar);
|
||||
}
|
||||
Fix *fix = modify->fix[ifix];
|
||||
|
||||
|
|
@ -3792,8 +3798,12 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
|
|||
// group to operate on
|
||||
|
||||
int igroup = group->find(args[0]);
|
||||
if (igroup == -1)
|
||||
print_var_error(FLERR,"Group ID in variable formula does not exist",ivar);
|
||||
if (igroup == -1) {
|
||||
std::string mesg = "Group ID '";
|
||||
mesg += args[0];
|
||||
mesg += "' in variable formula does not exist";
|
||||
print_var_error(FLERR,mesg.c_str(),ivar);
|
||||
}
|
||||
|
||||
// match word to group function
|
||||
|
||||
|
|
@ -4001,8 +4011,12 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
|
|||
int Variable::region_function(char *id, int ivar)
|
||||
{
|
||||
int iregion = domain->find_region(id);
|
||||
if (iregion == -1)
|
||||
print_var_error(FLERR,"Region ID in variable formula does not exist",ivar);
|
||||
if (iregion == -1) {
|
||||
std::string mesg = "Region ID '";
|
||||
mesg += id;
|
||||
mesg += "' in variable formula does not exist";
|
||||
print_var_error(FLERR,mesg.c_str(),ivar);
|
||||
}
|
||||
|
||||
// init region in case sub-regions have been deleted
|
||||
|
||||
|
|
@ -4080,9 +4094,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
|
|||
|
||||
int icompute = modify->find_compute(&args[0][2]);
|
||||
if (icompute < 0) {
|
||||
char msg[128];
|
||||
snprintf(msg,128,"Invalid compute ID '%s' in variable formula",word+2);
|
||||
print_var_error(FLERR,msg,ivar);
|
||||
std::string mesg = "Invalid compute ID '";
|
||||
mesg += (args[0]+2);
|
||||
mesg += "' in variable formula";
|
||||
print_var_error(FLERR,mesg.c_str(),ivar);
|
||||
}
|
||||
compute = modify->compute[icompute];
|
||||
if (index == 0 && compute->vector_flag) {
|
||||
|
|
@ -4123,13 +4138,20 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
|
|||
} else index = 0;
|
||||
|
||||
int ifix = modify->find_fix(&args[0][2]);
|
||||
if (ifix < 0)
|
||||
print_var_error(FLERR,"Invalid fix ID in variable formula",ivar);
|
||||
if (ifix < 0) {
|
||||
std::string mesg = "Invalid fix ID '";
|
||||
mesg += (args[0]+2);
|
||||
mesg += "' in variable formula";
|
||||
print_var_error(FLERR,mesg.c_str(),ivar);
|
||||
}
|
||||
fix = modify->fix[ifix];
|
||||
if (index == 0 && fix->vector_flag) {
|
||||
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
|
||||
print_var_error(FLERR,"Fix in variable not computed at "
|
||||
"compatible time",ivar);
|
||||
if (update->whichflag > 0 && update->ntimestep % fix->global_freq) {
|
||||
std::string mesg = "Fix with ID '";
|
||||
mesg += (args[0]+2);
|
||||
mesg += "' in variable formula not computed at compatible time";
|
||||
print_var_error(FLERR,mesg.c_str(),ivar);
|
||||
}
|
||||
nvec = fix->size_vector;
|
||||
nstride = 1;
|
||||
} else if (index && fix->array_flag) {
|
||||
|
|
@ -4336,9 +4358,12 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
|
|||
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
|
||||
|
||||
int ivar = find(args[0]);
|
||||
if (ivar < 0)
|
||||
print_var_error(FLERR,"Variable ID in "
|
||||
"variable formula does not exist",ivar);
|
||||
if (ivar < 0) {
|
||||
std::string mesg = "Variable ID '";
|
||||
mesg += args[0];
|
||||
mesg += "' in variable formula does not exist";
|
||||
print_var_error(FLERR,mesg.c_str(),ivar);
|
||||
}
|
||||
|
||||
// SCALARFILE has single current value, read next one
|
||||
// save value in tree or on argstack
|
||||
|
|
|
|||
Loading…
Reference in New Issue