forked from lijiext/lammps
Merge branch 'master' of https://github.com/lammps/lammps
This commit is contained in:
charlie sievers
commit
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../../potentials/CH.airebo
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../../potentials/CdTe.bop.table
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Cu functions (universal 3), SM Foiles et al, PRB, 33, 7983 (1986)
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29 63.550 3.6150 FCC
|
||||
500 5.0100200400801306e-04 500 1.0000000000000009e-02 4.9499999999999886e+00
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|
||||
3.5745755503880039e-02 3.4521007208912380e-02 3.3361833779917971e-02 3.2264023597108116e-02 3.1223635691821294e-02
|
||||
3.0236983660070216e-02 2.9300620393215571e-02 2.8411323597772320e-02 2.7566082075896281e-02 2.6762082737777249e-02
|
||||
2.5996698317105604e-02 2.5267475760840985e-02 2.4572125264713973e-02 2.3908509926274246e-02 2.3274635987705516e-02
|
||||
2.2668643641204911e-02 2.2088798370316409e-02 2.1533482801290083e-02 2.1001189039288493e-02 2.0490511464994254e-02
|
||||
2.0000139967999431e-02 1.9528853594166895e-02 1.9075514584991349e-02 1.8639062787818239e-02 1.8218510416650235e-02
|
||||
1.7812937144080498e-02 1.7421485505751177e-02 1.7043356599549031e-02 1.6677806062561751e-02 1.6324140309613155e-02
|
||||
1.5981713017976018e-02 1.5649921843605585e-02 1.5328205354974755e-02 1.5016040171312250e-02 1.4712938292708366e-02
|
||||
1.4418444610242331e-02 1.4132134584901757e-02 1.3853612084676337e-02 1.3582507369821917e-02 1.3318475216818060e-02
|
||||
1.3061193172097418e-02 1.2810359927147186e-02 1.2565693807050415e-02 1.2326931365025051e-02 1.2093826075940506e-02
|
||||
1.1866147122233661e-02 1.1643678266026136e-02 1.1426216801644407e-02 1.1213572583084475e-02 1.1005567121320226e-02
|
||||
1.0802032746662471e-02 1.0602811831688208e-02 1.0407756070544782e-02 1.0216725810699157e-02 1.0029589433467268e-02
|
||||
9.8462227798860602e-03 9.6665086187306404e-03 9.4903361536790021e-03 9.3176005668363371e-03 9.1482025960089031e-03
|
||||
8.9820481433065535e-03 8.8190479128032462e-03 8.6591170751522117e-03 8.5021749571883021e-03 8.3481447546937537e-03
|
||||
8.1969532666261724e-03 8.0485306492223962e-03 7.9028101885199598e-03 7.7597280899136256e-03 7.6192232834934315e-03
|
||||
7.4812372439735375e-03 7.3457138241272979e-03 7.2125991007052359e-03 7.0818412319012813e-03 6.9533903254870300e-03
|
||||
6.8271983168139705e-03 6.7032188559211503e-03 6.5814072030662141e-03 6.4617201320263939e-03 6.3441158405819764e-03
|
||||
6.2285538676237207e-03 6.1149950163802147e-03 6.0034012832899109e-03 5.8937357920846312e-03 5.7859627326801166e-03
|
||||
5.6800473044990030e-03 5.5759556638887986e-03 5.4736548753111791e-03 5.3731128660109428e-03 5.2742983838981461e-03
|
||||
5.1771809583849582e-03 5.0817308639591330e-03 4.9879190862693046e-03 4.8957172905357560e-03 4.8050977921015592e-03
|
||||
4.7160335289582467e-03 4.6284980360953021e-03 4.5424654215287241e-03 4.4579103438822931e-03 4.3748079913988880e-03
|
||||
4.2931340622749670e-03 4.2128647462132407e-03 4.1339767071033873e-03 4.0564470667446839e-03 3.9802533895282599e-03
|
||||
3.9053736680121076e-03 3.8317863093158128e-03 3.7594701222811860e-03 3.6884043053326127e-03 3.6185684349951674e-03
|
||||
3.5499424550168301e-03 3.4825066660512660e-03 3.4162417158645347e-03 3.3511285900229004e-03 3.2871486030347646e-03
|
||||
3.2242833899080170e-03 3.1625148980992668e-03 3.1018253798278661e-03 3.0421973847258310e-03 2.9836137528083811e-03
|
||||
2.9260576077371064e-03 2.8695123503632708e-03 2.8139616525287708e-03 2.7593894511106498e-03 2.7057799422959966e-03
|
||||
2.6531175760685227e-03 2.6013870509009052e-03 2.5505733086344240e-03 2.5006615295404683e-03 2.4516371275501436e-03
|
||||
2.4034857456453340e-03 2.3561932514012535e-03 2.3097457326723414e-03 2.2641294934160616e-03 2.2193310496436136e-03
|
||||
2.1753371254977782e-03 2.1321346494441173e-03 2.0897107505768314e-03 2.0480527550303662e-03 2.0071481824917164e-03
|
||||
1.9669847428123305e-03 1.9275503327108034e-03 1.8888330325659355e-03 1.8508211032951805e-03 1.8135029833145980e-03
|
||||
1.7768672855772646e-03 1.7409027946878666e-03 1.7055984640891586e-03 1.6709434133182904e-03 1.6369269253308227e-03
|
||||
1.6035384438881917e-03 1.5707675710093030e-03 1.5386040644797400e-03 1.5070378354209296e-03 1.4760589459142243e-03
|
||||
1.4456576066784674e-03 1.4158241748004133e-03 1.3865491515145517e-03 1.3578231800324136e-03 1.3296370434173130e-03
|
||||
1.3019816625059188e-03 1.2748480938728074e-03 1.2482275278369870e-03 1.2221112865106742e-03 1.1964908218862064e-03
|
||||
1.1713577139624703e-03 1.1467036689077198e-03 1.1225205172586891e-03 1.0988002121543120e-03 1.0755348276031765e-03
|
||||
1.0527165567835728e-03 1.0303377103750150e-03 1.0083907149206553e-03 9.8686811121878604e-04 9.6576255274356815e-04
|
||||
9.4506680409354657e-04 9.2477373946662708e-04 9.0487634116191706e-04 8.8536769810608137e-04 8.6624100440530968e-04
|
||||
8.4748955791986991e-04 8.2910675886310736e-04 8.1108610842155551e-04 7.9342120739794852e-04 7.7610575487466887e-04
|
||||
7.5913354689786591e-04 7.4249847518158968e-04 7.2619452583109687e-04 7.1021577808524222e-04 6.9455640307671332e-04
|
||||
6.7921066261025093e-04 6.6417290795844214e-04 6.4943757867335500e-04 6.3499920141575628e-04 6.2085238879914031e-04
|
||||
6.0699183824991856e-04 5.9341233088238896e-04 5.8010873038847818e-04 5.6707598194186137e-04 5.5430911111587280e-04
|
||||
5.4180322281523891e-04 5.2955350022104025e-04 5.1755520374872563e-04 5.0580367001857793e-04 4.9429431083891986e-04
|
||||
4.8302261220136561e-04 4.7198413328763435e-04 4.6117450548847222e-04 4.5058943143359842e-04 4.4022468403297037e-04
|
||||
4.3007610552883886e-04 4.2013960655883260e-04 4.1041116522908330e-04 4.0088682619821882e-04 3.9156269977118005e-04
|
||||
3.8243496100300207e-04 3.7349984881274514e-04 3.6475366510662147e-04 3.5619277391102898e-04 3.4781360051482253e-04
|
||||
3.3961263062063513e-04 3.3158640950565685e-04 3.2373154119109092e-04 3.1604468762060252e-04 3.0852256784754707e-04
|
||||
3.0116195723081836e-04 2.9395968663908575e-04 2.8691264166377101e-04 2.8001776184017647e-04 2.7327203987681688e-04
|
||||
2.6667252089326854e-04 2.6021630166557681e-04 2.5390052988028163e-04 2.4772240339593181e-04 2.4167916951265550e-04
|
||||
2.3576812424967210e-04 2.2998661163024531e-04 2.2433202297460642e-04 2.1880179620031078e-04 2.1339341513026532e-04
|
||||
2.0810440880823181e-04 2.0293235082175821e-04 1.9787485863260665e-04 1.9292959291436311e-04 1.8809425689761319e-04
|
||||
1.8336659572205580e-04 1.7874439579616125e-04 1.7422548416372047e-04 1.6980772787763936e-04 1.6548903338088530e-04
|
||||
1.6126734589430591e-04 1.5714064881157744e-04 1.5310696310104604e-04 1.4916434671449329e-04 1.4531089400280153e-04
|
||||
1.4154473513841234e-04 1.3786403554466153e-04 1.3426699533172857e-04 1.3075184873951283e-04 1.2731686358694039e-04
|
||||
1.2396034072819674e-04 1.2068061351527565e-04 1.1747604726729168e-04 1.1434503874632306e-04 1.1128601563955686e-04
|
||||
1.0829743604811193e-04 1.0537778798212988e-04 1.0252558886227753e-04 9.9739385027582898e-05 9.7017751249615057e-05
|
||||
9.4359290252773662e-05 9.1762632240957511e-05 8.9226434430383569e-05 8.6749380588361721e-05 8.4330180578390864e-05
|
||||
8.1967569911181246e-05 7.9660309301724484e-05 7.7407184232279429e-05 7.5207004521348451e-05 7.3058603898526649e-05
|
||||
7.0960839585107720e-05 6.8912591880629977e-05 6.6912763755002085e-05 6.4960280446513426e-05 6.3054089065330086e-05
|
||||
6.1193158202771814e-05 5.9376477546041213e-05 5.7603057498502742e-05 5.5871928805544500e-05 5.4182142185708361e-05
|
||||
5.2532767967318744e-05 5.0922895730446966e-05 4.9351633954125953e-05 4.7818109668823321e-05 4.6321468114150300e-05
|
||||
4.4860872401664663e-05 4.3435503182825573e-05 4.2044558321957873e-05 4.0687252574273750e-05 3.9362817268785450e-05
|
||||
3.8070499996214428e-05 3.6809564301621984e-05 3.5579289382025496e-05 3.4378969788611451e-05 3.3207915133769052e-05
|
||||
3.2065449802711312e-05 3.0950912669766876e-05 2.9863656819185611e-05 2.8803049270468119e-05 2.7768470708167169e-05
|
||||
2.6759315216115260e-05 2.5774990015931323e-05 2.4814915209964844e-05 2.3878523528387922e-05 2.2965260080560611e-05
|
||||
2.2074582110528148e-05 2.1205958756658535e-05 2.0358870815317476e-05 1.9532810508535560e-05 1.8727281255713447e-05
|
||||
1.7941797449145505e-05 1.7175884233475961e-05 1.6429077288930018e-05 1.5700922618341645e-05 1.4990976337865471e-05
|
||||
1.4298804471386687e-05 1.3623982748522034e-05 1.2966096406226424e-05 1.2324739993882115e-05 1.1699517181902770e-05
|
||||
1.1090040573734860e-05 1.0495931521266495e-05 9.9168199435395021e-06 9.3523441487842465e-06 8.8021506596591475e-06
|
||||
8.2658940417265321e-06 7.7432367350197678e-06 7.2338488887770244e-06 6.7374081991923703e-06 6.2535997501888662e-06
|
||||
5.7821158571569505e-06 5.3226559136389283e-06 4.8749262408651290e-06 4.4386399401326240e-06 4.0135167480073166e-06
|
||||
3.5992828942305738e-06 3.1956709623667747e-06 2.8024197531120341e-06 2.4192741502208947e-06 2.0459849890155880e-06
|
||||
1.6823089274468580e-06 1.3280083196495871e-06 9.8285109196557868e-07 6.4661062138351467e-07 3.1906561636122974e-07
|
||||
0. 0. 0. 0. 0.
|
||||
|
||||
|
||||
|
|
@ -0,0 +1 @@
|
|||
../../potentials/Cu_u3.eam
|
||||
43007
bench/POTENTIALS/Ni.adp
43007
bench/POTENTIALS/Ni.adp
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1 @@
|
|||
../../potentials/Ni.adp
|
||||
|
|
@ -52,10 +52,17 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
|
|||
include(CheckCCompilerFlag)
|
||||
include(CheckIncludeFileCXX)
|
||||
|
||||
if (${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
|
||||
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
|
||||
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
|
||||
endif()
|
||||
|
||||
option(DISABLE_CXX11_REQUIREMENT "Disable check that requires C++11 for compiling LAMMPS" OFF)
|
||||
if(DISABLE_CXX11_REQUIREMENT)
|
||||
add_definitions(-DLAMMPS_CXX98)
|
||||
else()
|
||||
set(CMAKE_CXX_STANDARD 11)
|
||||
endif()
|
||||
|
||||
# GNU compiler features
|
||||
if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
|
||||
option(ENABLE_COVERAGE "Enable code coverage" OFF)
|
||||
|
|
|
|||
|
|
@ -1,15 +1,21 @@
|
|||
if(PKG_KOKKOS)
|
||||
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
|
||||
set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
|
||||
option(EXTERNAL_KOKKOS "Build against external kokkos library")
|
||||
if(EXTERNAL_KOKKOS)
|
||||
find_package(Kokkos REQUIRED)
|
||||
list(APPEND LAMMPS_LINK_LIBS Kokkos::kokkos)
|
||||
else()
|
||||
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
|
||||
set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
|
||||
add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
|
||||
|
||||
set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
|
||||
${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
|
||||
${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
|
||||
${LAMMPS_LIB_KOKKOS_BIN_DIR})
|
||||
include_directories(${Kokkos_INCLUDE_DIRS})
|
||||
list(APPEND LAMMPS_LINK_LIBS kokkos)
|
||||
endif()
|
||||
add_definitions(-DLMP_KOKKOS)
|
||||
add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
|
||||
|
||||
set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
|
||||
${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
|
||||
${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
|
||||
${LAMMPS_LIB_KOKKOS_BIN_DIR})
|
||||
include_directories(${Kokkos_INCLUDE_DIRS})
|
||||
list(APPEND LAMMPS_LINK_LIBS kokkos)
|
||||
|
||||
set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS)
|
||||
set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
.TH LAMMPS "7 August 2019" "2019-08-07"
|
||||
.TH LAMMPS "19 September 2019" "2019-09-19"
|
||||
.SH NAME
|
||||
.B LAMMPS
|
||||
\- Molecular Dynamics Simulator.
|
||||
|
|
|
|||
|
|
@ -51,7 +51,7 @@ Serial build (see src/MAKE/Makefile.serial):
|
|||
|
||||
MPI_INC = -I../STUBS
|
||||
MPI_PATH = -L../STUBS
|
||||
MPI_LIB = -lmpi_stubs :pre
|
||||
MPI_LIB = -lmpi_stubs :pre
|
||||
|
||||
For a parallel build, if MPI is installed on your system in the usual
|
||||
place (e.g. under /usr/local), you do not need to specify the 3
|
||||
|
|
@ -183,17 +183,17 @@ want.
|
|||
|
||||
Parallel build (see src/MAKE/Makefile.mpi):
|
||||
|
||||
CC = mpicxx
|
||||
CCFLAGS = -g -O3
|
||||
LINK = mpicxx
|
||||
LINKFLAGS = -g -O :pre
|
||||
CC = mpicxx
|
||||
CCFLAGS = -g -O3
|
||||
LINK = mpicxx
|
||||
LINKFLAGS = -g -O :pre
|
||||
|
||||
Serial build (see src/MAKE/Makefile.serial):
|
||||
|
||||
CC = g++
|
||||
CCFLAGS = -g -O3
|
||||
LINK = g++
|
||||
LINKFLAGS = -g -O :pre
|
||||
CC = g++
|
||||
CCFLAGS = -g -O3
|
||||
LINK = g++
|
||||
LINKFLAGS = -g -O :pre
|
||||
|
||||
The "compiler/linker settings" section of a Makefile.machine lists
|
||||
compiler and linker settings for your C++ compiler, including
|
||||
|
|
|
|||
|
|
@ -50,7 +50,7 @@ Code Coverage and Testing :h4,link(testing)
|
|||
|
||||
We do extensive regression testing of the LAMMPS code base on a continuous
|
||||
basis. Some of the logic to do this has been added to the CMake build so
|
||||
developers can run the tests directly on their workstation.
|
||||
developers can run the tests directly on their workstation.
|
||||
|
||||
NOTE: this is incomplete and only represents a small subset of tests that we run
|
||||
|
||||
|
|
|
|||
|
|
@ -302,7 +302,7 @@ files.
|
|||
|
||||
KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
|
||||
export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
|
||||
CC = mpicxx :pre
|
||||
CC = mpicxx :pre
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -802,7 +802,7 @@ dir, using a command like these, which simply invoke the
|
|||
lib/h5md/Install.py script with the specified args:
|
||||
|
||||
make lib-h5md # print help message
|
||||
make lib-hm5d args="-m h5cc" # build with h5cc compiler :pre
|
||||
make lib-h5md args="-m h5cc" # build with h5cc compiler :pre
|
||||
|
||||
The build should produce two files: lib/h5md/libch5md.a and
|
||||
lib/h5md/Makefile.lammps. The latter is copied from an existing
|
||||
|
|
@ -849,15 +849,15 @@ additional information.
|
|||
For CPUs:
|
||||
|
||||
OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high
|
||||
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
|
||||
LINKFLAGS = -g -qopenmp $(OPTFLAGS)
|
||||
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
|
||||
LINKFLAGS = -g -qopenmp $(OPTFLAGS)
|
||||
LIB = -ltbbmalloc :pre
|
||||
|
||||
For KNLs:
|
||||
|
||||
OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
|
||||
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
|
||||
LINKFLAGS = -g -qopenmp $(OPTFLAGS)
|
||||
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
|
||||
LINKFLAGS = -g -qopenmp $(OPTFLAGS)
|
||||
LIB = -ltbbmalloc :pre
|
||||
|
||||
:line
|
||||
|
|
|
|||
|
|
@ -12,6 +12,7 @@ Optional build settings :h3
|
|||
LAMMPS can be built with several optional settings. Each sub-section
|
||||
explain how to do this for building both with CMake and make.
|
||||
|
||||
"C++11 standard compliance test"_#cxx11 when building all of LAMMPS
|
||||
"FFT library"_#fft for use with the "kspace_style pppm"_kspace_style.html command
|
||||
"Size of LAMMPS data types"_#size
|
||||
"Read or write compressed files"_#gzip
|
||||
|
|
@ -23,6 +24,28 @@ explain how to do this for building both with CMake and make.
|
|||
|
||||
:line
|
||||
|
||||
C++11 standard compliance test :h4,link(cxx11)
|
||||
|
||||
The LAMMPS developers plan to transition to make the C++11 standard the
|
||||
minimum requirement for compiling LAMMPS. Currently this only applies to
|
||||
some packages like KOKKOS while the rest aims to be compatible with the C++98
|
||||
standard. Most currently used compilers are compatible with C++11; some need
|
||||
to set extra flags to switch. To determine the impact of requiring C++11,
|
||||
we have added a simple compliance test to the source code, that will cause
|
||||
the compilation to abort, if C++11 compliance is not available or enabled.
|
||||
To bypass this check, you need to change a setting in the makefile or
|
||||
when calling CMake.
|
||||
|
||||
[CMake variable]:
|
||||
|
||||
-D DISABLE_CXX11_REQUIREMENT=yes
|
||||
|
||||
[Makefile.machine setting]:
|
||||
|
||||
LMP_INC = -DLAMMPS_CXX98
|
||||
|
||||
:line
|
||||
|
||||
FFT library :h4,link(fft)
|
||||
|
||||
When the KSPACE package is included in a LAMMPS build, the
|
||||
|
|
|
|||
|
|
@ -166,6 +166,7 @@ OPT.
|
|||
"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
|
||||
"lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html,
|
||||
"lj96/cut (go)"_pair_lj96.html,
|
||||
"local/density"_pair_local_density.html,
|
||||
"lubricate (o)"_pair_lubricate.html,
|
||||
"lubricate/poly (o)"_pair_lubricate.html,
|
||||
"lubricateU"_pair_lubricateU.html,
|
||||
|
|
|
|||
Binary file not shown.
|
After Width: | Height: | Size: 14 KiB |
|
|
@ -0,0 +1,15 @@
|
|||
\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath, amssymb, graphics, setspace}
|
||||
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{equation}
|
||||
|| \vec{F} ||_{inf}
|
||||
= {\rm max}\left(|F_1^1|, |F_1^2|, |F_1^3| \cdots,
|
||||
|F_N^1|, |F_N^2|, |F_N^3|\right)
|
||||
\nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 9.2 KiB |
|
|
@ -0,0 +1,15 @@
|
|||
\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath, amssymb, graphics, setspace}
|
||||
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{equation}
|
||||
% \left| \left| \vec{F} \right| \right|_2
|
||||
|| \vec{F} ||_{max}
|
||||
= {\rm max}\left(||\vec{F}_1||, \cdots, ||\vec{F}_N||\right)
|
||||
\nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 5.9 KiB |
|
|
@ -0,0 +1,15 @@
|
|||
\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath, amssymb, graphics, setspace}
|
||||
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{equation}
|
||||
% \left| \left| \vec{F} \right| \right|_2
|
||||
|| \vec{F} ||_{2}
|
||||
= \sqrt{\vec{F}_1+ \cdots + \vec{F}_N}
|
||||
\nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 3.0 KiB |
|
|
@ -0,0 +1,11 @@
|
|||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
U_{LD} = \sum_i F(\rho_i)
|
||||
$$
|
||||
|
||||
|
||||
\end{document}
|
||||
~
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 7.8 KiB |
|
|
@ -0,0 +1,9 @@
|
|||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
U_{LD} = \sum_k U_{LD}^{(k)} = \sum_i \left[ \sum_k a_\alpha^{(k)} F^{(k)} \left(\rho_i^{(k)}\right) \right]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 3.4 KiB |
|
|
@ -0,0 +1,9 @@
|
|||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
U_{LD} = \sum_i a_\alpha F(\rho_i)
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 8.8 KiB |
|
|
@ -0,0 +1,16 @@
|
|||
\documentclass[12pt]{article}
|
||||
\usepackage[utf8]{inputenc}
|
||||
\usepackage{amsmath}
|
||||
\usepackage{amsfonts}
|
||||
|
||||
\begin{document}
|
||||
\[
|
||||
\varphi(r) =
|
||||
\begin{cases}
|
||||
1 & r \le R_1 \\
|
||||
c_0 + c_2r^2 + c_4r^4 + c_6r^6 & r \in (R_1, R_2) \\
|
||||
0 & r \ge R_2
|
||||
\end{cases}
|
||||
\]
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 3.0 KiB |
|
|
@ -0,0 +1,10 @@
|
|||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
|
||||
$$
|
||||
\rho_i = \sum_{j \neq i} \varphi(r_{ij})
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 4.2 KiB |
|
|
@ -0,0 +1,10 @@
|
|||
\documentstyle[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
|
||||
$$
|
||||
\rho_i^{(k)} = \sum_j b_\beta^{(k)} \varphi^{(k)} (r_{ij})
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 3.4 KiB |
|
|
@ -0,0 +1,10 @@
|
|||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
|
||||
$$
|
||||
\rho_i = \sum_{j \neq i} b_\beta \varphi(r_{ij})
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
|
|
@ -4791,6 +4791,22 @@ Self-explanatory. :dd
|
|||
|
||||
This fix option cannot be used with point particles. :dd
|
||||
|
||||
{Fix langevin gjf and respa are not compatible} :dt
|
||||
|
||||
Self-explanatory. :dd
|
||||
|
||||
{Fix langevin gjf cannot have period equal to dt/2} :dt
|
||||
|
||||
If the period is equal to dt/2 then division by zero will happen. :dd
|
||||
|
||||
{Fix langevin gjf should come before fix nve} :dt
|
||||
|
||||
Self-explanatory. :dd
|
||||
|
||||
{Fix langevin gjf with tbias is not yet implemented with kokkos} :dt
|
||||
|
||||
This option is not yet available. :dd
|
||||
|
||||
{Fix langevin omega is not yet implemented with kokkos} :dt
|
||||
|
||||
This option is not yet available. :dd
|
||||
|
|
|
|||
|
|
@ -248,6 +248,10 @@ included one or more of the following: kspace, triclinic, a hybrid
|
|||
pair style, an eam pair style, or no "single" function for the pair
|
||||
style. :dd
|
||||
|
||||
{Fix langevin gjf using random gaussians is not implemented with kokkos} :dt
|
||||
|
||||
This will most likely cause errors in kinetic fluctuations.
|
||||
|
||||
{Fix property/atom mol or charge w/out ghost communication} :dt
|
||||
|
||||
A model typically needs these properties defined for ghost atoms. :dd
|
||||
|
|
|
|||
|
|
@ -43,19 +43,19 @@ langevin/spin"_fix_langevin_spin.html. It allows to either dissipate
|
|||
the thermal energy of the Langevin thermostat, or to perform a
|
||||
relaxation of the magnetic configuration toward an equilibrium state.
|
||||
|
||||
The command "fix setforce/spin"_fix_setforce.html allows to set the
|
||||
components of the magnetic precession vectors (while erasing and
|
||||
replacing the previously computed magnetic precession vectors on
|
||||
the atom).
|
||||
This command can be used to freeze the magnetic moment of certain
|
||||
atoms in the simulation by zeroing their precession vector.
|
||||
The command "fix setforce/spin"_fix_setforce.html allows to set the
|
||||
components of the magnetic precession vectors (while erasing and
|
||||
replacing the previously computed magnetic precession vectors on
|
||||
the atom).
|
||||
This command can be used to freeze the magnetic moment of certain
|
||||
atoms in the simulation by zeroing their precession vector.
|
||||
|
||||
The command "fix nve/spin"_fix_nve_spin.html can be used to
|
||||
perform a symplectic integration of the combined dynamics of spins
|
||||
perform a symplectic integration of the combined dynamics of spins
|
||||
and atomic motions.
|
||||
|
||||
The minimization style "min/spin"_min_spin.html can be applied
|
||||
to the spins to perform a minimization of the spin configuration.
|
||||
to the spins to perform a minimization of the spin configuration.
|
||||
|
||||
|
||||
All the computed magnetic properties can be output by two main
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
<!-- HTML_ONLY -->
|
||||
<HEAD>
|
||||
<TITLE>LAMMPS Users Manual</TITLE>
|
||||
<META NAME="docnumber" CONTENT="7 Aug 2019 version">
|
||||
<META NAME="docnumber" CONTENT="19 Sep 2019 version">
|
||||
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
|
||||
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
|
||||
</HEAD>
|
||||
|
|
@ -21,7 +21,7 @@
|
|||
:line
|
||||
|
||||
LAMMPS Documentation :c,h1
|
||||
7 Aug 2019 version :c,h2
|
||||
19 Sep 2019 version :c,h2
|
||||
|
||||
"What is a LAMMPS version?"_Manual_version.html
|
||||
|
||||
|
|
|
|||
|
|
@ -46,14 +46,14 @@ software version 7.5 or later must be installed on your system. See
|
|||
the discussion for the "GPU package"_Speed_gpu.html for details of how
|
||||
to check and do this.
|
||||
|
||||
NOTE: Kokkos with CUDA currently implicitly assumes that the MPI library
|
||||
is CUDA-aware. This is not always the case, especially when using
|
||||
pre-compiled MPI libraries provided by a Linux distribution. This is not
|
||||
a problem when using only a single GPU with a single MPI rank. When
|
||||
running with multiple MPI ranks, you may see segmentation faults without
|
||||
CUDA-aware MPI support. These can be avoided by adding the flags "-pk
|
||||
kokkos cuda/aware off"_Run_options.html to the LAMMPS command line or by
|
||||
using the command "package kokkos cuda/aware off"_package.html in the
|
||||
NOTE: Kokkos with CUDA currently implicitly assumes that the MPI library
|
||||
is CUDA-aware. This is not always the case, especially when using
|
||||
pre-compiled MPI libraries provided by a Linux distribution. This is not
|
||||
a problem when using only a single GPU with a single MPI rank. When
|
||||
running with multiple MPI ranks, you may see segmentation faults without
|
||||
CUDA-aware MPI support. These can be avoided by adding the flags "-pk
|
||||
kokkos cuda/aware off"_Run_options.html to the LAMMPS command line or by
|
||||
using the command "package kokkos cuda/aware off"_package.html in the
|
||||
input file.
|
||||
|
||||
[Building LAMMPS with the KOKKOS package:]
|
||||
|
|
@ -110,10 +110,10 @@ Makefile.kokkos_mpi_only) will give better performance than the OpenMP
|
|||
back end (i.e. Makefile.kokkos_omp) because some of the overhead to make
|
||||
the code thread-safe is removed.
|
||||
|
||||
NOTE: Use the "-pk kokkos" "command-line switch"_Run_options.html to
|
||||
change the default "package kokkos"_package.html options. See its doc
|
||||
page for details and default settings. Experimenting with its options
|
||||
can provide a speed-up for specific calculations. For example:
|
||||
NOTE: Use the "-pk kokkos" "command-line switch"_Run_options.html to
|
||||
change the default "package kokkos"_package.html options. See its doc
|
||||
page for details and default settings. Experimenting with its options
|
||||
can provide a speed-up for specific calculations. For example:
|
||||
|
||||
mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj # Newton on, Half neighbor list, non-threaded comm :pre
|
||||
|
||||
|
|
@ -183,15 +183,15 @@ tasks/node. The "-k on t Nt" command-line switch sets the number of
|
|||
threads/task as Nt. The product of these two values should be N, i.e.
|
||||
256 or 264.
|
||||
|
||||
NOTE: The default for the "package kokkos"_package.html command when
|
||||
running on KNL is to use "half" neighbor lists and set the Newton flag
|
||||
to "on" for both pairwise and bonded interactions. This will typically
|
||||
be best for many-body potentials. For simpler pair-wise potentials, it
|
||||
may be faster to use a "full" neighbor list with Newton flag to "off".
|
||||
Use the "-pk kokkos" "command-line switch"_Run_options.html to change
|
||||
the default "package kokkos"_package.html options. See its doc page for
|
||||
details and default settings. Experimenting with its options can provide
|
||||
a speed-up for specific calculations. For example:
|
||||
NOTE: The default for the "package kokkos"_package.html command when
|
||||
running on KNL is to use "half" neighbor lists and set the Newton flag
|
||||
to "on" for both pairwise and bonded interactions. This will typically
|
||||
be best for many-body potentials. For simpler pair-wise potentials, it
|
||||
may be faster to use a "full" neighbor list with Newton flag to "off".
|
||||
Use the "-pk kokkos" "command-line switch"_Run_options.html to change
|
||||
the default "package kokkos"_package.html options. See its doc page for
|
||||
details and default settings. Experimenting with its options can provide
|
||||
a speed-up for specific calculations. For example:
|
||||
|
||||
mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm host -in in.reax # Newton on, half neighbor list, threaded comm
|
||||
mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton off neigh full comm no -in in.lj # Newton off, full neighbor list, non-threaded comm :pre
|
||||
|
|
@ -206,19 +206,19 @@ supports.
|
|||
|
||||
[Running on GPUs:]
|
||||
|
||||
Use the "-k" "command-line switch"_Run_options.html to specify the
|
||||
number of GPUs per node. Typically the -np setting of the mpirun command
|
||||
should set the number of MPI tasks/node to be equal to the number of
|
||||
physical GPUs on the node. You can assign multiple MPI tasks to the same
|
||||
GPU with the KOKKOS package, but this is usually only faster if some
|
||||
portions of the input script have not been ported to use Kokkos. In this
|
||||
case, also packing/unpacking communication buffers on the host may give
|
||||
speedup (see the KOKKOS "package"_package.html command). Using CUDA MPS
|
||||
Use the "-k" "command-line switch"_Run_options.html to specify the
|
||||
number of GPUs per node. Typically the -np setting of the mpirun command
|
||||
should set the number of MPI tasks/node to be equal to the number of
|
||||
physical GPUs on the node. You can assign multiple MPI tasks to the same
|
||||
GPU with the KOKKOS package, but this is usually only faster if some
|
||||
portions of the input script have not been ported to use Kokkos. In this
|
||||
case, also packing/unpacking communication buffers on the host may give
|
||||
speedup (see the KOKKOS "package"_package.html command). Using CUDA MPS
|
||||
is recommended in this scenario.
|
||||
|
||||
Using a CUDA-aware MPI library is highly recommended. CUDA-aware MPI use can be
|
||||
avoided by using "-pk kokkos cuda/aware no"_package.html. As above for
|
||||
multi-core CPUs (and no GPU), if N is the number of physical cores/node,
|
||||
Using a CUDA-aware MPI library is highly recommended. CUDA-aware MPI use can be
|
||||
avoided by using "-pk kokkos cuda/aware no"_package.html. As above for
|
||||
multi-core CPUs (and no GPU), if N is the number of physical cores/node,
|
||||
then the number of MPI tasks/node should not exceed N.
|
||||
|
||||
-k on g Ng :pre
|
||||
|
|
@ -229,18 +229,18 @@ one or more nodes, each with two GPUs:
|
|||
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 2 GPUs/node
|
||||
mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total) :pre
|
||||
|
||||
NOTE: The default for the "package kokkos"_package.html command when
|
||||
running on GPUs is to use "full" neighbor lists and set the Newton flag
|
||||
to "off" for both pairwise and bonded interactions, along with threaded
|
||||
communication. When running on Maxwell or Kepler GPUs, this will
|
||||
typically be best. For Pascal GPUs, using "half" neighbor lists and
|
||||
setting the Newton flag to "on" may be faster. For many pair styles,
|
||||
setting the neighbor binsize equal to twice the CPU default value will
|
||||
give speedup, which is the default when running on GPUs. Use the "-pk
|
||||
kokkos" "command-line switch"_Run_options.html to change the default
|
||||
"package kokkos"_package.html options. See its doc page for details and
|
||||
default settings. Experimenting with its options can provide a speed-up
|
||||
for specific calculations. For example:
|
||||
NOTE: The default for the "package kokkos"_package.html command when
|
||||
running on GPUs is to use "full" neighbor lists and set the Newton flag
|
||||
to "off" for both pairwise and bonded interactions, along with threaded
|
||||
communication. When running on Maxwell or Kepler GPUs, this will
|
||||
typically be best. For Pascal GPUs, using "half" neighbor lists and
|
||||
setting the Newton flag to "on" may be faster. For many pair styles,
|
||||
setting the neighbor binsize equal to twice the CPU default value will
|
||||
give speedup, which is the default when running on GPUs. Use the "-pk
|
||||
kokkos" "command-line switch"_Run_options.html to change the default
|
||||
"package kokkos"_package.html options. See its doc page for details and
|
||||
default settings. Experimenting with its options can provide a speed-up
|
||||
for specific calculations. For example:
|
||||
|
||||
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighbor list, set binsize = neighbor ghost cutoff :pre
|
||||
|
||||
|
|
|
|||
|
|
@ -76,9 +76,10 @@ Post-processing tools :h3
|
|||
"pymol_asphere"_#pymol,
|
||||
"python"_#pythontools,
|
||||
"reax"_#reax_tool,
|
||||
"replica"_#replica,
|
||||
"smd"_#smd,
|
||||
"spin"_#spin,
|
||||
"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l)
|
||||
"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l)
|
||||
|
||||
Miscellaneous tools :h3
|
||||
|
||||
|
|
@ -485,6 +486,21 @@ README for more info on Pizza.py and how to use these scripts.
|
|||
|
||||
:line
|
||||
|
||||
replica tool :h4,link(replica)
|
||||
|
||||
The tools/replica directory contains the reorder_remd_traj python script which
|
||||
can be used to reorder the replica trajectories (resulting from the use of the
|
||||
temper command) according to temperature. This will produce discontinuous
|
||||
trajectories with all frames at the same temperature in each trajectory.
|
||||
Additional options can be used to calculate the canonical configurational
|
||||
log-weight for each frame at each temperature using the pymbar package. See
|
||||
the README.md file for further details. Try out the peptide example provided.
|
||||
|
||||
This tool was written by (and is maintained by) Tanmoy Sanyal,
|
||||
while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com)
|
||||
|
||||
:line
|
||||
|
||||
reax tool :h4,link(reax_tool)
|
||||
|
||||
The reax sub-directory contains stand-alone codes that can
|
||||
|
|
@ -515,13 +531,13 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
|
|||
spin tool :h4,link(spin)
|
||||
|
||||
The spin sub-directory contains a C file interpolate.c which can
|
||||
be compiled and used to perform a cubic polynomial interpolation of
|
||||
be compiled and used to perform a cubic polynomial interpolation of
|
||||
the MEP following a GNEB calculation.
|
||||
|
||||
See the README file in tools/spin/interpolate_gneb for more details.
|
||||
|
||||
This tool was written by the SPIN package author, Julien
|
||||
Tranchida at Sandia National Labs (jtranch at sandia.gov, and by Aleksei
|
||||
Tranchida at Sandia National Labs (jtranch at sandia.gov, and by Aleksei
|
||||
Ivanov, at University of Iceland (ali5 at hi.is).
|
||||
|
||||
:line
|
||||
|
|
@ -549,3 +565,4 @@ simulation.
|
|||
See the README file for details.
|
||||
|
||||
These files were provided by Vikas Varshney (vv0210 at gmail.com)
|
||||
|
||||
|
|
|
|||
|
|
@ -244,7 +244,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
|
|||
"plasticity/atom"_compute_plasticity_atom.html - Peridynamic plasticity for each atom
|
||||
"pressure"_compute_pressure.html - total pressure and pressure tensor
|
||||
"pressure/cylinder"_compute_pressure_cylinder.html - pressure tensor in cylindrical coordinates
|
||||
"pressure/uef"_compute_pressure_uef.html - pressure tensor in the reference frame of an applied flow field
|
||||
"pressure/uef"_compute_pressure_uef.html - pressure tensor in the reference frame of an applied flow field
|
||||
"property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays
|
||||
"property/chunk"_compute_property_chunk.html - extract various per-chunk attributes
|
||||
"property/local"_compute_property_local.html - convert local attributes to localvectors/arrays
|
||||
|
|
@ -284,7 +284,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
|
|||
"stress/mop"_compute_stress_mop.html - normal components of the local stress tensor using the method of planes
|
||||
"stress/mop/profile"_compute_stress_mop.html - profile of the normal components of the local stress tensor using the method of planes
|
||||
"stress/tally"_compute_tally.html -
|
||||
"tdpd/cc/atom"_compute_tdpd_cc_atom.html - per-atom chemical concentration of a specified species for each tDPD particle
|
||||
"tdpd/cc/atom"_compute_tdpd_cc_atom.html - per-atom chemical concentration of a specified species for each tDPD particle
|
||||
"temp"_compute_temp.html - temperature of group of atoms
|
||||
"temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles
|
||||
"temp/body"_compute_temp_body.html - temperature of body particles
|
||||
|
|
|
|||
|
|
@ -47,7 +47,7 @@ neighboring atoms, unless selected by type, type range, or group option,
|
|||
are included in the coordination number tally.
|
||||
|
||||
The optional {group} keyword allows to specify from which group atoms
|
||||
contribute to the coordination number. Default setting is group 'all'.
|
||||
contribute to the coordination number. Default setting is group 'all'.
|
||||
|
||||
The {typeN} keywords allow specification of which atom types
|
||||
contribute to each coordination number. One coordination number is
|
||||
|
|
|
|||
|
|
@ -34,7 +34,7 @@ compute 2 all hma 1 u cv :pre
|
|||
|
||||
Define a computation that calculates the properties of a solid (potential
|
||||
energy, pressure or heat capacity), using the harmonically-mapped averaging
|
||||
(HMA) method.
|
||||
(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,
|
||||
|
|
@ -52,7 +52,7 @@ 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
|
||||
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.
|
||||
|
|
@ -64,8 +64,8 @@ the list of pair styles that currently implement pair_hessian:
|
|||
: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.
|
||||
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\}
|
||||
|
|
@ -74,9 +74,9 @@ A detailed description of this method can be found in ("Moustafa"_#hma-Moustafa)
|
|||
|
||||
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.
|
||||
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:
|
||||
|
||||
|
|
@ -118,30 +118,30 @@ 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.
|
||||
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.
|
||||
|
||||
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
|
||||
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
|
||||
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
|
||||
|
|
@ -180,5 +180,5 @@ this compute.
|
|||
: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},
|
||||
[(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
|
||||
|
|
|
|||
|
|
@ -76,14 +76,14 @@ parameters up to {Q}12 for a range of commonly encountered
|
|||
high-symmetry structures are given in Table I of "Mickel et
|
||||
al."_#Mickel, and these can be reproduced with this compute
|
||||
|
||||
The optional keyword {wl} will output the third-order invariants {Wl}
|
||||
The optional keyword {wl} will output the third-order invariants {Wl}
|
||||
(see Eq. 1.4 in "Steinhardt"_#Steinhardt) for the same degrees as
|
||||
for the {Ql} parameters. For the FCC crystal with {nnn} =12,
|
||||
{W}4 = -sqrt(14/143).(49/4096)/Pi^1.5 = -0.0006722136...
|
||||
|
||||
The optional keyword {wl/hat} will output the normalized third-order
|
||||
invariants {Wlhat} (see Eq. 2.2 in "Steinhardt"_#Steinhardt)
|
||||
for the same degrees as for the {Ql} parameters. For the FCC crystal
|
||||
The optional keyword {wl/hat} will output the normalized third-order
|
||||
invariants {Wlhat} (see Eq. 2.2 in "Steinhardt"_#Steinhardt)
|
||||
for the same degrees as for the {Ql} parameters. For the FCC crystal
|
||||
with {nnn} =12, {W}4hat = -7/3*sqrt(2/429) = -0.159317...The numerical
|
||||
values of {Wlhat} for a range of commonly encountered high-symmetry
|
||||
structures are given in Table I of "Steinhardt"_#Steinhardt, and these
|
||||
|
|
@ -127,9 +127,9 @@ range 0 <= {Ql} <= 1.
|
|||
If the keyword {wl} is set to yes, then the {Wl} values for each
|
||||
atom will be added to the output array, which are real numbers.
|
||||
|
||||
If the keyword {wl/hat} is set to yes, then the {Wl_hat}
|
||||
If the keyword {wl/hat} is set to yes, then the {Wl_hat}
|
||||
values for each atom will be added to the output array, which are real numbers.
|
||||
|
||||
|
||||
If the keyword {components} is set, then the real and imaginary parts
|
||||
of each component of (normalized) {Ybar_lm} will be added to the
|
||||
output array in the following order: Re({Ybar_-m}) Im({Ybar_-m})
|
||||
|
|
|
|||
|
|
@ -64,6 +64,23 @@ which calculate the tangential force between two particles and return
|
|||
its components and magnitude acting on atom I for N = 1,2,3,4. See
|
||||
individual pair styles for details.
|
||||
|
||||
When using {pN} with pair style {hybrid}, the output will be the Nth
|
||||
quantity from the sub-style that computes the pairwise interaction
|
||||
(based on atom types). If that sub-style does not define a {pN},
|
||||
the output will be 0.0. The maximum allowed N is the maximum number
|
||||
of quantities provided by any sub-style.
|
||||
|
||||
When using {pN} with pair style {hybrid/overlay} the quantities
|
||||
from all sub-styles that provide them are concatenated together
|
||||
into one long list. For example, if there are 3 sub-styles and
|
||||
2 of them have additional output (with 3 and 4 quantities,
|
||||
respectively), then 7 values ({p1} up to {p7}) are defined.
|
||||
The values {p1} to {p3} refer to quantities defined by the first
|
||||
of the two sub-styles. Values {p4} to {p7} refer to quantities
|
||||
from the second of the two sub-styles. If the referenced {pN}
|
||||
is not computed for the specific pairwise interaction (based on
|
||||
atom types), then the output will be 0.0.
|
||||
|
||||
The value {dist} will be in distance "units"_units.html. The value
|
||||
{eng} will be in energy "units"_units.html. The values {force}, {fx},
|
||||
{fy}, and {fz} will be in force "units"_units.html. The values {pN}
|
||||
|
|
@ -126,7 +143,7 @@ options.
|
|||
The output for {dist} will be in distance "units"_units.html. The
|
||||
output for {eng} will be in energy "units"_units.html. The output for
|
||||
{force}, {fx}, {fy}, and {fz} will be in force "units"_units.html.
|
||||
The outpur for {pN} will be in whatever units the pair style defines.
|
||||
The output for {pN} will be in whatever units the pair style defines.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
|
|
|
|||
|
|
@ -196,7 +196,7 @@ for j1 in range(0,twojmax+1):
|
|||
if (j>=j1): print j1/2.,j2/2.,j/2. :pre
|
||||
|
||||
NOTE: the {diagonal} keyword allowing other possible choices
|
||||
for the number of bispectrum components was removed in 2019,
|
||||
for the number of bispectrum components was removed in 2019,
|
||||
since all potentials use the value of 3, corresponding to the
|
||||
above set of bispectrum components.
|
||||
|
||||
|
|
|
|||
|
|
@ -40,14 +40,14 @@ The simplest way to output the results of the compute spin calculation
|
|||
is to define some of the quantities as variables, and to use the thermo and
|
||||
thermo_style commands, for example:
|
||||
|
||||
compute out_mag all spin :pre
|
||||
compute out_mag all spin :pre
|
||||
|
||||
variable mag_z equal c_out_mag\[3\]
|
||||
variable mag_norm equal c_out_mag\[4\]
|
||||
variable temp_mag equal c_out_mag\[6\] :pre
|
||||
variable mag_z equal c_out_mag\[3\]
|
||||
variable mag_norm equal c_out_mag\[4\]
|
||||
variable temp_mag equal c_out_mag\[6\] :pre
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step v_mag_z v_mag_norm v_temp_mag :pre
|
||||
thermo 10
|
||||
thermo_style custom step v_mag_z v_mag_norm v_temp_mag :pre
|
||||
|
||||
This series of commands evaluates the total magnetization along z, the norm of
|
||||
the total magnetization, and the magnetic temperature. Three variables are
|
||||
|
|
|
|||
|
|
@ -21,7 +21,8 @@ dump ID group-ID style N file args :pre
|
|||
|
||||
ID = user-assigned name for the dump :ulb,l
|
||||
group-ID = ID of the group of atoms to be dumped :l
|
||||
style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or {local} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l
|
||||
style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or
|
||||
{cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or {local} or {local/gz} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l
|
||||
N = dump every this many timesteps :l
|
||||
file = name of file to write dump info to :l
|
||||
args = list of arguments for a particular style :l
|
||||
|
|
|
|||
|
|
@ -50,6 +50,7 @@ keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fi
|
|||
{sfactor} arg = coordinate scaling factor (> 0.0)
|
||||
{thermo} arg = {yes} or {no}
|
||||
{tfactor} arg = time scaling factor (> 0.0)
|
||||
{units} arg = {yes} or {no}
|
||||
{sort} arg = {off} or {id} or N or -N
|
||||
off = no sorting of per-atom lines within a snapshot
|
||||
id = sort per-atom lines by atom ID
|
||||
|
|
@ -620,6 +621,21 @@ threshold criterion is met. Otherwise it is not met.
|
|||
|
||||
:line
|
||||
|
||||
The {units} keyword only applies to the dump {atom}, {custom}, and
|
||||
{local} styles (and their COMPRESS package versions {atom/gz},
|
||||
{custom/gz} and {local/gz}). If set to {yes}, each individual dump
|
||||
file will contain two extra lines at the very beginning with:
|
||||
|
||||
ITEM: UNITS
|
||||
\<units style\> :pre
|
||||
|
||||
This will output the current selected "units"_units.html style
|
||||
to the dump file and thus allows visualization and post-processing
|
||||
tools to determine the choice of units of the data in the dump file.
|
||||
The default setting is {no}.
|
||||
|
||||
:line
|
||||
|
||||
The {unwrap} keyword only applies to the dump {dcd} and {xtc} styles.
|
||||
If set to {yes}, coordinates will be written "unwrapped" by the image
|
||||
flags for each atom. Unwrapped means that if the atom has passed through
|
||||
|
|
@ -924,6 +940,7 @@ scale = yes
|
|||
sort = off for dump styles {atom}, {custom}, {cfg}, and {local}
|
||||
sort = id for dump styles {dcd}, {xtc}, and {xyz}
|
||||
thresh = none
|
||||
units = no
|
||||
unwrap = no :ul
|
||||
|
||||
acolor = * red/green/blue/yellow/aqua/cyan
|
||||
|
|
|
|||
|
|
@ -52,4 +52,4 @@ provided by Pair's single_hessian.
|
|||
|
||||
[Default:]
|
||||
|
||||
The default settings are file = "dynmat.dyn", binary = no
|
||||
The default settings are file = "dynmat.dyn", binary = no
|
||||
|
|
|
|||
|
|
@ -221,7 +221,7 @@ accelerated styles exist.
|
|||
"heat"_fix_heat.html - add/subtract momentum-conserving heat
|
||||
"hyper/global"_fix_hyper_global.html - global hyperdynamics
|
||||
"hyper/local"_fix_hyper_local.html - local hyperdynamics
|
||||
"imd"_fix_imd.html - implements the “Interactive MD” (IMD) protocol
|
||||
"imd"_fix_imd.html - implements the “Interactive MD” (IMD) protocol
|
||||
"indent"_fix_indent.html - impose force due to an indenter
|
||||
"ipi"_fix_ipi.html - enable LAMMPS to run as a client for i-PI path-integral simulations
|
||||
"langevin"_fix_langevin.html - Langevin temperature control
|
||||
|
|
@ -327,7 +327,7 @@ accelerated styles exist.
|
|||
"rigid/nvt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration
|
||||
"rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration
|
||||
"rx"_fix_rx.html -
|
||||
"saed/vtk"_fix_saed_vtk.html -
|
||||
"saed/vtk"_fix_saed_vtk.html -
|
||||
"setforce"_fix_setforce.html - set the force on each atom
|
||||
"shake"_fix_shake.html - SHAKE constraints on bonds and/or angles
|
||||
"shardlow"_fix_shardlow.html - integration of DPD equations of motion using the Shardlow splitting
|
||||
|
|
|
|||
|
|
@ -186,20 +186,25 @@ reacting atoms.
|
|||
|
||||
Some atoms in the pre-reacted template that are not reacting may have
|
||||
missing topology with respect to the simulation. For example, the
|
||||
pre-reacted template may contain an atom that would connect to the
|
||||
rest of a long polymer chain. These are referred to as edge atoms, and
|
||||
are also specified in the map file. When the pre-reaction template
|
||||
contains edge atoms, not all atoms, bonds, charges, etc. specified in
|
||||
the reaction templates will be updated. Specifically, topology that
|
||||
involves only atoms that are 'too near' to template edges will not be
|
||||
updated. The definition of 'too near the edge' depends on which
|
||||
interactions are defined in the simulation. If the simulation has
|
||||
defined dihedrals, atoms within two bonds of edge atoms are considered
|
||||
'too near the edge.' If the simulation defines angles, but not
|
||||
dihedrals, atoms within one bond of edge atoms are considered 'too
|
||||
near the edge.' If just bonds are defined, only edge atoms are
|
||||
pre-reacted template may contain an atom that, in the simulation, is
|
||||
currently connected to the rest of a long polymer chain. These are
|
||||
referred to as edge atoms, and are also specified in the map file. All
|
||||
pre-reaction template atoms should be linked to a bonding atom, via at
|
||||
least one path that does not involve edge atoms. When the pre-reaction
|
||||
template contains edge atoms, not all atoms, bonds, charges, etc.
|
||||
specified in the reaction templates will be updated. Specifically,
|
||||
topology that involves only atoms that are 'too near' to template
|
||||
edges will not be updated. The definition of 'too near the edge'
|
||||
depends on which interactions are defined in the simulation. If the
|
||||
simulation has defined dihedrals, atoms within two bonds of edge atoms
|
||||
are considered 'too near the edge.' If the simulation defines angles,
|
||||
but not dihedrals, atoms within one bond of edge atoms are considered
|
||||
'too near the edge.' If just bonds are defined, only edge atoms are
|
||||
considered 'too near the edge.'
|
||||
|
||||
NOTE: Small molecules, i.e. ones that have all their atoms contained
|
||||
within the reaction templates, never have edge atoms.
|
||||
|
||||
Note that some care must be taken when a building a molecule template
|
||||
for a given simulation. All atom types in the pre-reacted template
|
||||
must be the same as those of a potential reaction site in the
|
||||
|
|
@ -261,7 +266,7 @@ either 'none' or 'charges.' Further details are provided in the
|
|||
discussion of the 'update_edges' keyword. The fourth optional section
|
||||
begins with the keyword 'Constraints' and lists additional criteria
|
||||
that must be satisfied in order for the reaction to occur. Currently,
|
||||
there is one type of constraint available, as discussed below.
|
||||
there are two types of constraints available, as discussed below.
|
||||
|
||||
A sample map file is given below:
|
||||
|
||||
|
|
@ -295,14 +300,23 @@ Equivalences :pre
|
|||
:line
|
||||
|
||||
Any number of additional constraints may be specified in the
|
||||
Constraints section of the map file. Currently there is one type of
|
||||
additional constraint, of type 'distance', whose syntax is as follows:
|
||||
Constraints section of the map file. The constraint of type 'distance'
|
||||
has syntax as follows:
|
||||
|
||||
distance {ID1} {ID2} {rmin} {rmax} :pre
|
||||
|
||||
where 'distance' is the required keyword, {ID1} and {ID2} are
|
||||
pre-reaction atom IDs, and these two atoms must be separated by a
|
||||
distance between {rmin} and {rmax} for the reaction to occur. This
|
||||
distance between {rmin} and {rmax} for the reaction to occur.
|
||||
|
||||
The constraint of type 'angle' has the following syntax:
|
||||
|
||||
angle {ID1} {ID2} {ID3} {amin} {amax} :pre
|
||||
|
||||
where 'angle' is the required keyword, {ID1}, {ID2} and {ID3} are
|
||||
pre-reaction atom IDs, and these three atoms must form an angle
|
||||
between {amin} and {amax} for the reaction to occur (where {ID2} is
|
||||
the central atom). Angles must be specified in degrees. This
|
||||
constraint can be used to enforce a certain orientation between
|
||||
reacting molecules.
|
||||
|
||||
|
|
@ -392,10 +406,11 @@ local command.
|
|||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html, aside from internally-created per-atom
|
||||
properties. None of the "fix_modify"_fix_modify.html options are
|
||||
relevant to this fix.
|
||||
Cumulative reaction counts for each reaction are written to "binary
|
||||
restart files"_restart.html. These values are associated with the
|
||||
reaction name (react-ID). Additionally, internally-created per-atom
|
||||
properties are stored to allow for smooth restarts. None of the
|
||||
"fix_modify"_fix_modify.html options are relevant to this fix.
|
||||
|
||||
This fix computes one statistic for each {react} argument that it
|
||||
stores in a global vector, of length 'number of react arguments', that
|
||||
|
|
@ -406,8 +421,8 @@ These is 1 quantity for each react argument:
|
|||
|
||||
(1) cumulative # of reactions occurred :ul
|
||||
|
||||
No parameter of this fix can be used with the {start/stop} keywords of
|
||||
the "run"_run.html command. This fix is not invoked during "energy
|
||||
No parameter of this fix can be used with the {start/stop} keywords
|
||||
of the "run"_run.html command. This fix is not invoked during "energy
|
||||
minimization"_minimize.html.
|
||||
|
||||
When fix bond/react is 'unfixed,' all internally-created groups are
|
||||
|
|
@ -417,18 +432,20 @@ all other fixes that use any group created by fix bond/react.
|
|||
[Restrictions:]
|
||||
|
||||
This fix is part of the USER-MISC package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
LAMMPS was built with that package. See the
|
||||
"Build package"_Build_package.html doc page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix bond/create"_fix_bond_create.html, "fix
|
||||
bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html,
|
||||
"fix bond/create"_fix_bond_create.html,
|
||||
"fix bond/break"_fix_bond_break.html,
|
||||
"fix bond/swap"_fix_bond_swap.html,
|
||||
"dump local"_dump.html, "special_bonds"_special_bonds.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60, update_edges = none
|
||||
The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60,
|
||||
update_edges = none
|
||||
|
||||
:line
|
||||
|
||||
|
|
|
|||
|
|
@ -31,7 +31,6 @@ cvar = name of control variable :l
|
|||
|
||||
[Examples:]
|
||||
|
||||
|
||||
fix 1 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol
|
||||
fix 1 all controller 100 0.2 0.5 0 100.0 v_pxxwall 1.01325 xwall
|
||||
fix 1 all controller 10000 0.2 0.5 0 2000 v_avpe -3.785 tcontrol :pre
|
||||
|
|
|
|||
|
|
@ -24,9 +24,10 @@ keyword = {angmom} or {omega} or {scale} or {tally} or {zero} :l
|
|||
{angmom} value = {no} or factor
|
||||
{no} = do not thermostat rotational degrees of freedom via the angular momentum
|
||||
factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below
|
||||
{gjf} value = {no} or {yes}
|
||||
{gjf} value = {no} or {vfull} or {vhalf}
|
||||
{no} = use standard formulation
|
||||
{yes} = use Gronbech-Jensen/Farago formulation
|
||||
{vfull} = use Gronbech-Jensen/Farago formulation
|
||||
{vhalf} = use 2GJ formulation
|
||||
{omega} value = {no} or {yes}
|
||||
{no} = do not thermostat rotational degrees of freedom via the angular velocity
|
||||
{yes} = do thermostat rotational degrees of freedom via the angular velocity
|
||||
|
|
@ -217,6 +218,10 @@ the particles. As described below, this energy can then be printed
|
|||
out or added to the potential energy of the system to monitor energy
|
||||
conservation.
|
||||
|
||||
NOTE: this accumulated energy does NOT include kinetic energy removed
|
||||
by the {zero} flag. LAMMPS will print a warning when both options are
|
||||
active.
|
||||
|
||||
The keyword {zero} can be used to eliminate drift due to the
|
||||
thermostat. Because the random forces on different atoms are
|
||||
independent, they do not sum exactly to zero. As a result, this fix
|
||||
|
|
@ -232,29 +237,24 @@ The keyword {gjf} can be used to run the "Gronbech-Jensen/Farago
|
|||
described in the papers cited below, the purpose of this method is to
|
||||
enable longer timesteps to be used (up to the numerical stability
|
||||
limit of the integrator), while still producing the correct Boltzmann
|
||||
distribution of atom positions. It is implemented within LAMMPS, by
|
||||
changing how the random force is applied so that it is composed of
|
||||
the average of two random forces representing half-contributions from
|
||||
the previous and current time intervals.
|
||||
distribution of atom positions.
|
||||
|
||||
In common with all methods based on Verlet integration, the
|
||||
discretized velocities generated by this method in conjunction with
|
||||
velocity-Verlet time integration are not exactly conjugate to the
|
||||
positions. As a result the temperature (computed from the discretized
|
||||
velocities) will be systematically lower than the target temperature,
|
||||
by a small amount which grows with the timestep. Nonetheless, the
|
||||
distribution of atom positions will still be consistent with the
|
||||
The current implementation provides the user with the option to output
|
||||
the velocity in one of two forms: {vfull} or {vhalf}, which replaces
|
||||
the outdated option {yes}. The {gjf} option {vfull} outputs the on-site
|
||||
velocity given in "Gronbech-Jensen/Farago"_#Gronbech-Jensen; this velocity
|
||||
is shown to be systematically lower than the target temperature by a small
|
||||
amount, which grows quadratically with the timestep.
|
||||
The {gjf} option {vhalf} outputs the 2GJ half-step velocity given in
|
||||
"Gronbech Jensen/Gronbech-Jensen"_#2Gronbech-Jensen; this velocity is shown
|
||||
to not have any linear statistical errors for any stable time step.
|
||||
An overview of statistically correct Boltzmann and Maxwell-Boltzmann
|
||||
sampling of true on-site and true half-step velocities is given in
|
||||
"Gronbech-Jensen_#1Gronbech-Jensen.
|
||||
Regardless of the choice of output velocity, the sampling of the configurational
|
||||
distribution of atom positions is the same, and linearly consistent with the
|
||||
target temperature.
|
||||
|
||||
As an example of using the {gjf} keyword, for molecules containing C-H
|
||||
bonds, configurational properties generated with dt = 2.5 fs and tdamp
|
||||
= 100 fs are indistinguishable from dt = 0.5 fs. Because the velocity
|
||||
distribution systematically decreases with increasing timestep, the
|
||||
method should not be used to generate properties that depend on the
|
||||
velocity distribution, such as the velocity auto-correlation function
|
||||
(VACF). In this example, the velocity distribution at dt = 2.5fs
|
||||
generates an average temperature of 220 K, instead of 300 K.
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
|
|
@ -312,7 +312,10 @@ This fix can ramp its target temperature over multiple runs, using the
|
|||
|
||||
This fix is not invoked during "energy minimization"_minimize.html.
|
||||
|
||||
[Restrictions:] none
|
||||
[Restrictions:]
|
||||
|
||||
For {gjf} do not choose damp=dt/2. {gjf} is not compatible
|
||||
with run_style respa.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
@ -335,5 +338,10 @@ types, tally = no, zero = no, gjf = no.
|
|||
|
||||
:link(Gronbech-Jensen)
|
||||
[(Gronbech-Jensen)] Gronbech-Jensen and Farago, Mol Phys, 111, 983
|
||||
(2013); Gronbech-Jensen, Hayre, and Farago, Comp Phys Comm,
|
||||
185, 524 (2014)
|
||||
(2013); Gronbech-Jensen, Hayre, and Farago, Comp Phys Comm, 185, 524 (2014)
|
||||
|
||||
:link(2Gronbech-Jensen)
|
||||
[(Gronbech-Jensen)] Gronbech Jensen and Gronbech-Jensen, Mol Phys, 117, 2511 (2019)
|
||||
|
||||
:link(1Gronbech-Jensen)
|
||||
[(Gronbech-Jensen)] Gronbech-Jensen, Mol Phys (2019); https://doi.org/10.1080/00268976.2019.1662506
|
||||
|
|
|
|||
|
|
@ -50,7 +50,7 @@ As an example:
|
|||
|
||||
fix 1 all precession/spin zeeman 0.01 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 300.0 0.01 21
|
||||
fix 3 all nve/spin lattice yes :pre
|
||||
fix 3 all nve/spin lattice moving :pre
|
||||
|
||||
is correct, but defining a force/spin command after the langevin/spin command
|
||||
would give an error message.
|
||||
|
|
|
|||
|
|
@ -24,18 +24,18 @@ fix 1 active neb/spin 1.0
|
|||
[Description:]
|
||||
|
||||
Add nudging forces to spins in the group for a multi-replica
|
||||
simulation run via the "neb/spin"_neb_spin.html command to perform a
|
||||
geodesic nudged elastic band (GNEB) calculation for finding the
|
||||
simulation run via the "neb/spin"_neb_spin.html command to perform a
|
||||
geodesic nudged elastic band (GNEB) calculation for finding the
|
||||
transition state.
|
||||
Hi-level explanations of GNEB are given with the
|
||||
"neb/spin"_neb_spin.html command and on the
|
||||
"Howto replica"_Howto_replica.html doc page.
|
||||
The fix neb/spin command must be used with the "neb/spin" command and
|
||||
defines how inter-replica nudging forces are computed. A GNEB
|
||||
calculation is divided in two stages. In the first stage n replicas
|
||||
are relaxed toward a MEP until convergence. In the second stage, the
|
||||
climbing image scheme is enabled, so that the replica having the highest
|
||||
energy relaxes toward the saddle point (i.e. the point of highest energy
|
||||
Hi-level explanations of GNEB are given with the
|
||||
"neb/spin"_neb_spin.html command and on the
|
||||
"Howto replica"_Howto_replica.html doc page.
|
||||
The fix neb/spin command must be used with the "neb/spin" command and
|
||||
defines how inter-replica nudging forces are computed. A GNEB
|
||||
calculation is divided in two stages. In the first stage n replicas
|
||||
are relaxed toward a MEP until convergence. In the second stage, the
|
||||
climbing image scheme is enabled, so that the replica having the highest
|
||||
energy relaxes toward the saddle point (i.e. the point of highest energy
|
||||
along the MEP), and a second relaxation is performed.
|
||||
|
||||
The nudging forces are calculated as explained in
|
||||
|
|
|
|||
|
|
@ -15,22 +15,26 @@ fix ID group-ID nve/spin keyword values :pre
|
|||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
nve/spin = style name of this fix command :l
|
||||
keyword = {lattice} :l
|
||||
{lattice} value = {no} or {yes} :pre
|
||||
{lattice} value = {moving} or {frozen}
|
||||
moving = integrate both spin and atomic degress of freedom
|
||||
frozen = integrate spins on a fixed lattice :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
fix 1 all nve/spin lattice no :pre
|
||||
fix 3 all nve/spin lattice moving
|
||||
fix 1 all nve/spin lattice frozen :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Perform a symplectic integration for the spin or spin-lattice system.
|
||||
|
||||
The {lattice} keyword defines if the spins are integrated on a lattice
|
||||
of fixed atoms (lattice = no), or if atoms are moving (lattice = yes).
|
||||
|
||||
By default (lattice = yes), a spin-lattice integration is performed.
|
||||
of fixed atoms (lattice = frozen), or if atoms are moving
|
||||
(lattice = moving).
|
||||
The first case corresponds to a spin dynamics calculation, and
|
||||
the second to a spin-lattice calculation.
|
||||
By default a spin-lattice integration is performed (lattice = moving).
|
||||
|
||||
The {nve/spin} fix applies a Suzuki-Trotter decomposition to
|
||||
the equations of motion of the spin lattice system, following the scheme:
|
||||
|
|
@ -63,7 +67,9 @@ instead of "array" is also valid.
|
|||
|
||||
"atom_style spin"_atom_style.html, "fix nve"_fix_nve.html
|
||||
|
||||
[Default:] none
|
||||
[Default:]
|
||||
|
||||
The option default is lattice = moving.
|
||||
|
||||
:line
|
||||
|
||||
|
|
|
|||
|
|
@ -21,7 +21,7 @@ style = {zeeman} or {anisotropy} or {cubic} :l
|
|||
{anisotropy} args = K x y z
|
||||
K = intensity of the magnetic anisotropy (in eV)
|
||||
x y z = vector direction of the anisotropy :pre
|
||||
{cubic} args = K1 K2c n1x n1y n1x n2x n2y n2z n3x n3y n3z
|
||||
{cubic} args = K1 K2c n1x n1y n1x n2x n2y n2z n3x n3y n3z
|
||||
K1 and K2c = intensity of the magnetic anisotropy (in eV)
|
||||
n1x to n3z = three direction vectors of the cubic anisotropy :pre
|
||||
:ule
|
||||
|
|
@ -55,24 +55,24 @@ with n defining the direction of the anisotropy, and K (in eV) its intensity.
|
|||
If K>0, an easy axis is defined, and if K<0, an easy plane is defined.
|
||||
|
||||
Style {cubic} is used to simulate a cubic anisotropy, with three
|
||||
possible easy axis for the magnetic spins in the defined group:
|
||||
possible easy axis for the magnetic spins in the defined group:
|
||||
|
||||
:c,image(Eqs/fix_spin_cubic.jpg)
|
||||
|
||||
with K1 and K2c (in eV) the intensity coefficients and
|
||||
with K1 and K2c (in eV) the intensity coefficients and
|
||||
n1, n2 and n3 defining the three anisotropic directions
|
||||
defined by the command (from n1x to n3z).
|
||||
For n1 = (100), n2 = (010), and n3 = (001), K1 < 0 defines an
|
||||
defined by the command (from n1x to n3z).
|
||||
For n1 = (100), n2 = (010), and n3 = (001), K1 < 0 defines an
|
||||
iron type anisotropy (easy axis along the (001)-type cube
|
||||
edges), and K1 > 0 defines a nickel type anisotropy (easy axis
|
||||
along the (111)-type cube diagonals).
|
||||
along the (111)-type cube diagonals).
|
||||
K2^c > 0 also defines easy axis along the (111)-type cube
|
||||
diagonals.
|
||||
See chapter 2 of "(Skomski)"_#Skomski1 for more details on cubic
|
||||
anisotropies.
|
||||
|
||||
In all cases, the choice of (x y z) only imposes the vector
|
||||
directions for the forces. Only the direction of the vector is
|
||||
directions for the forces. Only the direction of the vector is
|
||||
important; it's length is ignored (the entered vectors are
|
||||
normalized).
|
||||
|
||||
|
|
|
|||
|
|
@ -44,7 +44,7 @@ fix 1 rods rigid/meso molecule
|
|||
fix 1 spheres rigid/meso single force 1 off off on
|
||||
fix 1 particles rigid/meso molecule force 1*5 off off off force 6*10 off off on
|
||||
fix 2 spheres rigid/meso group 3 sphere1 sphere2 sphere3 torque * off off off :pre
|
||||
|
||||
|
||||
[Description:]
|
||||
|
||||
Treat one or more sets of mesoscopic SPH/SDPD particles as independent
|
||||
|
|
|
|||
|
|
@ -67,15 +67,15 @@ to it.
|
|||
|
||||
:line
|
||||
|
||||
Style {spin} suffix sets the components of the magnetic precession
|
||||
vectors instead of the mechanical forces. This also erases all
|
||||
previously computed magnetic precession vectors on the atom, though
|
||||
Style {spin} suffix sets the components of the magnetic precession
|
||||
vectors instead of the mechanical forces. This also erases all
|
||||
previously computed magnetic precession vectors on the atom, though
|
||||
additional magnetic fixes could add new forces.
|
||||
|
||||
This command can be used to freeze the magnetic moment of certain
|
||||
atoms in the simulation by zeroing their precession vector.
|
||||
This command can be used to freeze the magnetic moment of certain
|
||||
atoms in the simulation by zeroing their precession vector.
|
||||
|
||||
All options defined above remain valid, they just apply to the magnetic
|
||||
All options defined above remain valid, they just apply to the magnetic
|
||||
precession vectors instead of the forces.
|
||||
|
||||
:line
|
||||
|
|
@ -132,7 +132,7 @@ forces to any value besides zero when performing a minimization. Use
|
|||
the "fix addforce"_fix_addforce.html command if you want to apply a
|
||||
non-zero force to atoms during a minimization.
|
||||
|
||||
[Restrictions:]
|
||||
[Restrictions:]
|
||||
|
||||
The fix {setforce/spin} only makes sense when LAMMPS was built with the
|
||||
SPIN package.
|
||||
|
|
|
|||
|
|
@ -16,7 +16,7 @@ improper_style fourier :pre
|
|||
[Examples:]
|
||||
|
||||
improper_style fourier
|
||||
improper_coeff 1 100.0 180.0 :pre
|
||||
improper_coeff 1 100.0 0.0 1.0 0.5 1 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
|
@ -24,12 +24,12 @@ The {fourier} improper style uses the following potential:
|
|||
|
||||
:c,image(Eqs/improper_fourier.jpg)
|
||||
|
||||
where K is the force constant and omega is the angle between the IL
|
||||
axis and the IJK plane:
|
||||
where K is the force constant, C0, C1, C2 are dimensionless coefficients,
|
||||
and omega is the angle between the IL axis and the IJK plane:
|
||||
|
||||
:c,image(JPG/umbrella.jpg)
|
||||
|
||||
If all parameter (see bellow) is not zero, the all the three possible angles will taken in account.
|
||||
If all parameter (see below) is not zero, the all the three possible angles will taken in account.
|
||||
|
||||
The following coefficients must be defined for each improper type via
|
||||
the "improper_coeff"_improper_coeff.html command as in the example
|
||||
|
|
@ -38,10 +38,10 @@ above, or in the data file or restart files read by the
|
|||
commands:
|
||||
|
||||
K (energy)
|
||||
C0 (real)
|
||||
C1 (real)
|
||||
C2 (real)
|
||||
all (integer >= 0) :ul
|
||||
C0 (unitless)
|
||||
C1 (unitless)
|
||||
C2 (unitless)
|
||||
all (0 or 1, optional) :ul
|
||||
|
||||
:line
|
||||
|
||||
|
|
|
|||
|
|
@ -116,10 +116,10 @@ used without a cutoff, i.e. they become full long-range potentials.
|
|||
The {ewald/disp} style can also be used with point-dipoles, see
|
||||
"(Toukmaji)"_#Toukmaji.
|
||||
|
||||
The {ewald/dipole} style adds long-range standard Ewald summations
|
||||
The {ewald/dipole} style adds long-range standard Ewald summations
|
||||
for dipole-dipole interactions, see "(Toukmaji)"_#Toukmaji.
|
||||
|
||||
The {ewald/dipole/spin} style adds long-range standard Ewald
|
||||
The {ewald/dipole/spin} style adds long-range standard Ewald
|
||||
summations for magnetic dipole-dipole interactions between
|
||||
magnetic spins.
|
||||
|
||||
|
|
@ -142,11 +142,11 @@ The optional {smallq} argument defines the cutoff for the absolute
|
|||
charge value which determines whether a particle is considered charged
|
||||
or not. Its default value is 1.0e-5.
|
||||
|
||||
The {pppm/dipole} style invokes a particle-particle particle-mesh solver
|
||||
The {pppm/dipole} style invokes a particle-particle particle-mesh solver
|
||||
for dipole-dipole interactions, following the method of "(Cerda)"_#Cerda2008.
|
||||
|
||||
The {pppm/dipole/spin} style invokes a particle-particle particle-mesh solver
|
||||
for magnetic dipole-dipole interactions between magnetic spins.
|
||||
The {pppm/dipole/spin} style invokes a particle-particle particle-mesh solver
|
||||
for magnetic dipole-dipole interactions between magnetic spins.
|
||||
|
||||
The {pppm/tip4p} style is identical to the {pppm} style except that it
|
||||
adds a charge at the massless 4th site in each TIP4P water molecule.
|
||||
|
|
|
|||
|
|
@ -611,6 +611,7 @@ pair_lj_smooth.html
|
|||
pair_lj_smooth_linear.html
|
||||
pair_fep_soft.html
|
||||
pair_lj_switch3_coulgauss.html
|
||||
pair_local_density.html
|
||||
pair_lubricate.html
|
||||
pair_lubricateU.html
|
||||
pair_mdf.html
|
||||
|
|
|
|||
|
|
@ -13,11 +13,15 @@ min_modify command :h3
|
|||
min_modify keyword values ... :pre
|
||||
|
||||
one or more keyword/value pairs may be listed :ulb,l
|
||||
keyword = {dmax} or {line} or {alpha_damp} or {discrete_factor}
|
||||
keyword = {dmax} or {line} or {norm} or {alpha_damp} or {discrete_factor}
|
||||
{dmax} value = max
|
||||
max = maximum distance for line search to move (distance units)
|
||||
{line} value = {backtrack} or {quadratic} or {forcezero}
|
||||
backtrack,quadratic,forcezero = style of linesearch to use
|
||||
{line} value = {backtrack} or {quadratic} or {forcezero} or {spin_cubic} or {spin_none}
|
||||
backtrack,quadratic,forcezero,spin_cubic,spin_none = style of linesearch to use
|
||||
{norm} value = {two} or {max}
|
||||
two = Euclidean two-norm (length of 3N vector)
|
||||
inf = max force component across all 3-vectors
|
||||
max = max force norm across all 3-vectors
|
||||
{alpha_damp} value = damping
|
||||
damping = fictitious Gilbert damping for spin minimization (adim)
|
||||
{discrete_factor} value = factor
|
||||
|
|
@ -69,18 +73,54 @@ difference of two large values (energy before and energy after) and
|
|||
that difference may be smaller than machine epsilon even if atoms
|
||||
could move in the gradient direction to reduce forces further.
|
||||
|
||||
The choice of a norm can be modified for the min styles {cg}, {sd},
|
||||
{quickmin}, {fire}, {spin}, {spin/cg} and {spin/lbfgs} using
|
||||
the {norm} keyword.
|
||||
The default {two} norm computes the 2-norm (Euclidean length) of the
|
||||
global force vector:
|
||||
|
||||
:c,image(Eqs/norm_two.jpg)
|
||||
|
||||
The {max} norm computes the length of the 3-vector force
|
||||
for each atom (2-norm), and takes the maximum value of those across
|
||||
all atoms
|
||||
|
||||
:c,image(Eqs/norm_max.jpg)
|
||||
|
||||
The {inf} norm takes the maximum component across the forces of
|
||||
all atoms in the system:
|
||||
|
||||
:c,image(Eqs/norm_inf.jpg)
|
||||
|
||||
For the min styles {spin}, {spin/cg} and {spin/lbfgs}, the force
|
||||
norm is replaced by the spin-torque norm.
|
||||
|
||||
Keywords {alpha_damp} and {discrete_factor} only make sense when
|
||||
a "min_spin"_min_spin.html command is declared.
|
||||
a "min_spin"_min_spin.html command is declared.
|
||||
Keyword {alpha_damp} defines an analog of a magnetic Gilbert
|
||||
damping. It defines a relaxation rate toward an equilibrium for
|
||||
a given magnetic system.
|
||||
a given magnetic system.
|
||||
Keyword {discrete_factor} defines a discretization factor for the
|
||||
adaptive timestep used in the {spin} minimization.
|
||||
adaptive timestep used in the {spin} minimization.
|
||||
See "min_spin"_min_spin.html for more information about those
|
||||
quantities.
|
||||
Default values are {alpha_damp} = 1.0 and {discrete_factor} = 10.0.
|
||||
|
||||
[Restrictions:] none
|
||||
The choice of a line search algorithm for the {spin/cg} and
|
||||
{spin/lbfgs} styles can be specified via the {line} keyword.
|
||||
The {spin_cubic} and {spin_none} only make sense when one of those
|
||||
two minimization styles is declared.
|
||||
The {spin_cubic} performs the line search based on a cubic interpolation
|
||||
of the energy along the search direction. The {spin_none} keyword
|
||||
deactivates the line search procedure.
|
||||
The {spin_none} is a default value for {line} keyword for both {spin/lbfgs}
|
||||
and {spin/cg}. Convergence of {spin/lbfgs} can be more robust if
|
||||
{spin_cubic} line search is used.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
For magnetic GNEB calculations, only {spin_none} value for {line} keyword can be used
|
||||
when styles {spin/cg} and {spin/lbfgs} are employed.
|
||||
See "neb/spin"_neb_spin.html for more explanation.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
@ -88,4 +128,8 @@ Default values are {alpha_damp} = 1.0 and {discrete_factor} = 10.0.
|
|||
|
||||
[Default:]
|
||||
|
||||
The option defaults are dmax = 0.1 and line = quadratic.
|
||||
The option defaults are dmax = 0.1, line = quadratic and norm = two.
|
||||
|
||||
For the {spin}, {spin/cg} and {spin/lbfgs} styles, the
|
||||
option defaults are alpha_damp = 1.0, discrete_factor = 10.0,
|
||||
line = spin_none, and norm = euclidean.
|
||||
|
|
|
|||
|
|
@ -6,14 +6,19 @@
|
|||
:line
|
||||
|
||||
min_style spin command :h3
|
||||
min_style spin/cg command :h3
|
||||
min_style spin/lbfgs command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
min_style spin :pre
|
||||
min_style spin
|
||||
min_style spin/cg
|
||||
min_style spin/lbfgs :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
min_style spin :pre
|
||||
min_style spin/lbfgs
|
||||
min_modify line spin_cubic discrete_factor 10.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
|
@ -27,28 +32,57 @@ timestep, according to:
|
|||
|
||||
with lambda a damping coefficient (similar to a Gilbert
|
||||
damping).
|
||||
Lambda can be defined by setting the {alpha_damp} keyword with the
|
||||
"min_modify"_min_modify.html command.
|
||||
Lambda can be defined by setting the {alpha_damp} keyword with the
|
||||
"min_modify"_min_modify.html command.
|
||||
|
||||
The minimization procedure solves this equation using an
|
||||
adaptive timestep. The value of this timestep is defined
|
||||
by the largest precession frequency that has to be solved in the
|
||||
adaptive timestep. The value of this timestep is defined
|
||||
by the largest precession frequency that has to be solved in the
|
||||
system:
|
||||
|
||||
:c,image(Eqs/min_spin_timestep.jpg)
|
||||
|
||||
with {|omega|_{max}} the norm of the largest precession frequency
|
||||
in the system (across all processes, and across all replicas if a
|
||||
spin/neb calculation is performed).
|
||||
spin/neb calculation is performed).
|
||||
|
||||
Kappa defines a discretization factor {discrete_factor} for the
|
||||
definition of this timestep.
|
||||
Kappa defines a discretization factor {discrete_factor} for the
|
||||
definition of this timestep.
|
||||
{discrete_factor} can be defined with the "min_modify"_min_modify.html
|
||||
command.
|
||||
|
||||
NOTE: The {spin} style replaces the force tolerance by a torque
|
||||
Style {spin/cg} defines an orthogonal spin optimization
|
||||
(OSO) combined to a conjugate gradient (CG) algorithm.
|
||||
The "min_modify"_min_modify.html command can be used to
|
||||
couple the {spin/cg} to a line search procedure, and to modify the
|
||||
discretization factor {discrete_factor}.
|
||||
By default, style {spin/cg} does not employ the line search procedure
|
||||
and uses the adaptive time-step technique in the same way as style {spin}.
|
||||
|
||||
Style {spin/lbfgs} defines an orthogonal spin optimization
|
||||
(OSO) combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno
|
||||
(L-BFGS) algorithm.
|
||||
By default, style {spin/lbfgs} does not employ line search procedure.
|
||||
If the line search procedure is not used then the discrete factor defines
|
||||
the maximum root mean squared rotation angle of spins by equation {pi/(5*Kappa)}.
|
||||
The default value for Kappa is 10.
|
||||
The {spin_cubic} line search can improve the convergence of the
|
||||
{spin/lbfgs} algorithm.
|
||||
|
||||
The "min_modify"_min_modify.html command can be used to
|
||||
activate the line search procedure, and to modify the
|
||||
discretization factor {discrete_factor}.
|
||||
|
||||
For more information about styles {spin/cg} and {spin/lbfgs},
|
||||
see their implementation reported in "(Ivanov)"_#Ivanov1.
|
||||
|
||||
NOTE: All the {spin} styles replace the force tolerance by a torque
|
||||
tolerance. See "minimize"_minimize.html for more explanation.
|
||||
|
||||
NOTE: The {spin/cg} and {spin/lbfgs} styles can be used
|
||||
for magnetic NEB calculations only if the line search procedure
|
||||
is deactivated. See "neb/spin"_neb_spin.html for more explanation.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This minimization procedure is only applied to spin degrees of
|
||||
|
|
@ -56,10 +90,15 @@ freedom for a frozen lattice configuration.
|
|||
|
||||
[Related commands:]
|
||||
|
||||
"min_style"_min_style.html, "minimize"_minimize.html,
|
||||
"min_style"_min_style.html, "minimize"_minimize.html,
|
||||
"min_modify"_min_modify.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The option defaults are {alpha_damp} = 1.0 and {discrete_factor} =
|
||||
10.0.
|
||||
The option defaults are {alpha_damp} = 1.0, {discrete_factor} =
|
||||
10.0, {line} = spin_none and {norm} = euclidean.
|
||||
|
||||
:line
|
||||
|
||||
:link(Ivanov1)
|
||||
[(Ivanov)] Ivanov, Uzdin, Jonsson. arXiv preprint arXiv:1904.02669, (2019).
|
||||
|
|
|
|||
|
|
@ -11,7 +11,7 @@ min_style command :h3
|
|||
|
||||
min_style style :pre
|
||||
|
||||
style = {cg} or {cg/kk} or {hftn} or {sd} or {quickmin} or {fire} or {spin} :ul
|
||||
style = {cg} or {hftn} or {sd} or {quickmin} or {fire} or {spin} or {spin/cg} or {spin/lbfgs} :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
|
|
@ -62,22 +62,36 @@ the velocity non-parallel to the current force vector. The velocity
|
|||
of each atom is initialized to 0.0 by this style, at the beginning of
|
||||
a minimization.
|
||||
|
||||
Style {spin} is a damped spin dynamics with an adaptive
|
||||
Style {spin} is a damped spin dynamics with an adaptive
|
||||
timestep.
|
||||
See the "min/spin"_min_spin.html doc page for more information.
|
||||
|
||||
Style {spin/cg} uses an orthogonal spin optimization (OSO)
|
||||
combined to a conjugate gradient (CG) approach to minimize spin
|
||||
configurations.
|
||||
|
||||
Style {spin/lbfgs} uses an orthogonal spin optimization (OSO)
|
||||
combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno
|
||||
(LBFGS) approach to minimize spin configurations.
|
||||
|
||||
See the "min/spin"_min_spin.html doc page for more information
|
||||
about the {spin}, {spin/cg} and {spin/lbfgs} styles.
|
||||
|
||||
Either the {quickmin} and {fire} styles are useful in the context of
|
||||
nudged elastic band (NEB) calculations via the "neb"_neb.html command.
|
||||
|
||||
Either the {spin}, {spin/cg} and {spin/lbfgs} styles are useful
|
||||
in the context of magnetic geodesic nudged elastic band (GNEB) calculations
|
||||
via the "neb/spin"_neb_spin.html command.
|
||||
|
||||
NOTE: The damped dynamic minimizers use whatever timestep you have
|
||||
defined via the "timestep"_timestep.html command. Often they will
|
||||
converge more quickly if you use a timestep about 10x larger than you
|
||||
would normally use for dynamics simulations.
|
||||
|
||||
NOTE: The {quickmin}, {fire}, {hftn}, and {cg/kk} styles do not yet
|
||||
support the use of the "fix box/relax"_fix_box_relax.html command or
|
||||
minimizations involving the electron radius in "eFF"_pair_eff.html
|
||||
models.
|
||||
NOTE: The {quickmin}, {fire}, {hftn}, and {cg/kk} styles do not yet
|
||||
support the use of the "fix box/relax"_fix_box_relax.html command or
|
||||
minimizations involving the electron radius in "eFF"_pair_eff.html
|
||||
models.
|
||||
|
||||
:line
|
||||
|
||||
|
|
|
|||
|
|
@ -104,12 +104,13 @@ the line search fails because the step distance backtracks to 0.0
|
|||
the number of outer iterations or timesteps exceeds {maxiter}
|
||||
the number of total force evaluations exceeds {maxeval} :ul
|
||||
|
||||
NOTE: the "minimization style"_min_style.html {spin} replaces
|
||||
NOTE: the "minimization style"_min_style.html {spin},
|
||||
{spin/cg}, and {spin/lbfgs} replace
|
||||
the force tolerance {ftol} by a torque tolerance.
|
||||
The minimization procedure stops if the 2-norm (length) of the
|
||||
global torque vector (defined as the cross product between the
|
||||
spins and their precession vectors omega) is less than {ftol},
|
||||
or if any of the other criteria are met.
|
||||
The minimization procedure stops if the 2-norm (length) of the torque vector on atom
|
||||
(defined as the cross product between the
|
||||
atomic spin and its precession vectors omega) is less than {ftol},
|
||||
or if any of the other criteria are met. Torque have the same units as the energy.
|
||||
|
||||
NOTE: You can also use the "fix halt"_fix_halt.html command to specify
|
||||
a general criterion for exiting a minimization, that is a calculation
|
||||
|
|
|
|||
|
|
@ -45,7 +45,7 @@ and last are the end points of the transition path.
|
|||
GNEB is a method for finding both the spin configurations and height
|
||||
of the energy barrier associated with a transition state, e.g.
|
||||
spins to perform a collective rotation from one energy basin to
|
||||
another.
|
||||
another.
|
||||
The implementation in LAMMPS follows the discussion in the
|
||||
following paper: "(BessarabA)"_#BessarabA.
|
||||
|
||||
|
|
@ -59,35 +59,35 @@ performance speed-up you would see with one or more physical
|
|||
processors per replica. See the "Howto replica"_Howto_replica.html
|
||||
doc page for further discussion.
|
||||
|
||||
NOTE: As explained below, a GNEB calculation performs a damped dynamics
|
||||
minimization across all the replicas. The "spin"_min_spin.html
|
||||
style minimizer has to be defined in your input script.
|
||||
NOTE: As explained below, a GNEB calculation performs a
|
||||
minimization across all the replicas. One of the "spin"_min_spin.html
|
||||
style minimizers has to be defined in your input script.
|
||||
|
||||
When a GNEB calculation is performed, it is assumed that each replica
|
||||
is running the same system, though LAMMPS does not check for this.
|
||||
I.e. the simulation domain, the number of magnetic atoms, the
|
||||
interaction potentials, and the starting configuration when the neb
|
||||
I.e. the simulation domain, the number of magnetic atoms, the
|
||||
interaction potentials, and the starting configuration when the neb
|
||||
command is issued should be the same for every replica.
|
||||
|
||||
In a GNEB calculation each replica is connected to other replicas by
|
||||
inter-replica nudging forces. These forces are imposed by the "fix
|
||||
neb/spin"_fix_neb_spin.html command, which must be used in conjunction
|
||||
with the neb command.
|
||||
neb/spin"_fix_neb_spin.html command, which must be used in conjunction
|
||||
with the neb command.
|
||||
The group used to define the fix neb/spin command defines the
|
||||
GNEB magnetic atoms which are the only ones that inter-replica springs
|
||||
are applied to.
|
||||
GNEB magnetic atoms which are the only ones that inter-replica springs
|
||||
are applied to.
|
||||
If the group does not include all magnetic atoms, then non-GNEB
|
||||
magnetic atoms have no inter-replica springs and the torques they feel
|
||||
and their precession motion is computed in the usual way due only
|
||||
to other magnetic atoms within their replica.
|
||||
Conceptually, the non-GNEB atoms provide a background force field for
|
||||
the GNEB atoms.
|
||||
Their magnetic spins can be allowed to evolve during the GNEB
|
||||
magnetic atoms have no inter-replica springs and the torques they feel
|
||||
and their precession motion is computed in the usual way due only
|
||||
to other magnetic atoms within their replica.
|
||||
Conceptually, the non-GNEB atoms provide a background force field for
|
||||
the GNEB atoms.
|
||||
Their magnetic spins can be allowed to evolve during the GNEB
|
||||
minimization procedure.
|
||||
|
||||
The initial spin configuration for each of the replicas can be
|
||||
specified in different manners via the {file-style} setting, as
|
||||
discussed below. Only atomic spins whose initial coordinates should
|
||||
discussed below. Only atomic spins whose initial coordinates should
|
||||
differ from the current configuration need to be specified.
|
||||
|
||||
Conceptually, the initial and final configurations for the first
|
||||
|
|
@ -106,21 +106,21 @@ closer to the MEP and read them in.
|
|||
:line
|
||||
|
||||
For a {file-style} setting of {final}, a filename is specified which
|
||||
contains atomic and spin coordinates for zero or more atoms, in the
|
||||
format described below.
|
||||
For each atom that appears in the file, the new coordinates are
|
||||
assigned to that atom in the final replica. Each intermediate replica
|
||||
also assigns a new spin to that atom in an interpolated manner.
|
||||
This is done by using the current direction of the spin at the starting
|
||||
point and the read-in direction as the final point.
|
||||
The "angular distance" between them is calculated, and the new direction
|
||||
contains atomic and spin coordinates for zero or more atoms, in the
|
||||
format described below.
|
||||
For each atom that appears in the file, the new coordinates are
|
||||
assigned to that atom in the final replica. Each intermediate replica
|
||||
also assigns a new spin to that atom in an interpolated manner.
|
||||
This is done by using the current direction of the spin at the starting
|
||||
point and the read-in direction as the final point.
|
||||
The "angular distance" between them is calculated, and the new direction
|
||||
is assigned to be a fraction of the angular distance.
|
||||
|
||||
NOTE: The "angular distance" between the starting and final point is
|
||||
evaluated in the geodesic sense, as described in
|
||||
"(BessarabA)"_#BessarabA.
|
||||
NOTE: The "angular distance" between the starting and final point is
|
||||
evaluated in the geodesic sense, as described in
|
||||
"(BessarabA)"_#BessarabA.
|
||||
|
||||
NOTE: The angular interpolation between the starting and final point
|
||||
NOTE: The angular interpolation between the starting and final point
|
||||
is achieved using Rodrigues formula:
|
||||
|
||||
:c,image(Eqs/neb_spin_rodrigues_formula.jpg)
|
||||
|
|
@ -130,7 +130,7 @@ omega_i^nu is a rotation angle defined as:
|
|||
|
||||
:c,image(Eqs/neb_spin_angle.jpg)
|
||||
|
||||
with nu the image number, Q the total number of images, and
|
||||
with nu the image number, Q the total number of images, and
|
||||
omega_i the total rotation between the initial and final spins.
|
||||
k_i defines a rotation axis such as:
|
||||
|
||||
|
|
@ -139,16 +139,16 @@ k_i defines a rotation axis such as:
|
|||
if the initial and final spins are not aligned.
|
||||
If the initial and final spins are aligned, then their cross
|
||||
product is null, and the expression above does not apply.
|
||||
If they point toward the same direction, the intermediate images
|
||||
If they point toward the same direction, the intermediate images
|
||||
conserve the same orientation.
|
||||
If the initial and final spins are aligned, but point toward
|
||||
opposite directions, an arbitrary rotation vector belonging to
|
||||
the plane perpendicular to initial and final spins is chosen.
|
||||
the plane perpendicular to initial and final spins is chosen.
|
||||
In this case, a warning message is displayed.
|
||||
|
||||
For a {file-style} setting of {each}, a filename is specified which is
|
||||
assumed to be unique to each replica.
|
||||
See the "neb"_neb.html documentation page for more information about this
|
||||
assumed to be unique to each replica.
|
||||
See the "neb"_neb.html documentation page for more information about this
|
||||
option.
|
||||
|
||||
For a {file-style} setting of {none}, no filename is specified. Each
|
||||
|
|
@ -170,9 +170,10 @@ command is issued.
|
|||
:line
|
||||
|
||||
A NEB calculation proceeds in two stages, each of which is a
|
||||
minimization procedure, performed via damped dynamics. To enable
|
||||
this, you must first define a damped spin dynamics
|
||||
"min_style"_min_style.html, using the {spin} style (see
|
||||
minimization procedure. To enable
|
||||
this, you must first define a
|
||||
"min_style"_min_style.html, using either the {spin},
|
||||
{spin/cg}, or {spin/lbfgs} style (see
|
||||
"min_spin"_min_spin.html for more information).
|
||||
The other styles cannot be used, since they relax the lattice
|
||||
degrees of freedom instead of the spins.
|
||||
|
|
@ -195,9 +196,9 @@ damped dynamics is like a single timestep in a dynamics
|
|||
replica and its normalized distance along the reaction path (reaction
|
||||
coordinate RD) will be printed to the screen and log file every
|
||||
{Nevery} timesteps. The RD is 0 and 1 for the first and last replica.
|
||||
For intermediate replicas, it is the cumulative angular distance
|
||||
(normalized by the total cumulative angular distance) between adjacent
|
||||
replicas, where "distance" is defined as the length of the 3N-vector of
|
||||
For intermediate replicas, it is the cumulative angular distance
|
||||
(normalized by the total cumulative angular distance) between adjacent
|
||||
replicas, where "distance" is defined as the length of the 3N-vector of
|
||||
the geodesic distances in spin coordinates, with N the number of
|
||||
GNEB spins involved (see equation (13) in "(BessarabA)"_#BessarabA).
|
||||
These outputs allow you to monitor NEB's progress in
|
||||
|
|
@ -207,11 +208,11 @@ of {Nevery}.
|
|||
In the first stage of GNEB, the set of replicas should converge toward
|
||||
a minimum energy path (MEP) of conformational states that transition
|
||||
over a barrier. The MEP for a transition is defined as a sequence of
|
||||
3N-dimensional spin states, each of which has a potential energy
|
||||
gradient parallel to the MEP itself.
|
||||
The configuration of highest energy along a MEP corresponds to a saddle
|
||||
point. The replica states will also be roughly equally spaced along
|
||||
the MEP due to the inter-replica nudging force added by the
|
||||
3N-dimensional spin states, each of which has a potential energy
|
||||
gradient parallel to the MEP itself.
|
||||
The configuration of highest energy along a MEP corresponds to a saddle
|
||||
point. The replica states will also be roughly equally spaced along
|
||||
the MEP due to the inter-replica nudging force added by the
|
||||
"fix neb"_fix_neb.html command.
|
||||
|
||||
In the second stage of GNEB, the replica with the highest energy is
|
||||
|
|
@ -234,12 +235,12 @@ An atom map must be defined which it is not by default for "atom_style
|
|||
atomic"_atom_style.html problems. The "atom_modify
|
||||
map"_atom_modify.html command can be used to do this.
|
||||
|
||||
An initial value can be defined for the timestep. Although, the {spin}
|
||||
minimization algorithm is an adaptive timestep methodology, so that
|
||||
this timestep is likely to evolve during the calculation.
|
||||
An initial value can be defined for the timestep. Although, the {spin}
|
||||
minimization algorithm is an adaptive timestep methodology, so that
|
||||
this timestep is likely to evolve during the calculation.
|
||||
|
||||
The minimizers in LAMMPS operate on all spins in your system, even
|
||||
non-GNEB atoms, as defined above.
|
||||
non-GNEB atoms, as defined above.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -257,7 +258,7 @@ ID2 g2 x2 y2 z2 sx2 sy2 sz2
|
|||
...
|
||||
IDN gN yN zN sxN syN szN :pre
|
||||
|
||||
The fields are the atom ID, the norm of the associated magnetic spin,
|
||||
The fields are the atom ID, the norm of the associated magnetic spin,
|
||||
followed by the {x,y,z} coordinates and the {sx,sy,sz} spin coordinates.
|
||||
The lines can be listed in any order. Additional trailing information on
|
||||
the line is OK, such as a comment.
|
||||
|
|
@ -290,22 +291,22 @@ reaction coordinate and potential energy of each replica.
|
|||
|
||||
The "maximum torque per replica" is the two-norm of the
|
||||
3N-length vector given by the cross product of a spin by its
|
||||
precession vector omega, in each replica, maximized across replicas,
|
||||
precession vector omega, in each replica, maximized across replicas,
|
||||
which is what the {ttol} setting is checking against. In this case, N is
|
||||
all the atoms in each replica. The "maximum torque per atom" is the
|
||||
maximum torque component of any atom in any replica. The potential
|
||||
gradients are the two-norm of the 3N-length magnetic precession vector
|
||||
solely due to the interaction potential i.e. without adding in
|
||||
inter-replica forces, and projected along the path tangent (as detailed
|
||||
gradients are the two-norm of the 3N-length magnetic precession vector
|
||||
solely due to the interaction potential i.e. without adding in
|
||||
inter-replica forces, and projected along the path tangent (as detailed
|
||||
in Appendix D of "(BessarabA)"_#BessarabA).
|
||||
|
||||
The "reaction coordinate" (RD) for each replica is the two-norm of the
|
||||
3N-length vector of geodesic distances between its spins and the preceding
|
||||
replica's spins (see equation (13) of "(BessarabA)"_#BessarabA), added to
|
||||
the RD of the preceding replica. The RD of the first replica RD1 = 0.0;
|
||||
the RD of the final replica RDN = RDT, the total reaction coordinate.
|
||||
The normalized RDs are divided by RDT, so that they form a monotonically
|
||||
increasing sequence from zero to one. When computing RD, N only includes
|
||||
replica's spins (see equation (13) of "(BessarabA)"_#BessarabA), added to
|
||||
the RD of the preceding replica. The RD of the first replica RD1 = 0.0;
|
||||
the RD of the final replica RDN = RDT, the total reaction coordinate.
|
||||
The normalized RDs are divided by RDT, so that they form a monotonically
|
||||
increasing sequence from zero to one. When computing RD, N only includes
|
||||
the spins being operated on by the fix neb/spin command.
|
||||
|
||||
The forward (reverse) energy barrier is the potential energy of the
|
||||
|
|
@ -313,17 +314,17 @@ highest replica minus the energy of the first (last) replica.
|
|||
|
||||
Supplementary information for all replicas can be printed out to the
|
||||
screen and master log.lammps file by adding the verbose keyword. This
|
||||
information include the following.
|
||||
The "GradVidottan" are the projections of the potential gradient for
|
||||
the replica i on its tangent vector (as detailed in Appendix D of
|
||||
information include the following.
|
||||
The "GradVidottan" are the projections of the potential gradient for
|
||||
the replica i on its tangent vector (as detailed in Appendix D of
|
||||
"(BessarabA)"_#BessarabA).
|
||||
The "DNi" are the non normalized geodesic distances (see equation (13)
|
||||
of "(BessarabA)"_#BessarabA), between a replica i and the next replica
|
||||
The "DNi" are the non normalized geodesic distances (see equation (13)
|
||||
of "(BessarabA)"_#BessarabA), between a replica i and the next replica
|
||||
i+1. For the last replica, this distance is not defined and a "NAN"
|
||||
value is the corresponding output.
|
||||
value is the corresponding output.
|
||||
|
||||
When a NEB calculation does not converge properly, the supplementary
|
||||
information can help understanding what is going wrong.
|
||||
information can help understanding what is going wrong.
|
||||
|
||||
When running on multiple partitions, LAMMPS produces additional log
|
||||
files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a
|
||||
|
|
@ -346,9 +347,9 @@ restart the calculation from an intermediate point with altered
|
|||
parameters.
|
||||
|
||||
A c file script in provided in the tool/spin/interpolate_gneb
|
||||
directory, that interpolates the MEP given the information provided
|
||||
directory, that interpolates the MEP given the information provided
|
||||
by the verbose output option (as detailed in Appendix D of
|
||||
"(BessarabA)"_#BessarabA).
|
||||
"(BessarabA)"_#BessarabA).
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -358,6 +359,9 @@ This command can only be used if LAMMPS was built with the SPIN
|
|||
package. See the "Build package"_Build_package.html doc
|
||||
page for more info.
|
||||
|
||||
For magnetic GNEB calculations, only {spin_none} value for {line} keyword can be used
|
||||
when styles {spin/cg} and {spin/lbfgs} are employed.
|
||||
|
||||
:line
|
||||
|
||||
[Related commands:]
|
||||
|
|
|
|||
|
|
@ -423,115 +423,115 @@ processes/threads used for LAMMPS.
|
|||
|
||||
:line
|
||||
|
||||
The {kokkos} style invokes settings associated with the use of the
|
||||
KOKKOS package.
|
||||
The {kokkos} style invokes settings associated with the use of the
|
||||
KOKKOS package.
|
||||
|
||||
All of the settings are optional keyword/value pairs. Each has a default
|
||||
value as listed below.
|
||||
All of the settings are optional keyword/value pairs. Each has a default
|
||||
value as listed below.
|
||||
|
||||
The {neigh} keyword determines how neighbor lists are built. A value of
|
||||
{half} uses a thread-safe variant of half-neighbor lists, the same as
|
||||
used by most pair styles in LAMMPS, which is the default when running on
|
||||
CPUs (i.e. the Kokkos CUDA back end is not enabled).
|
||||
The {neigh} keyword determines how neighbor lists are built. A value of
|
||||
{half} uses a thread-safe variant of half-neighbor lists, the same as
|
||||
used by most pair styles in LAMMPS, which is the default when running on
|
||||
CPUs (i.e. the Kokkos CUDA back end is not enabled).
|
||||
|
||||
A value of {full} uses a full neighbor lists and is the default when
|
||||
running on GPUs. This performs twice as much computation as the {half}
|
||||
option, however that is often a win because it is thread-safe and
|
||||
doesn't require atomic operations in the calculation of pair forces. For
|
||||
that reason, {full} is the default setting for GPUs. However, when
|
||||
running on CPUs, a {half} neighbor list is the default because it are
|
||||
often faster, just as it is for non-accelerated pair styles. Similarly,
|
||||
the {neigh/qeq} keyword determines how neighbor lists are built for "fix
|
||||
qeq/reax/kk"_fix_qeq_reax.html. If not explicitly set, the value of
|
||||
A value of {full} uses a full neighbor lists and is the default when
|
||||
running on GPUs. This performs twice as much computation as the {half}
|
||||
option, however that is often a win because it is thread-safe and
|
||||
doesn't require atomic operations in the calculation of pair forces. For
|
||||
that reason, {full} is the default setting for GPUs. However, when
|
||||
running on CPUs, a {half} neighbor list is the default because it are
|
||||
often faster, just as it is for non-accelerated pair styles. Similarly,
|
||||
the {neigh/qeq} keyword determines how neighbor lists are built for "fix
|
||||
qeq/reax/kk"_fix_qeq_reax.html. If not explicitly set, the value of
|
||||
{neigh/qeq} will match {neigh}.
|
||||
|
||||
If the {neigh/thread} keyword is set to {off}, then the KOKKOS package
|
||||
threads only over atoms. However, for small systems, this may not expose
|
||||
enough parallelism to keep a GPU busy. When this keyword is set to {on},
|
||||
the KOKKOS package threads over both atoms and neighbors of atoms. When
|
||||
using {neigh/thread} {on}, a full neighbor list must also be used. Using
|
||||
{neigh/thread} {on} may be slower for large systems, so this this option
|
||||
is turned on by default only when there are 16K atoms or less owned by
|
||||
an MPI rank and when using a full neighbor list. Not all KOKKOS-enabled
|
||||
potentials support this keyword yet, and only thread over atoms. Many
|
||||
simple pair-wise potentials such as Lennard-Jones do support threading
|
||||
If the {neigh/thread} keyword is set to {off}, then the KOKKOS package
|
||||
threads only over atoms. However, for small systems, this may not expose
|
||||
enough parallelism to keep a GPU busy. When this keyword is set to {on},
|
||||
the KOKKOS package threads over both atoms and neighbors of atoms. When
|
||||
using {neigh/thread} {on}, a full neighbor list must also be used. Using
|
||||
{neigh/thread} {on} may be slower for large systems, so this this option
|
||||
is turned on by default only when there are 16K atoms or less owned by
|
||||
an MPI rank and when using a full neighbor list. Not all KOKKOS-enabled
|
||||
potentials support this keyword yet, and only thread over atoms. Many
|
||||
simple pair-wise potentials such as Lennard-Jones do support threading
|
||||
over both atoms and neighbors.
|
||||
|
||||
The {newton} keyword sets the Newton flags for pairwise and bonded
|
||||
interactions to {off} or {on}, the same as the "newton"_newton.html
|
||||
command allows. The default for GPUs is {off} because this will almost
|
||||
always give better performance for the KOKKOS package. This means more
|
||||
computation is done, but less communication. However, when running on
|
||||
CPUs a value of {on} is the default since it can often be faster, just
|
||||
as it is for non-accelerated pair styles
|
||||
The {newton} keyword sets the Newton flags for pairwise and bonded
|
||||
interactions to {off} or {on}, the same as the "newton"_newton.html
|
||||
command allows. The default for GPUs is {off} because this will almost
|
||||
always give better performance for the KOKKOS package. This means more
|
||||
computation is done, but less communication. However, when running on
|
||||
CPUs a value of {on} is the default since it can often be faster, just
|
||||
as it is for non-accelerated pair styles
|
||||
|
||||
The {binsize} keyword sets the size of bins used to bin atoms in
|
||||
neighbor list builds. The same value can be set by the "neigh_modify
|
||||
binsize"_neigh_modify.html command. Making it an option in the package
|
||||
kokkos command allows it to be set from the command line. The default
|
||||
value for CPUs is 0.0, which means the LAMMPS default will be used,
|
||||
which is bins = 1/2 the size of the pairwise cutoff + neighbor skin
|
||||
distance. This is fine when neighbor lists are built on the CPU. For GPU
|
||||
builds, a 2x larger binsize equal to the pairwise cutoff + neighbor skin
|
||||
is often faster, which is the default. Note that if you use a
|
||||
longer-than-usual pairwise cutoff, e.g. to allow for a smaller fraction
|
||||
of KSpace work with a "long-range Coulombic solver"_kspace_style.html
|
||||
because the GPU is faster at performing pairwise interactions, then this
|
||||
rule of thumb may give too large a binsize and the default should be
|
||||
overridden with a smaller value.
|
||||
The {binsize} keyword sets the size of bins used to bin atoms in
|
||||
neighbor list builds. The same value can be set by the "neigh_modify
|
||||
binsize"_neigh_modify.html command. Making it an option in the package
|
||||
kokkos command allows it to be set from the command line. The default
|
||||
value for CPUs is 0.0, which means the LAMMPS default will be used,
|
||||
which is bins = 1/2 the size of the pairwise cutoff + neighbor skin
|
||||
distance. This is fine when neighbor lists are built on the CPU. For GPU
|
||||
builds, a 2x larger binsize equal to the pairwise cutoff + neighbor skin
|
||||
is often faster, which is the default. Note that if you use a
|
||||
longer-than-usual pairwise cutoff, e.g. to allow for a smaller fraction
|
||||
of KSpace work with a "long-range Coulombic solver"_kspace_style.html
|
||||
because the GPU is faster at performing pairwise interactions, then this
|
||||
rule of thumb may give too large a binsize and the default should be
|
||||
overridden with a smaller value.
|
||||
|
||||
The {comm} and {comm/exchange} and {comm/forward} and {comm/reverse}
|
||||
keywords determine whether the host or device performs the packing and
|
||||
unpacking of data when communicating per-atom data between processors.
|
||||
"Exchange" communication happens only on timesteps that neighbor lists
|
||||
are rebuilt. The data is only for atoms that migrate to new processors.
|
||||
"Forward" communication happens every timestep. "Reverse" communication
|
||||
happens every timestep if the {newton} option is on. The data is for
|
||||
atom coordinates and any other atom properties that needs to be updated
|
||||
The {comm} and {comm/exchange} and {comm/forward} and {comm/reverse}
|
||||
keywords determine whether the host or device performs the packing and
|
||||
unpacking of data when communicating per-atom data between processors.
|
||||
"Exchange" communication happens only on timesteps that neighbor lists
|
||||
are rebuilt. The data is only for atoms that migrate to new processors.
|
||||
"Forward" communication happens every timestep. "Reverse" communication
|
||||
happens every timestep if the {newton} option is on. The data is for
|
||||
atom coordinates and any other atom properties that needs to be updated
|
||||
for ghost atoms owned by each processor.
|
||||
|
||||
The {comm} keyword is simply a short-cut to set the same value for both
|
||||
The {comm} keyword is simply a short-cut to set the same value for both
|
||||
the {comm/exchange} and {comm/forward} and {comm/reverse} keywords.
|
||||
|
||||
The value options for all 3 keywords are {no} or {host} or {device}. A
|
||||
value of {no} means to use the standard non-KOKKOS method of
|
||||
packing/unpacking data for the communication. A value of {host} means to
|
||||
use the host, typically a multi-core CPU, and perform the
|
||||
packing/unpacking in parallel with threads. A value of {device} means to
|
||||
use the device, typically a GPU, to perform the packing/unpacking
|
||||
The value options for all 3 keywords are {no} or {host} or {device}. A
|
||||
value of {no} means to use the standard non-KOKKOS method of
|
||||
packing/unpacking data for the communication. A value of {host} means to
|
||||
use the host, typically a multi-core CPU, and perform the
|
||||
packing/unpacking in parallel with threads. A value of {device} means to
|
||||
use the device, typically a GPU, to perform the packing/unpacking
|
||||
operation.
|
||||
|
||||
The optimal choice for these keywords depends on the input script and
|
||||
the hardware used. The {no} value is useful for verifying that the
|
||||
Kokkos-based {host} and {device} values are working correctly. It is the
|
||||
The optimal choice for these keywords depends on the input script and
|
||||
the hardware used. The {no} value is useful for verifying that the
|
||||
Kokkos-based {host} and {device} values are working correctly. It is the
|
||||
default when running on CPUs since it is usually the fastest.
|
||||
|
||||
When running on CPUs or Xeon Phi, the {host} and {device} values work
|
||||
identically. When using GPUs, the {device} value is the default since it
|
||||
will typically be optimal if all of your styles used in your input
|
||||
script are supported by the KOKKOS package. In this case data can stay
|
||||
on the GPU for many timesteps without being moved between the host and
|
||||
GPU, if you use the {device} value. If your script uses styles (e.g.
|
||||
fixes) which are not yet supported by the KOKKOS package, then data has
|
||||
to be move between the host and device anyway, so it is typically faster
|
||||
to let the host handle communication, by using the {host} value. Using
|
||||
{host} instead of {no} will enable use of multiple threads to
|
||||
pack/unpack communicated data. When running small systems on a GPU,
|
||||
performing the exchange pack/unpack on the host CPU can give speedup
|
||||
When running on CPUs or Xeon Phi, the {host} and {device} values work
|
||||
identically. When using GPUs, the {device} value is the default since it
|
||||
will typically be optimal if all of your styles used in your input
|
||||
script are supported by the KOKKOS package. In this case data can stay
|
||||
on the GPU for many timesteps without being moved between the host and
|
||||
GPU, if you use the {device} value. If your script uses styles (e.g.
|
||||
fixes) which are not yet supported by the KOKKOS package, then data has
|
||||
to be move between the host and device anyway, so it is typically faster
|
||||
to let the host handle communication, by using the {host} value. Using
|
||||
{host} instead of {no} will enable use of multiple threads to
|
||||
pack/unpack communicated data. When running small systems on a GPU,
|
||||
performing the exchange pack/unpack on the host CPU can give speedup
|
||||
since it reduces the number of CUDA kernel launches.
|
||||
|
||||
The {cuda/aware} keyword chooses whether CUDA-aware MPI will be used. When
|
||||
this keyword is set to {on}, buffers in GPU memory are passed directly
|
||||
through MPI send/receive calls. This reduces overhead of first copying
|
||||
the data to the host CPU. However CUDA-aware MPI is not supported on all
|
||||
systems, which can lead to segmentation faults and would require using a
|
||||
value of {off}. If LAMMPS can safely detect that CUDA-aware MPI is not
|
||||
available (currently only possible with OpenMPI v2.0.0 or later), then
|
||||
the {cuda/aware} keyword is automatically set to {off} by default. When
|
||||
the {cuda/aware} keyword is set to {off} while any of the {comm}
|
||||
keywords are set to {device}, the value for these {comm} keywords will
|
||||
be automatically changed to {host}. This setting has no effect if not
|
||||
running on GPUs. CUDA-aware MPI is available for OpenMPI 1.8 (or later
|
||||
The {cuda/aware} keyword chooses whether CUDA-aware MPI will be used. When
|
||||
this keyword is set to {on}, buffers in GPU memory are passed directly
|
||||
through MPI send/receive calls. This reduces overhead of first copying
|
||||
the data to the host CPU. However CUDA-aware MPI is not supported on all
|
||||
systems, which can lead to segmentation faults and would require using a
|
||||
value of {off}. If LAMMPS can safely detect that CUDA-aware MPI is not
|
||||
available (currently only possible with OpenMPI v2.0.0 or later), then
|
||||
the {cuda/aware} keyword is automatically set to {off} by default. When
|
||||
the {cuda/aware} keyword is set to {off} while any of the {comm}
|
||||
keywords are set to {device}, the value for these {comm} keywords will
|
||||
be automatically changed to {host}. This setting has no effect if not
|
||||
running on GPUs. CUDA-aware MPI is available for OpenMPI 1.8 (or later
|
||||
versions), Mvapich2 1.9 (or later) when the "MV2_USE_CUDA" environment
|
||||
variable is set to "1", CrayMPI, and IBM Spectrum MPI when the "-gpu"
|
||||
flag is used.
|
||||
|
|
@ -641,16 +641,16 @@ not used, you must invoke the package intel command in your input
|
|||
script or via the "-pk intel" "command-line
|
||||
switch"_Run_options.html.
|
||||
|
||||
For the KOKKOS package, the option defaults for GPUs are neigh = full,
|
||||
neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default
|
||||
value, comm = device, cuda/aware = on. When LAMMPS can safely detect
|
||||
that CUDA-aware MPI is not available, the default value of cuda/aware
|
||||
becomes "off". For CPUs or Xeon Phis, the option defaults are neigh =
|
||||
half, neigh/qeq = half, newton = on, binsize = 0.0, and comm = no. The
|
||||
option neigh/thread = on when there are 16K atoms or less on an MPI
|
||||
rank, otherwise it is "off". These settings are made automatically by
|
||||
the required "-k on" "command-line switch"_Run_options.html. You can
|
||||
change them by using the package kokkos command in your input script or
|
||||
For the KOKKOS package, the option defaults for GPUs are neigh = full,
|
||||
neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default
|
||||
value, comm = device, cuda/aware = on. When LAMMPS can safely detect
|
||||
that CUDA-aware MPI is not available, the default value of cuda/aware
|
||||
becomes "off". For CPUs or Xeon Phis, the option defaults are neigh =
|
||||
half, neigh/qeq = half, newton = on, binsize = 0.0, and comm = no. The
|
||||
option neigh/thread = on when there are 16K atoms or less on an MPI
|
||||
rank, otherwise it is "off". These settings are made automatically by
|
||||
the required "-k on" "command-line switch"_Run_options.html. You can
|
||||
change them by using the package kokkos command in your input script or
|
||||
via the "-pk kokkos command-line switch"_Run_options.html.
|
||||
|
||||
For the OMP package, the default is Nthreads = 0 and the option
|
||||
|
|
|
|||
|
|
@ -20,8 +20,8 @@ If the {preset} keyword is given, no others are needed.
|
|||
Otherwise, all are mandatory except for {neigh}.
|
||||
The {neigh} keyword is always optional. :l
|
||||
{preset} arg = {2011} or {2015} = which set of predefined parameters to use
|
||||
2011 = use the potential parameters from "(Tainter 2011)"_#Tainter2011
|
||||
2015 = use the potential parameters from "(Tainter 2015)"_#Tainter2015
|
||||
2011 = use the potential parameters from "(Tainter 2011)"_#Tainter2011
|
||||
2015 = use the potential parameters from "(Tainter 2015)"_#Tainter2015
|
||||
{Ea} arg = three-body energy for type A hydrogen bonding interactions (energy units)
|
||||
{Eb} arg = three-body energy for type B hydrogen bonding interactions (energy units)
|
||||
{Ec} arg = three-body energy for type C hydrogen bonding interactions (energy units)
|
||||
|
|
|
|||
|
|
@ -790,4 +790,4 @@ alternative contact force models during inelastic collisions. Powder
|
|||
Technology, 233, 30-46.
|
||||
|
||||
:link(WaltonPC)
|
||||
[(Otis R. Walton)] Walton, O.R., Personal Communication
|
||||
[(Otis R. Walton)] Walton, O.R., Personal Communication
|
||||
|
|
|
|||
|
|
@ -43,8 +43,8 @@ when the tapper function is turned off. The formula of taper function
|
|||
can be found in pair style "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
|
||||
|
||||
NOTE: This potential (ILP) is intended for interlayer interactions between two
|
||||
different layers of graphene. To perform a realistic simulation, this potential
|
||||
must be used in combination with intralayer potential, such as
|
||||
different layers of graphene. To perform a realistic simulation, this potential
|
||||
must be used in combination with intralayer potential, such as
|
||||
"AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential.
|
||||
To keep the intralayer properties unaffected, the interlayer interaction
|
||||
within the same layers should be avoided. Hence, each atom has to have a layer
|
||||
|
|
|
|||
|
|
@ -0,0 +1,207 @@
|
|||
"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 local/density command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style style arg :pre
|
||||
|
||||
style = {local/density}
|
||||
arg = name of file containing tabulated values of local density and the potential :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style local/density benzene_water.localdensity.table :pre
|
||||
|
||||
pair_style hybrid/overlay table spline 500 local/density
|
||||
pair_coeff * * local/density benzene_water.localdensity.table :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The local density (LD) potential is a mean-field manybody potential, and, in some
|
||||
sense,a generalization of embedded atom models (EAM). The name "local density
|
||||
potential" arises from the fact that it assigns an energy to an atom depending
|
||||
on the number of neighboring atoms of given type around it within a predefined
|
||||
spherical volume (i.e., within a cutoff). The bottom-up coarse-graining (CG)
|
||||
literature suggests that such potentials can be widely useful in capturing
|
||||
effective multibody forces in a computationally efficient manner so as to
|
||||
improve the quality of CG models of implicit solvation"(Sanyal1)"_#Sanyal1 and
|
||||
phase-segregation in liquid mixtures"(Sanyal2)"_#Sanyal2, and provide guidelines
|
||||
to determine the extent of manybody correlations present in a CG
|
||||
model."(Rosenberger)"_#Rosenberger The LD potential in LAMMPS is primarily
|
||||
intended to be used as a corrective potential over traditional pair potentials
|
||||
in bottom-up CG models, i.e., as a hybrid pair style with
|
||||
other explicit pair interaction terms (e.g., table spline, Lennard Jones, etc.).
|
||||
Because the LD potential is not a pair potential per se, it is implemented
|
||||
simply as a single auxiliary file with all specifications that will be read
|
||||
upon initialization.
|
||||
|
||||
NOTE: Thus when used as the only interaction in the system, there is no
|
||||
corresponding pair_coeff command and when used with other pair styles using the
|
||||
hybrid/overlay option, the corresponding pair_coeff command must be supplied
|
||||
* * as placeholders for the atom types.
|
||||
|
||||
:line
|
||||
|
||||
[System with a single CG atom type:]
|
||||
|
||||
A system of a single atom type (e.g., LJ argon) with a single local density (LD)
|
||||
potential would have an energy given by:
|
||||
|
||||
:c,image(Eqs/pair_local_density_energy.jpg)
|
||||
|
||||
where rho_i is the LD at atom i and F(rho) is similar in spirit to the
|
||||
embedding function used in EAM potentials. The LD at atom i is given by the sum
|
||||
|
||||
:c,image(Eqs/pair_local_density_ld.jpg)
|
||||
|
||||
where phi is an indicator function that is one at r=0 and zero beyond a cutoff
|
||||
distance R2. The choice of the functional form of phi is somewhat arbitrary,
|
||||
but the following piecewise cubic function has proven sufficiently general:
|
||||
"(Sanyal1)"_#Sanyal1, "(Sanyal2)"_#Sanyal2 "(Rosenberger)"_#Rosenberger
|
||||
|
||||
:c,image(Eqs/pair_local_density_indicator_func.jpg)
|
||||
|
||||
The constants {c} are chosen so that the indicator function smoothly
|
||||
interpolates between 1 and 0 between the distances R1 and R2, which are
|
||||
called the inner and outer cutoffs, respectively. Thus phi satisfies
|
||||
phi(R1) = 1, phi(R2) = dphi/dr @ (r=R1) = dphi/dr @ (r=R2) = 0. The embedding
|
||||
function F(rho) may or may not have a closed-form expression. To maintain
|
||||
generality, it is practically represented with a spline-interpolated table
|
||||
over a predetermined range of rho. Outside of that range it simply adopts zero
|
||||
values at the endpoints.
|
||||
|
||||
It can be shown that the total force between two atoms due to the LD potential
|
||||
takes the form of a pair force, which motivates its designation as a LAMMPS
|
||||
pair style. Please see "(Sanyal1)"_#Sanyal1 for details of the derivation.
|
||||
|
||||
:line
|
||||
|
||||
[Systems with arbitrary numbers of atom types:]
|
||||
|
||||
The potential is easily generalized to systems involving multiple atom types:
|
||||
|
||||
:c,image(Eqs/pair_local_density_energy_multi.jpg)
|
||||
|
||||
with the LD expressed as
|
||||
|
||||
:c,image(Eqs/pair_local_density_ld_multi.jpg)
|
||||
|
||||
where alpha gives the type of atom i, beta the type of atom j, and the
|
||||
coefficients a and b filter for atom types as specified by the user. a is
|
||||
called the central atom filter as it determines to which atoms the
|
||||
potential applies; a_alpha = 1 if the LD potential applies to atom type alpha
|
||||
else zero. On the other hand, b is called the neighbor atom filter because it
|
||||
specifies which atom types to use in the calculation of the LD; b_beta = 1 if
|
||||
atom type beta contributes to the LD and zero otherwise.
|
||||
|
||||
NOTE: Note that the potentials need not be symmetric with respect to atom types,
|
||||
which is the reason for two distinct sets of coefficients a and b. An atom type
|
||||
may contribute to the LD but not the potential, or to the potential but not the
|
||||
LD. Such decisions are made by the user and should (ideally) be motivated on
|
||||
physical grounds for the problem at hand.
|
||||
|
||||
:line
|
||||
|
||||
[General form for implementation in LAMMPS:]
|
||||
|
||||
Of course, a system with many atom types may have many different possible LD
|
||||
potentials, each with their own atom type filters, cutoffs, and embedding
|
||||
functions. The most general form of this potential as implemented in the
|
||||
pair_style local/density is:
|
||||
|
||||
:c,image(Eqs/pair_local_density_energy_implement.jpg)
|
||||
|
||||
where, k is an index that spans the (arbitrary) number of applied LD potentials
|
||||
N_LD. Each LD is calculated as before with:
|
||||
|
||||
:c,image(Eqs/pair_local_density_ld_implement.jpg)
|
||||
|
||||
The superscript on the indicator function phi simply indicates that it is
|
||||
associated with specific values of the cutoff distances R1(k) and R2(k). In
|
||||
summary, there may be N_LD distinct LD potentials. With each potential type (k),
|
||||
one must specify:
|
||||
|
||||
the inner and outer cutoffs as R1 and R2
|
||||
the central type filter a(k), where k = 1,2,...N_LD
|
||||
the neighbor type filter b(k), where k = 1,2,...N_LD
|
||||
the LD potential function F(k)(rho), typically as a table that is later spline-interpolated :ul
|
||||
|
||||
:line
|
||||
|
||||
[Tabulated input file format:]
|
||||
|
||||
Line 1: comment or blank (ignored)
|
||||
Line 2: comment or blank (ignored)
|
||||
Line 3: N_LD N_rho (# of LD potentials and # of tabulated values, single space separated)
|
||||
Line 4: blank (ignored)
|
||||
Line 5: R1(k) R2(k) (lower and upper cutoffs, single space separated)
|
||||
Line 6: central-types (central atom types, single space separated)
|
||||
Line 7: neighbor-types (neighbor atom types single space separated)
|
||||
Line 8: rho_min rho_max drho (min, max and diff. in tabulated rho values, single space separated)
|
||||
Line 9: F(k)(rho_min + 0.drho)
|
||||
Line 10: F(k)(rho_min + 1.drho)
|
||||
Line 11: F(k)(rho_min + 2.drho)
|
||||
...
|
||||
Line 9+N_rho: F(k)(rho_min + N_rho . drho)
|
||||
Line 10+N_rho: blank (ignored) :pre
|
||||
|
||||
Block 2 :pre
|
||||
|
||||
Block 3 :pre
|
||||
|
||||
Block N_LD :pre
|
||||
|
||||
Lines 5 to 9+N_rho constitute the first block. Thus the input file is separated
|
||||
(by blank lines) into N_LD blocks each representing a separate LD potential and
|
||||
each specifying its own upper and lower cutoffs, central and neighbor atoms,
|
||||
and potential. In general, blank lines anywhere are ignored.
|
||||
|
||||
:line
|
||||
|
||||
[Mixing, shift, table, tail correction, restart, info]:
|
||||
This pair style does not support automatic mixing. For atom type pairs alpha,
|
||||
beta and alpha != beta, even if LD potentials of type (alpha, alpha) and
|
||||
(beta, beta) are provided, you will need to explicitly provide LD potential
|
||||
types (alpha, beta) and (beta, alpha) if need be (Here, the notation (alpha,
|
||||
beta) means that alpha is the central atom to which the LD potential is applied
|
||||
and beta is the neighbor atom which contributes to the LD potential on alpha).
|
||||
|
||||
This pair style does not support the "pair_modify"_pair_modify.html
|
||||
shift, table, and tail options.
|
||||
|
||||
The local/density pair style does not write its information to "binary restart
|
||||
files"_restart.html, since it is stored in tabulated potential files.
|
||||
Thus, you need to re-specify the pair_style and pair_coeff commands in
|
||||
an input script that reads a restart file.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The local/density pair style is a part of the USER-MISC package. It is only
|
||||
enabled if LAMMPS was built with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
|
||||
:link(Sanyal1)
|
||||
[(Sanyal1)] Sanyal and Shell, Journal of Chemical Physics, 2016, 145 (3), 034109.
|
||||
:link(Sanyal2)
|
||||
[(Sanyal2)] Sanyal and Shell, Journal of Physical Chemistry B, 122 (21), 5678-5693.
|
||||
|
||||
:link(Rosenberger)
|
||||
[(Rosenberger)] Rosenberger, Sanyal, Shell and van der Vegt, Journal of Chemical Physics, 2019, 151 (4), 044111.
|
||||
|
|
@ -68,7 +68,7 @@ gamma (distance) :ul
|
|||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
Mixing rules are fixed for this style as defined above.
|
||||
Mixing rules are fixed for this style as defined above.
|
||||
|
||||
Shifting the potential energy is not necessary because the switching
|
||||
function ensures that the potential is zero at the cut-off.
|
||||
|
|
|
|||
|
|
@ -27,8 +27,8 @@ args = list of arguments for these particular styles :ul
|
|||
{oxdna2/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
|
||||
T = temperature (oxDNA units, 0.1 = 300 K)
|
||||
xi = temperature-independent coefficient in stacking strength
|
||||
kappa = coefficient of linear temperature dependence in stacking strength
|
||||
xi = temperature-independent coefficient in stacking strength
|
||||
kappa = coefficient of linear temperature dependence in stacking strength
|
||||
{oxdna2/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
|
||||
eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
|
||||
|
|
|
|||
|
|
@ -50,7 +50,7 @@ the SNAP potential files themselves.
|
|||
Only a single pair_coeff command is used with the {snap} style which
|
||||
specifies a SNAP coefficient file followed by a SNAP parameter file
|
||||
and then N additional arguments specifying the mapping of SNAP
|
||||
elements to LAMMPS atom types, where N is the number of
|
||||
elements to LAMMPS atom types, where N is the number of
|
||||
LAMMPS atom types:
|
||||
|
||||
SNAP coefficient file
|
||||
|
|
@ -79,7 +79,7 @@ The name of the SNAP coefficient file usually ends in the
|
|||
".snapcoeff" extension. It may contain coefficients
|
||||
for many SNAP elements. The only requirement is that it
|
||||
contain at least those element names appearing in the
|
||||
LAMMPS mapping list.
|
||||
LAMMPS mapping list.
|
||||
The name of the SNAP parameter file usually ends in the ".snapparam"
|
||||
extension. It contains a small number
|
||||
of parameters that define the overall form of the SNAP potential.
|
||||
|
|
|
|||
|
|
@ -11,7 +11,7 @@ pair_style spin/dipole/long command :h3
|
|||
|
||||
[Syntax:]
|
||||
|
||||
pair_style spin/dipole/cut cutoff
|
||||
pair_style spin/dipole/cut cutoff
|
||||
pair_style spin/dipole/long cutoff :pre
|
||||
|
||||
cutoff = global cutoff for magnetic dipole energy and forces
|
||||
|
|
@ -21,35 +21,34 @@ cutoff = global cutoff for magnetic dipole energy and forces
|
|||
[Examples:]
|
||||
|
||||
pair_style spin/dipole/cut 10.0
|
||||
pair_coeff * * 10.0
|
||||
pair_coeff * * 10.0
|
||||
pair_coeff 2 3 8.0 :pre
|
||||
|
||||
pair_style spin/dipole/long 9.0
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_coeff 2 3 1.0 1.0 2.5 4.0 scale 0.5
|
||||
pair_coeff 2 3 1.0 1.0 2.5 4.0 :pre
|
||||
pair_coeff * * 10.0
|
||||
pair_coeff 2 3 6.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {spin/dipole/cut} computes a short-range dipole-dipole
|
||||
interaction between pairs of magnetic particles that each
|
||||
have a magnetic spin.
|
||||
interaction between pairs of magnetic particles that each
|
||||
have a magnetic spin.
|
||||
The magnetic dipole-dipole interactions are computed by the
|
||||
following formulas for the magnetic energy, magnetic precession
|
||||
following formulas for the magnetic energy, magnetic precession
|
||||
vector omega and mechanical force between particles I and J.
|
||||
|
||||
:c,image(Eqs/pair_spin_dipole.jpg)
|
||||
|
||||
where si and sj are the spin on two magnetic particles,
|
||||
r is their separation distance, and the vector e = (Ri - Rj)/|Ri - Rj|
|
||||
is the direction vector between the two particles.
|
||||
where si and sj are the spin on two magnetic particles,
|
||||
r is their separation distance, and the vector e = (Ri - Rj)/|Ri - Rj|
|
||||
is the direction vector between the two particles.
|
||||
|
||||
Style {spin/dipole/long} computes long-range magnetic dipole-dipole
|
||||
interaction.
|
||||
A "kspace_style"_kspace_style.html must be defined to
|
||||
use this pair style. Currently, "kspace_style
|
||||
use this pair style. Currently, "kspace_style
|
||||
ewald/dipole/spin"_kspace_style.html and "kspace_style
|
||||
pppm/dipole/spin"_kspace_style.html support long-range magnetic
|
||||
pppm/dipole/spin"_kspace_style.html support long-range magnetic
|
||||
dipole-dipole interactions.
|
||||
|
||||
:line
|
||||
|
|
@ -68,8 +67,8 @@ to be specified in an input script that reads a restart file.
|
|||
[Restrictions:]
|
||||
|
||||
The {spin/dipole/cut} and {spin/dipole/long} styles are part of
|
||||
the SPIN package. They are only enabled if LAMMPS was built with that
|
||||
package. See the "Build package"_Build_package.html doc page for more
|
||||
the SPIN package. They are only enabled if LAMMPS was built with that
|
||||
package. See the "Build package"_Build_package.html doc page for more
|
||||
info.
|
||||
|
||||
Using dipole/spin pair styles with {electron} "units"_units.html is not
|
||||
|
|
|
|||
|
|
@ -15,11 +15,11 @@ pair_style spin/dmi cutoff :pre
|
|||
cutoff = global cutoff pair (distance in metal units) :ulb,l
|
||||
|
||||
:ule
|
||||
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style spin/dmi 4.0
|
||||
pair_coeff * * dmi 2.6 0.001 1.0 0.0 0.0
|
||||
pair_coeff * * dmi 2.6 0.001 1.0 0.0 0.0
|
||||
pair_coeff 1 2 dmi 4.0 0.00109 0.0 0.0 1.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
|
|
|||
|
|
@ -15,7 +15,7 @@ pair_style spin/neel cutoff :pre
|
|||
cutoff = global cutoff pair (distance in metal units) :ulb,l
|
||||
|
||||
:ule
|
||||
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style spin/neel 4.0
|
||||
|
|
|
|||
|
|
@ -228,6 +228,7 @@ accelerated styles exist.
|
|||
"lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed LJ potential
|
||||
"lj/switch3/coulgauss"_pair_lj_switch3_coulgauss - smoothed LJ vdW potential with Gaussian electrostatics
|
||||
"lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential
|
||||
"local/density"_pair_local_density.html - generalized basic local density potential
|
||||
"lubricate"_pair_lubricate.html - hydrodynamic lubrication forces
|
||||
"lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity
|
||||
"lubricateU"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication Dynamics
|
||||
|
|
|
|||
|
|
@ -66,6 +66,7 @@ Pair Styles :h1
|
|||
pair_lj_smooth
|
||||
pair_lj_smooth_linear
|
||||
pair_lj_switch3_coulgauss
|
||||
pair_local_density
|
||||
pair_lubricate
|
||||
pair_lubricateU
|
||||
pair_mdf
|
||||
|
|
|
|||
|
|
@ -110,7 +110,13 @@ the information from the log.lammps file. E.g. you could produce one
|
|||
dump file with snapshots at 300K (from all replicas), another with
|
||||
snapshots at 310K, etc. Note that these new dump files will not
|
||||
contain "continuous trajectories" for individual atoms, because two
|
||||
successive snapshots (in time) may be from different replicas.
|
||||
successive snapshots (in time) may be from different replicas. The
|
||||
reorder_remd_traj python script can do the reordering for you
|
||||
(and additionally also calculated configurational log-weights of
|
||||
trajectory snapshots in the canonical ensemble). The script can be found
|
||||
in the tools/replica directory while instructions on how to use it is
|
||||
available in doc/Tools (in brief) and as a README file in tools/replica
|
||||
(in detail).
|
||||
|
||||
The last argument {index} in the temper command is optional and is
|
||||
used when restarting a tempering run from a set of restart files (one
|
||||
|
|
|
|||
|
|
@ -275,6 +275,7 @@ Broadwell
|
|||
Broglie
|
||||
brownian
|
||||
brownw
|
||||
Broyden
|
||||
Bryantsev
|
||||
Btarget
|
||||
btype
|
||||
|
|
@ -305,6 +306,7 @@ Cavium
|
|||
Cawkwell
|
||||
cbecker
|
||||
ccache
|
||||
ccachepiecewise
|
||||
ccmake
|
||||
ccNspecies
|
||||
CCu
|
||||
|
|
@ -622,6 +624,7 @@ Doye
|
|||
dpd
|
||||
DPD
|
||||
dpdTheta
|
||||
dphi
|
||||
DPhil
|
||||
dr
|
||||
dR
|
||||
|
|
@ -986,6 +989,7 @@ gmask
|
|||
Gmask
|
||||
gneb
|
||||
GNEB
|
||||
Goldfarb
|
||||
googlemail
|
||||
Gordan
|
||||
GPa
|
||||
|
|
@ -1403,6 +1407,7 @@ Laupretre
|
|||
lavenderblush
|
||||
lawngreen
|
||||
lB
|
||||
lbfgs
|
||||
lbl
|
||||
LBtype
|
||||
lcbop
|
||||
|
|
@ -2039,12 +2044,12 @@ Orsi
|
|||
ortho
|
||||
orthonormal
|
||||
orthorhombic
|
||||
oso
|
||||
ot
|
||||
Otype
|
||||
Ouldridge
|
||||
outfile
|
||||
outmost
|
||||
outpur
|
||||
outputss
|
||||
Ouyang
|
||||
overlayed
|
||||
|
|
@ -2137,6 +2142,7 @@ picograms
|
|||
picosecond
|
||||
picoseconds
|
||||
pid
|
||||
piecewise
|
||||
Pieniazek
|
||||
Pieter
|
||||
pimd
|
||||
|
|
@ -2239,6 +2245,7 @@ Py
|
|||
pydir
|
||||
pylammps
|
||||
PyLammps
|
||||
pymbar
|
||||
pymodule
|
||||
pymol
|
||||
pypar
|
||||
|
|
@ -2269,6 +2276,7 @@ qoffload
|
|||
qopenmp
|
||||
qoverride
|
||||
qtb
|
||||
quadratically
|
||||
quadrupolar
|
||||
Quant
|
||||
quartic
|
||||
|
|
@ -2325,6 +2333,7 @@ reinit
|
|||
relink
|
||||
relTol
|
||||
remappings
|
||||
remd
|
||||
Ren
|
||||
Rendon
|
||||
reneighbor
|
||||
|
|
@ -2417,6 +2426,7 @@ Rodrigues
|
|||
Rohart
|
||||
Ronchetti
|
||||
Rosati
|
||||
Rosenberger
|
||||
Rossky
|
||||
rosybrown
|
||||
rotationally
|
||||
|
|
@ -2456,6 +2466,7 @@ Sandia
|
|||
sandybrown
|
||||
Sanitizer
|
||||
sanitizers
|
||||
Sanyal
|
||||
sc
|
||||
scafacos
|
||||
SCAFACOS
|
||||
|
|
@ -2480,6 +2491,7 @@ Scripta
|
|||
sdk
|
||||
sdpd
|
||||
SDPD
|
||||
se
|
||||
seagreen
|
||||
Secor
|
||||
sectoring
|
||||
|
|
@ -2506,6 +2518,7 @@ setvel
|
|||
sfftw
|
||||
Sg
|
||||
Shan
|
||||
Shanno
|
||||
shapex
|
||||
shapey
|
||||
shapez
|
||||
|
|
@ -2573,6 +2586,7 @@ Snodin
|
|||
Sodani
|
||||
Soderlind
|
||||
solvated
|
||||
solvation
|
||||
Sorensen
|
||||
soundspeed
|
||||
Souza
|
||||
|
|
@ -2689,6 +2703,8 @@ Tajkhorshid
|
|||
Tamaskovics
|
||||
Tanaka
|
||||
tanh
|
||||
tanmoy
|
||||
Tanmoy
|
||||
Tartakovsky
|
||||
taskset
|
||||
taubi
|
||||
|
|
@ -2931,6 +2947,7 @@ vectorial
|
|||
vectorization
|
||||
Vectorization
|
||||
vectorized
|
||||
Vegt
|
||||
vel
|
||||
Verlag
|
||||
verlet
|
||||
|
|
|
|||
|
|
@ -99,12 +99,12 @@ pour: pouring of granular particles into a 3d box, then chute flow
|
|||
prd: parallel replica dynamics of vacancy diffusion in bulk Si
|
||||
python: use of PYTHON package to invoke Python code from input script
|
||||
qeq: use of QEQ package for charge equilibration
|
||||
reax: RDX and TATB models using the ReaxFF
|
||||
reax: RDX and TATB and several other models using ReaxFF
|
||||
rigid: rigid bodies modeled as independent or coupled
|
||||
shear: sideways shear applied to 2d solid, with and without a void
|
||||
snap: use of SNAP potential for Ta
|
||||
snap: examples for using several bundled SNAP potentials
|
||||
srd: stochastic rotation dynamics (SRD) particles as solvent
|
||||
snap: NVE dynamics for BCC tantalum crystal using SNAP potential
|
||||
steinhardt: Steinhardt-Nelson Q_l and W_l parameters usng orientorder/atom
|
||||
streitz: Streitz-Mintmire potential for Al2O3
|
||||
tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
|
||||
threebody: regression test input for a variety of manybody potentials
|
||||
|
|
|
|||
|
|
@ -32,7 +32,7 @@ neigh_modify every 10 check yes delay 20
|
|||
|
||||
fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.1 21
|
||||
fix 3 all nve/spin lattice no
|
||||
fix 3 all nve/spin lattice frozen
|
||||
|
||||
timestep 0.0002
|
||||
|
||||
|
|
|
|||
|
|
@ -35,7 +35,7 @@ fix_modify 1 energy yes
|
|||
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
|
|
|||
|
|
@ -37,7 +37,7 @@ neigh_modify every 10 check yes delay 20
|
|||
fix 1 all precession/spin anisotropy 0.01 0.0 0.0 1.0
|
||||
#fix 2 all langevin/spin 0.0 0.0 21
|
||||
fix 2 all langevin/spin 0.0 0.1 21
|
||||
fix 3 all nve/spin lattice yes
|
||||
fix 3 all nve/spin lattice moving
|
||||
|
||||
timestep 0.0001
|
||||
|
||||
|
|
|
|||
|
|
@ -33,7 +33,7 @@ fix 1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1
|
|||
fix_modify 1 energy yes
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
|
|
|||
|
|
@ -35,7 +35,7 @@ fix 1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1
|
|||
fix_modify 1 energy yes
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
|
|
|||
|
|
@ -36,7 +36,7 @@ fix 1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1
|
|||
fix_modify 1 energy yes
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
|
|
|||
|
|
@ -33,7 +33,7 @@ neigh_modify every 10 check yes delay 20
|
|||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
|
|
|||
|
|
@ -31,7 +31,7 @@ fix 1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1
|
|||
fix_modify 1 energy yes
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
|
|
|||
|
|
@ -33,7 +33,7 @@ neigh_modify every 10 check yes delay 20
|
|||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
|
|
|||
|
|
@ -35,7 +35,7 @@ fix 1 all precession/spin cubic -0.0001 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.
|
|||
fix_modify 1 energy yes
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
|
|
|||
|
|
@ -20,7 +20,7 @@ neigh_modify every 1 check no delay 0
|
|||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
|
||||
# define outputs and computes
|
||||
|
|
|
|||
|
|
@ -24,7 +24,7 @@ neigh_modify every 1 check no delay 0
|
|||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
fix 3 all nve/spin lattice moving
|
||||
timestep 0.0001
|
||||
|
||||
# define outputs
|
||||
|
|
|
|||
|
|
@ -29,7 +29,7 @@ neigh_modify every 10 check yes delay 20
|
|||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 100.0 0.01 21
|
||||
|
||||
fix 3 all nve/spin lattice no
|
||||
fix 3 all nve/spin lattice frozen
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
|
|
|||
|
|
@ -35,7 +35,7 @@ fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 anisotropy 5e-05 0.0 0.0 1.0
|
|||
fix_modify 1 energy yes
|
||||
fix 2 fixed_spin setforce/spin 0.0 0.0 0.0
|
||||
fix 3 all langevin/spin 0.0 0.1 21
|
||||
fix 4 all nve/spin lattice no
|
||||
fix 4 all nve/spin lattice frozen
|
||||
|
||||
timestep 0.0001
|
||||
|
||||
|
|
|
|||
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in New Issue