Jacob Gissinger
File diff suppressed because it is too large
Load Diff
1
bench/POTENTIALS/CH.airebo
Symbolic link
1
bench/POTENTIALS/CH.airebo
Symbolic link
@ -0,0 +1 @@
|
||||
../../potentials/CH.airebo
|
||||
File diff suppressed because it is too large
Load Diff
1
bench/POTENTIALS/CdTe.bop.table
Symbolic link
1
bench/POTENTIALS/CdTe.bop.table
Symbolic link
@ -0,0 +1 @@
|
||||
../../potentials/CdTe.bop.table
|
||||
@ -1,305 +0,0 @@
|
||||
Cu functions (universal 3), SM Foiles et al, PRB, 33, 7983 (1986)
|
||||
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.
|
||||
|
||||
|
||||
1
bench/POTENTIALS/Cu_u3.eam
Symbolic link
1
bench/POTENTIALS/Cu_u3.eam
Symbolic link
@ -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
1
bench/POTENTIALS/Ni.adp
Symbolic link
1
bench/POTENTIALS/Ni.adp
Symbolic link
@ -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)
|
||||
|
||||
@ -17,6 +17,8 @@ if(PKG_KOKKOS)
|
||||
${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
|
||||
${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
|
||||
${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
|
||||
${KOKKOS_PKG_SOURCES_DIR}/min_kokkos.cpp
|
||||
${KOKKOS_PKG_SOURCES_DIR}/min_linesearch_kokkos.cpp
|
||||
${KOKKOS_PKG_SOURCES_DIR}/neighbor_kokkos.cpp
|
||||
${KOKKOS_PKG_SOURCES_DIR}/neigh_list_kokkos.cpp
|
||||
${KOKKOS_PKG_SOURCES_DIR}/neigh_bond_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
|
||||
|
||||
@ -108,7 +108,7 @@ OPT.
|
||||
"class2 (ko)"_dihedral_class2.html,
|
||||
"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
|
||||
"fourier (io)"_dihedral_fourier.html,
|
||||
"harmonic (io)"_dihedral_harmonic.html,
|
||||
"harmonic (iko)"_dihedral_harmonic.html,
|
||||
"helix (o)"_dihedral_helix.html,
|
||||
"multi/harmonic (o)"_dihedral_multi_harmonic.html,
|
||||
"nharmonic (o)"_dihedral_nharmonic.html,
|
||||
|
||||
@ -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,
|
||||
|
||||
BIN
doc/src/Eqs/pair_local_density_energy.jpg
Normal file
BIN
doc/src/Eqs/pair_local_density_energy.jpg
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 3.0 KiB |
11
doc/src/Eqs/pair_local_density_energy.tex
Normal file
11
doc/src/Eqs/pair_local_density_energy.tex
Normal file
@ -0,0 +1,11 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
U_{LD} = \sum_i F(\rho_i)
|
||||
$$
|
||||
|
||||
|
||||
\end{document}
|
||||
~
|
||||
BIN
doc/src/Eqs/pair_local_density_energy_implement.jpg
Normal file
BIN
doc/src/Eqs/pair_local_density_energy_implement.jpg
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 7.8 KiB |
9
doc/src/Eqs/pair_local_density_energy_implement.tex
Normal file
9
doc/src/Eqs/pair_local_density_energy_implement.tex
Normal file
@ -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}
|
||||
BIN
doc/src/Eqs/pair_local_density_energy_multi.jpg
Normal file
BIN
doc/src/Eqs/pair_local_density_energy_multi.jpg
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 3.4 KiB |
9
doc/src/Eqs/pair_local_density_energy_multi.tex
Normal file
9
doc/src/Eqs/pair_local_density_energy_multi.tex
Normal file
@ -0,0 +1,9 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
U_{LD} = \sum_i a_\alpha F(\rho_i)
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
BIN
doc/src/Eqs/pair_local_density_indicator_func.jpg
Normal file
BIN
doc/src/Eqs/pair_local_density_indicator_func.jpg
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 8.8 KiB |
16
doc/src/Eqs/pair_local_density_indicator_func.tex
Normal file
16
doc/src/Eqs/pair_local_density_indicator_func.tex
Normal file
@ -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}
|
||||
BIN
doc/src/Eqs/pair_local_density_ld.jpg
Normal file
BIN
doc/src/Eqs/pair_local_density_ld.jpg
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 3.0 KiB |
10
doc/src/Eqs/pair_local_density_ld.tex
Normal file
10
doc/src/Eqs/pair_local_density_ld.tex
Normal file
@ -0,0 +1,10 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
|
||||
$$
|
||||
\rho_i = \sum_{j \neq i} \varphi(r_{ij})
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
BIN
doc/src/Eqs/pair_local_density_ld_implement.jpg
Normal file
BIN
doc/src/Eqs/pair_local_density_ld_implement.jpg
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 4.2 KiB |
10
doc/src/Eqs/pair_local_density_ld_implement.tex
Normal file
10
doc/src/Eqs/pair_local_density_ld_implement.tex
Normal file
@ -0,0 +1,10 @@
|
||||
\documentstyle[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
|
||||
$$
|
||||
\rho_i^{(k)} = \sum_j b_\beta^{(k)} \varphi^{(k)} (r_{ij})
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
BIN
doc/src/Eqs/pair_local_density_ld_multi.jpg
Normal file
BIN
doc/src/Eqs/pair_local_density_ld_multi.jpg
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 3.4 KiB |
10
doc/src/Eqs/pair_local_density_ld_multi.tex
Normal file
10
doc/src/Eqs/pair_local_density_ld_multi.tex
Normal file
@ -0,0 +1,10 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
|
||||
$$
|
||||
\rho_i = \sum_{j \neq i} b_\beta \varphi(r_{ij})
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
@ -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
|
||||
|
||||
|
||||
@ -126,9 +126,10 @@ are intended for computational work like running LAMMPS. By default
|
||||
Ng = 1 and Ns is not set.
|
||||
|
||||
Depending on which flavor of MPI you are running, LAMMPS will look for
|
||||
one of these 3 environment variables
|
||||
one of these 4 environment variables
|
||||
|
||||
SLURM_LOCALID (various MPI variants compiled with SLURM support)
|
||||
MPT_LRANK (HPE MPI)
|
||||
MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
|
||||
OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI) :pre
|
||||
|
||||
|
||||
@ -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)
|
||||
|
||||
|
||||
@ -40,11 +40,12 @@ coordinates and other properties are exchanged between neighboring
|
||||
processors and stored as properties of ghost atoms.
|
||||
|
||||
NOTE: These options apply to the currently defined comm style. When
|
||||
you specify a "comm_style"_comm_style.html command, all communication
|
||||
settings are restored to their default values, including those
|
||||
you specify a "comm_style"_comm_style.html or
|
||||
"read_restart"_read_restart.html command, all communication settings
|
||||
are restored to their default or stored values, including those
|
||||
previously reset by a comm_modify command. Thus if your input script
|
||||
specifies a comm_style command, you should use the comm_modify command
|
||||
after it.
|
||||
specifies a comm_style or read_restart command, you should use the
|
||||
comm_modify command after it.
|
||||
|
||||
The {mode} keyword determines whether a single or multiple cutoff
|
||||
distances are used to determine which atoms to communicate.
|
||||
|
||||
@ -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
|
||||
|
||||
@ -15,10 +15,11 @@ compute ID group-ID bond/local value1 value2 ... keyword args ... :pre
|
||||
ID, group-ID are documented in "compute"_compute.html command :ulb,l
|
||||
bond/local = style name of this compute command :l
|
||||
one or more values may be appended :l
|
||||
value = {dist} or {engpot} or {force} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} or {v_name} :l
|
||||
value = {dist} or {engpot} or {force} or {fx} or {fy} or {fz} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} or {v_name} :l
|
||||
{dist} = bond distance
|
||||
{engpot} = bond potential energy
|
||||
{force} = bond force :pre
|
||||
{fx},{fy},{fz} = components of bond force
|
||||
{engvib} = bond kinetic energy of vibration
|
||||
{engrot} = bond kinetic energy of rotation
|
||||
{engtrans} = bond kinetic energy of translation
|
||||
@ -38,6 +39,7 @@ keyword = {set} :l
|
||||
|
||||
compute 1 all bond/local engpot
|
||||
compute 1 all bond/local dist engpot force :pre
|
||||
compute 1 all bond/local dist fx fy fz :pre
|
||||
compute 1 all angle/local dist v_distsq set dist d :pre
|
||||
|
||||
[Description:]
|
||||
@ -59,6 +61,9 @@ based on the current separation of the pair of atoms in the bond.
|
||||
The value {force} is the magnitude of the force acting between the
|
||||
pair of atoms in the bond.
|
||||
|
||||
The values {fx}, {fy}, and {fz} are the xyz components of
|
||||
{force} between the pair of atoms in the bond.
|
||||
|
||||
The remaining properties are all computed for motion of the two atoms
|
||||
relative to the center of mass (COM) velocity of the 2 atoms in the
|
||||
bond.
|
||||
|
||||
@ -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
|
||||
|
||||
@ -19,6 +19,8 @@ keyword = {cutoff} or {nnn} or {degrees} or {components}
|
||||
{cutoff} value = distance cutoff
|
||||
{nnn} value = number of nearest neighbors
|
||||
{degrees} values = nlvalues, l1, l2,...
|
||||
{wl} value = yes or no
|
||||
{wl/hat} value = yes or no
|
||||
{components} value = ldegree :pre
|
||||
|
||||
:ule
|
||||
@ -27,7 +29,8 @@ keyword = {cutoff} or {nnn} or {degrees} or {components}
|
||||
|
||||
compute 1 all orientorder/atom
|
||||
compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5
|
||||
compute 1 all orientorder/atom degrees 4 6 components 6 nnn NULL cutoff 3.0 :pre
|
||||
compute 1 all orientorder/atom wl/hat yes
|
||||
compute 1 all orientorder/atom components 6 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
@ -48,7 +51,7 @@ neighbors of the central atom.
|
||||
The angles theta and phi are the standard spherical polar angles
|
||||
defining the direction of the bond vector {rij}.
|
||||
The second equation defines {Ql}, which is a
|
||||
rotationally invariant scalar quantity obtained by summing
|
||||
rotationally invariant non-negative amplitude obtained by summing
|
||||
over all the components of degree {l}.
|
||||
|
||||
The optional keyword {cutoff} defines the distance cutoff
|
||||
@ -63,7 +66,7 @@ specified distance cutoff are used.
|
||||
|
||||
The optional keyword {degrees} defines the list of order parameters to
|
||||
be computed. The first argument {nlvalues} is the number of order
|
||||
parameters. This is followed by that number of integers giving the
|
||||
parameters. This is followed by that number of non-negative integers giving the
|
||||
degree of each order parameter. Because {Q}2 and all odd-degree order
|
||||
parameters are zero for atoms in cubic crystals (see
|
||||
"Steinhardt"_#Steinhardt), the default order parameters are {Q}4,
|
||||
@ -71,7 +74,20 @@ parameters are zero for atoms in cubic crystals (see
|
||||
= sqrt(7/3)/8 = 0.19094.... The numerical values of all order
|
||||
parameters up to {Q}12 for a range of commonly encountered
|
||||
high-symmetry structures are given in Table I of "Mickel et
|
||||
al."_#Mickel.
|
||||
al."_#Mickel, and these can be reproduced with this compute
|
||||
|
||||
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
|
||||
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
|
||||
can be reproduced with this keyword.
|
||||
|
||||
The optional keyword {components} will output the components of the
|
||||
normalized complex vector {Ybar_lm} of degree {ldegree}, which must be
|
||||
@ -82,7 +98,7 @@ particles, as discussed in "ten Wolde"_#tenWolde2.
|
||||
|
||||
The value of {Ql} is set to zero for atoms not in the
|
||||
specified compute group, as well as for atoms that have less than
|
||||
{nnn} neighbors within the distance cutoff.
|
||||
{nnn} neighbors within the distance cutoff, unless {nnn} is NULL.
|
||||
|
||||
The neighbor list needed to compute this quantity is constructed each
|
||||
time the calculation is performed (i.e. each time a snapshot of atoms
|
||||
@ -108,6 +124,12 @@ This compute calculates a per-atom array with {nlvalues} columns,
|
||||
giving the {Ql} values for each atom, which are real numbers on the
|
||||
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}
|
||||
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})
|
||||
@ -130,7 +152,8 @@ hexorder/atom"_compute_hexorder_atom.html
|
||||
[Default:]
|
||||
|
||||
The option defaults are {cutoff} = pair style cutoff, {nnn} = 12,
|
||||
{degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.
|
||||
{degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12,
|
||||
{wl} = no, {wl/hat} = no, and {components} off
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -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
|
||||
|
||||
@ -8,6 +8,7 @@
|
||||
|
||||
dihedral_style harmonic command :h3
|
||||
dihedral_style harmonic/intel command :h3
|
||||
dihedral_style harmonic/kk command :h3
|
||||
dihedral_style harmonic/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
@ -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
|
||||
@ -392,10 +397,11 @@ 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 +412,8 @@ 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 +423,20 @@ 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
|
||||
|
||||
@ -24,18 +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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -17,7 +17,7 @@ keyword = {dmax} or {line} 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
|
||||
backtrack,quadratic,forcezero = style of linesearch to use
|
||||
{alpha_damp} value = damping
|
||||
damping = fictitious Gilbert damping for spin minimization (adim)
|
||||
{discrete_factor} value = factor
|
||||
@ -70,14 +70,14 @@ that difference may be smaller than machine epsilon even if atoms
|
||||
could move in the gradient direction to reduce forces further.
|
||||
|
||||
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.
|
||||
quantities.
|
||||
Default values are {alpha_damp} = 1.0 and {discrete_factor} = 10.0.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
@ -13,7 +13,7 @@ min_style spin :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
min_style spin :pre
|
||||
min_style spin :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
@ -27,36 +27,36 @@ 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
|
||||
tolerance. See "minimize"_minimize.html for more explanation.
|
||||
tolerance. See "minimize"_minimize.html for more explanation.
|
||||
|
||||
[Restrictions:]
|
||||
[Restrictions:]
|
||||
|
||||
This minimization procedure is only applied to spin degrees of
|
||||
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:]
|
||||
|
||||
@ -11,7 +11,7 @@ min_style command :h3
|
||||
|
||||
min_style style :pre
|
||||
|
||||
style = {cg} or {hftn} or {sd} or {quickmin} or {fire} or {spin} :ul
|
||||
style = {cg} or {cg/kk} or {hftn} or {sd} or {quickmin} or {fire} or {spin} :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
@ -62,7 +62,7 @@ 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.
|
||||
|
||||
@ -74,9 +74,34 @@ 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}, and {hftn} 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
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
|
||||
@ -7,6 +7,7 @@
|
||||
:line
|
||||
|
||||
minimize command :h3
|
||||
minimize/kk command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
@ -105,9 +106,9 @@ the number of total force evaluations exceeds {maxeval} :ul
|
||||
|
||||
NOTE: the "minimization style"_min_style.html {spin} replaces
|
||||
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},
|
||||
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.
|
||||
|
||||
NOTE: You can also use the "fix halt"_fix_halt.html command to specify
|
||||
@ -256,6 +257,28 @@ info in the Restrictions section below.
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
Features that are not yet implemented are listed here, in case someone
|
||||
|
||||
@ -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.
|
||||
|
||||
@ -61,33 +61,33 @@ 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.
|
||||
style minimizer 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
|
||||
@ -173,7 +173,7 @@ 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
|
||||
"min_spin"_min_spin.html for more information).
|
||||
"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 +195,9 @@ 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 +207,11 @@ 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 +234,12 @@ 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 +257,7 @@ 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 +290,22 @@ 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 +313,17 @@ 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 +346,9 @@ 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
|
||||
|
||||
|
||||
@ -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
|
||||
|
||||
207
doc/src/pair_local_density.txt
Normal file
207
doc/src/pair_local_density.txt
Normal file
@ -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
|
||||
@ -21,7 +21,7 @@ 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
|
||||
@ -32,24 +32,24 @@ pair_coeff 2 3 1.0 1.0 2.5 4.0 :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 +68,8 @@ 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
|
||||
|
||||
@ -305,6 +305,7 @@ Cavium
|
||||
Cawkwell
|
||||
cbecker
|
||||
ccache
|
||||
ccachepiecewise
|
||||
ccmake
|
||||
ccNspecies
|
||||
CCu
|
||||
@ -622,6 +623,7 @@ Doye
|
||||
dpd
|
||||
DPD
|
||||
dpdTheta
|
||||
dphi
|
||||
DPhil
|
||||
dr
|
||||
dR
|
||||
@ -2044,7 +2046,6 @@ Otype
|
||||
Ouldridge
|
||||
outfile
|
||||
outmost
|
||||
outpur
|
||||
outputss
|
||||
Ouyang
|
||||
overlayed
|
||||
@ -2137,6 +2138,7 @@ picograms
|
||||
picosecond
|
||||
picoseconds
|
||||
pid
|
||||
piecewise
|
||||
Pieniazek
|
||||
Pieter
|
||||
pimd
|
||||
@ -2239,6 +2241,7 @@ Py
|
||||
pydir
|
||||
pylammps
|
||||
PyLammps
|
||||
pymbar
|
||||
pymodule
|
||||
pymol
|
||||
pypar
|
||||
@ -2325,6 +2328,7 @@ reinit
|
||||
relink
|
||||
relTol
|
||||
remappings
|
||||
remd
|
||||
Ren
|
||||
Rendon
|
||||
reneighbor
|
||||
@ -2417,6 +2421,7 @@ Rodrigues
|
||||
Rohart
|
||||
Ronchetti
|
||||
Rosati
|
||||
Rosenberger
|
||||
Rossky
|
||||
rosybrown
|
||||
rotationally
|
||||
@ -2456,6 +2461,7 @@ Sandia
|
||||
sandybrown
|
||||
Sanitizer
|
||||
sanitizers
|
||||
Sanyal
|
||||
sc
|
||||
scafacos
|
||||
SCAFACOS
|
||||
@ -2480,6 +2486,7 @@ Scripta
|
||||
sdk
|
||||
sdpd
|
||||
SDPD
|
||||
se
|
||||
seagreen
|
||||
Secor
|
||||
sectoring
|
||||
@ -2573,6 +2580,7 @@ Snodin
|
||||
Sodani
|
||||
Soderlind
|
||||
solvated
|
||||
solvation
|
||||
Sorensen
|
||||
soundspeed
|
||||
Souza
|
||||
@ -2689,6 +2697,8 @@ Tajkhorshid
|
||||
Tamaskovics
|
||||
Tanaka
|
||||
tanh
|
||||
tanmoy
|
||||
Tanmoy
|
||||
Tartakovsky
|
||||
taskset
|
||||
taubi
|
||||
@ -2931,6 +2941,7 @@ 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
|
||||
|
||||
@ -79,10 +79,10 @@ Dihedral Coeffs
|
||||
|
||||
Improper Coeffs
|
||||
|
||||
1 0.0000 2.1999 0.0000 0.0000 # CAO-CAO-CAT-CTT
|
||||
2 0.0000 2.1999 0.0000 0.0000 # CAT-CAM-CAO-HAT
|
||||
3 0.0000 2.1999 0.0000 0.0000 # CAO-CAP-CAM-HAT
|
||||
4 0.0000 2.1999 0.0000 0.0000 # CAM-CAM-CAP-HAT
|
||||
1 2.1999 0.0000 0.0000 -1.0000 0 # CAO-CAO-CAT-CTT
|
||||
2 2.1999 0.0000 0.0000 -1.0000 0 # CAT-CAM-CAO-HAT
|
||||
3 2.1999 0.0000 0.0000 -1.0000 0 # CAO-CAP-CAM-HAT
|
||||
4 2.1999 0.0000 0.0000 -1.0000 0 # CAM-CAM-CAP-HAT
|
||||
|
||||
Atoms
|
||||
|
||||
|
||||
@ -7,7 +7,7 @@ atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
improper_style opls
|
||||
improper_style fourier
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style lj/cut/thole/long 2.600 8.0 8.0
|
||||
@ -109,7 +109,7 @@ fix fNPH all nve
|
||||
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo 50
|
||||
|
||||
timestep 0.5
|
||||
|
||||
@ -7,7 +7,7 @@ atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
improper_style opls
|
||||
improper_style fourier
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style lj/cut/thole/long 2.600 8.0 8.0
|
||||
@ -115,7 +115,7 @@ fix fINVERSE all drude/transform/inverse
|
||||
|
||||
fix fMOMENTUM all momentum 100 linear 1 1 1
|
||||
|
||||
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo 50
|
||||
|
||||
timestep 0.5
|
||||
|
||||
@ -1,14 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 250 toluene system for drude polarizability example (Langevin)
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
improper_style opls
|
||||
ERROR: Unknown improper style opls (src/force.cpp:634)
|
||||
Last command: improper_style opls
|
||||
@ -1,14 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 250 toluene system for drude polarizability example (Langevin)
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
improper_style opls
|
||||
ERROR: Unknown improper style opls (src/force.cpp:634)
|
||||
Last command: improper_style opls
|
||||
@ -1,14 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 250 toluene system for drude polarizability example (Nose-Hoover)
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
improper_style opls
|
||||
ERROR: Unknown improper style opls (src/force.cpp:634)
|
||||
Last command: improper_style opls
|
||||
@ -1,14 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 250 toluene system for drude polarizability example (Nose-Hoover)
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
improper_style opls
|
||||
ERROR: Unknown improper style opls (src/force.cpp:634)
|
||||
Last command: improper_style opls
|
||||
254
examples/USER/drude/toluene/log.7Aug19.toluene.lang.g++.1
Normal file
254
examples/USER/drude/toluene/log.7Aug19.toluene.lang.g++.1
Normal file
@ -0,0 +1,254 @@
|
||||
LAMMPS (7 Aug 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 250 toluene system for drude polarizability example (Langevin)
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
improper_style fourier
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style lj/cut/thole/long 2.600 8.0 8.0
|
||||
pair_modify mix geometric tail yes
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
read_data data.toluene extra/special/per/atom 1
|
||||
orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
5500 atoms
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
8 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
2 = max impropers/atom
|
||||
reading bonds ...
|
||||
5500 bonds
|
||||
reading angles ...
|
||||
6000 angles
|
||||
reading dihedrals ...
|
||||
6000 dihedrals
|
||||
reading impropers ...
|
||||
1500 impropers
|
||||
5 = max # of 1-2 neighbors
|
||||
10 = max # of 1-3 neighbors
|
||||
16 = max # of 1-4 neighbors
|
||||
20 = max # of special neighbors
|
||||
special bonds CPU = 0.00199628 secs
|
||||
read_data CPU = 0.0169649 secs
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
group gTOLUENE molecule 1:250
|
||||
5500 atoms in group gTOLUENE
|
||||
group gCORES type 1 2 3 4 5 6 7
|
||||
3750 atoms in group gCORES
|
||||
group gDRUDES type 8 9 10 11 12
|
||||
1750 atoms in group gDRUDES
|
||||
|
||||
pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT
|
||||
pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO
|
||||
pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM
|
||||
pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP
|
||||
pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT
|
||||
pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT
|
||||
pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT
|
||||
pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO
|
||||
pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM
|
||||
pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP
|
||||
pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT
|
||||
pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT
|
||||
pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT
|
||||
pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM
|
||||
pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP
|
||||
pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT
|
||||
pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT
|
||||
pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT
|
||||
pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP
|
||||
pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT
|
||||
pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT
|
||||
pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT
|
||||
pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT
|
||||
pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT
|
||||
pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT
|
||||
pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT
|
||||
pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT
|
||||
pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT
|
||||
pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT
|
||||
pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO
|
||||
pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM
|
||||
pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP
|
||||
pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT
|
||||
pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT
|
||||
pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO
|
||||
pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM
|
||||
pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP
|
||||
pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT
|
||||
pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT
|
||||
pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO
|
||||
pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM
|
||||
pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP
|
||||
pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT
|
||||
pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT
|
||||
pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO
|
||||
pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM
|
||||
pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP
|
||||
pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT
|
||||
pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT
|
||||
pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO
|
||||
pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM
|
||||
pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP
|
||||
pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT
|
||||
pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT
|
||||
pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO
|
||||
pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM
|
||||
pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP
|
||||
pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT
|
||||
pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO
|
||||
pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM
|
||||
pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP
|
||||
pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT
|
||||
pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM
|
||||
pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP
|
||||
pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT
|
||||
pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP
|
||||
pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT
|
||||
pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 260.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gCORES create ${vTEMP} 12345
|
||||
velocity gCORES create 260 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C C C C N N D D D D D
|
||||
|
||||
fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
|
||||
1250 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
250 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
find clusters CPU = 0.000807762 secs
|
||||
|
||||
fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
|
||||
fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
|
||||
fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
|
||||
fix fNPH all nve
|
||||
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo 50
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:323)
|
||||
G vector (1/distance) = 0.382011
|
||||
grid = 40 40 40
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0325934
|
||||
estimated relative force accuracy = 9.8154e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 103823 64000
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 19
|
||||
New max number of 1-2 to 1-4 neighbors: 20 (+1)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/thole/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 42.06 | 42.06 | 42.06 Mbytes
|
||||
Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2]
|
||||
0 11086.347 2910.7282 202.07402 8175.6191 6565.4851 20.333365 1.0706727e-06 -3299.85 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821
|
||||
50 4782.1702 4728.7435 328.28767 53.426722 1812.2203 685.37824 683.70917 -3277.1645 797.34329 1305983.2 -1306631.2 16874.358 48631.318 448.52419 116.25477
|
||||
100 2906.0879 3699.8031 256.85465 -793.7152 978.15364 778.36908 862.30899 -3270.1722 468.44888 1306096.8 -1306707.6 15631.384 48631.318 382.26408 35.748403
|
||||
150 2089.0918 3593.0499 249.44342 -1503.9581 751.32283 803.47802 668.4757 -3277.5983 128.17444 1306138.5 -1306716.3 15193.04 48631.318 384.75632 10.892446
|
||||
200 1547.3302 3248.639 225.53309 -1701.3089 699.65977 814.31164 692.83227 -3276.3957 -66.671816 1306160.9 -1306725.9 13787.676 48631.318 351.28242 3.8458668
|
||||
250 1177.9323 3095.949 214.93276 -1918.0167 688.87262 842.44531 615.89218 -3278.4465 -210.06178 1306154.3 -1306731 8808.5835 48631.318 335.8115 1.8330994
|
||||
300 895.90313 2870.3451 199.27046 -1974.442 734.95873 858.58147 624.00862 -3278.6022 -342.01951 1306163.6 -1306735 3388.4841 48631.318 311.56815 1.2987715
|
||||
350 669.25785 2764.9587 191.95413 -2095.7009 662.44028 860.79714 602.69567 -3278.776 -376.37081 1306172.3 -1306738.8 8494.9184 48631.318 300.19414 1.1358594
|
||||
400 531.21609 2722.6775 189.01881 -2191.4614 684.34049 868.77818 576.86096 -3280.1649 -459.66591 1306160 -1306741.6 6726.3087 48631.318 295.59622 1.1315427
|
||||
450 427.05425 2611.7588 181.3184 -2184.7046 719.2042 891.88178 591.2282 -3279.339 -534.65069 1306172.2 -1306745.2 2398.5394 48631.318 283.56126 1.0726045
|
||||
500 310.44891 2556.0967 177.45412 -2245.6477 720.86526 841.50195 586.3417 -3279.3029 -539.81715 1306169.5 -1306744.8 3028.595 48631.318 277.52314 1.0406334
|
||||
550 207.83114 2531.3051 175.73299 -2323.4739 674.71188 855.2132 555.53227 -3280.0378 -553.93222 1306171.9 -1306746.9 4609.4408 48631.318 274.80629 1.0748601
|
||||
600 88.81557 2459.9059 170.77619 -2371.0903 692.4485 834.47484 550.85905 -3280.9086 -595.31802 1306171.4 -1306744 2107.9995 48631.318 267.06312 1.0301965
|
||||
650 75.616307 2416.9747 167.79573 -2341.3584 703.57186 869.98959 564.81201 -3280.7522 -619.8016 1306168 -1306747.2 1236.4829 48631.318 262.3542 1.0968447
|
||||
700 49.832719 2415.7344 167.70963 -2365.9017 683.61663 882.67915 555.23571 -3280.7778 -615.06862 1306159.9 -1306751.4 2985.7048 48631.318 262.23095 1.0762424
|
||||
750 41.513638 2427.218 168.50687 -2385.7044 698.87619 863.2938 564.58197 -3280.0156 -637.29964 1306160.1 -1306755.3 1653.117 48631.318 263.49803 1.0451977
|
||||
800 109.53032 2481.9041 172.30339 -2372.3738 697.22709 897.36555 561.28745 -3280.6784 -651.29564 1306155 -1306751.3 1219.8761 48631.318 269.43698 1.0647792
|
||||
850 98.142203 2502.3132 173.72026 -2404.171 696.5382 878.83293 566.44302 -3280.2837 -663.94587 1306155.6 -1306757.4 1122.7487 48631.318 271.67716 1.030267
|
||||
900 62.992675 2409.7324 167.29295 -2346.7397 722.00541 896.64662 560.66083 -3279.4915 -644.05458 1306153.6 -1306756.1 1604.295 48631.318 261.58656 1.0609836
|
||||
950 5.6677468 2403.5067 166.86073 -2397.839 725.07222 891.00249 556.81977 -3279.7848 -672.66389 1306141 -1306759.2 1019.1694 48631.318 260.91187 1.0562387
|
||||
1000 38.526968 2444.97 169.73928 -2406.4431 704.72993 920.68493 534.59035 -3281.2673 -667.78091 1306141.1 -1306758.5 486.79846 48631.318 265.39928 1.098473
|
||||
1050 21.698026 2388.6306 165.82798 -2366.9326 712.15539 934.39244 546.92027 -3281.1469 -654.7449 1306137.4 -1306761.9 1556.1256 48631.318 259.28203 1.0760765
|
||||
1100 -26.971225 2433.8428 168.96678 -2460.814 710.11081 881.19212 524.51547 -3281.7925 -667.53202 1306137.1 -1306764.4 1203.8971 48631.318 264.20441 1.0706085
|
||||
1150 -49.171269 2375.9688 164.94895 -2425.14 729.78127 918.79575 518.21967 -3281.6542 -675.7239 1306130.4 -1306765 229.44016 48631.318 257.89845 1.086519
|
||||
1200 -53.421342 2422.0091 168.14524 -2475.4304 710.67274 884.2589 523.32524 -3282.2275 -674.49333 1306130.9 -1306767.9 -131.09655 48631.318 262.91124 1.0804821
|
||||
1250 -58.534776 2394.4031 166.22873 -2452.9378 680.27486 909.58096 532.81959 -3281.5551 -653.13731 1306127 -1306767.9 546.96357 48631.318 259.92916 1.0424914
|
||||
1300 -24.151217 2431.9902 168.83817 -2456.1414 681.27127 919.39245 536.41899 -3281.3717 -661.90875 1306121.6 -1306771.5 1455.7512 48631.318 264.00712 1.0630558
|
||||
1350 -38.973062 2438.6194 169.2984 -2477.5925 707.96118 912.62518 519.44533 -3281.6739 -687.67183 1306126.1 -1306774.4 -1470.4442 48631.318 264.70225 1.1091537
|
||||
1400 11.896539 2384.5407 165.54404 -2372.6442 719.03374 950.93261 550.5639 -3280.4581 -663.4921 1306122 -1306771.3 465.12854 48631.318 258.83564 1.0785364
|
||||
1450 -13.118691 2436.6246 169.15991 -2449.7433 661.04397 933.07103 561.29537 -3280.6997 -672.68495 1306123.9 -1306775.7 -108.46564 48631.318 264.50636 1.0718787
|
||||
1500 -38.151755 2417.4849 167.83116 -2455.6367 688.81484 892.35701 565.29013 -3279.6716 -662.1817 1306116.9 -1306777.2 517.89634 48631.318 262.44549 1.0338083
|
||||
1550 -71.663334 2405.7016 167.01311 -2477.3649 681.78925 876.31247 559.003 -3280.451 -649.16641 1306112.8 -1306777.7 925.49349 48631.318 261.148 1.0609731
|
||||
1600 -13.900431 2419.481 167.96973 -2433.3814 718.46559 909.67964 559.06779 -3280.8163 -667.6092 1306108 -1306780.2 13.95808 48631.318 262.63632 1.080229
|
||||
1650 -16.403222 2431.075 168.77464 -2447.4783 710.99509 907.65662 551.60307 -3279.8852 -661.52624 1306104.5 -1306780.8 726.89923 48631.318 263.91553 1.0489963
|
||||
1700 -18.555086 2438.2062 169.26971 -2456.7613 665.90475 943.02217 542.86579 -3280.9017 -657.99229 1306108 -1306777.7 801.41078 48631.318 264.67663 1.0750708
|
||||
1750 -6.9249446 2443.9707 169.6699 -2450.8956 733.23573 890.06857 560.83229 -3280.362 -670.93883 1306098.3 -1306782.1 47.037748 48631.318 265.30892 1.0661143
|
||||
1800 -21.686222 2434.3375 169.00113 -2456.0237 729.35297 899.9733 561.59516 -3280.4727 -680.98901 1306096.5 -1306782 495.63617 48631.318 264.25723 1.0723683
|
||||
1850 -72.916947 2408.8254 167.22998 -2481.7423 683.24984 904.13282 549.97726 -3279.6699 -652.63212 1306099.2 -1306786 -120.61674 48631.318 261.48504 1.0659808
|
||||
1900 -55.4099 2415.455 167.69023 -2470.8649 700.4473 904.72264 565.5266 -3280.4533 -673.23082 1306099.6 -1306787.4 202.15936 48631.318 262.20353 1.0709756
|
||||
1950 -79.877997 2409.2307 167.25812 -2489.1087 695.9536 894.4541 564.7034 -3279.3581 -680.33472 1306100.8 -1306785.3 213.72828 48631.318 261.52921 1.0658433
|
||||
2000 -102.20457 2399.4263 166.57746 -2501.6309 689.67819 894.58596 565.53233 -3280.7595 -680.39032 1306096.4 -1306786.6 1113.7499 48631.318 260.46311 1.0647045
|
||||
Loop time of 68.4185 on 1 procs for 2000 steps with 5500 atoms
|
||||
|
||||
Performance: 1.263 ns/day, 19.005 hours/ns, 29.232 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 48.825 | 48.825 | 48.825 | 0.0 | 71.36
|
||||
Bond | 2.8852 | 2.8852 | 2.8852 | 0.0 | 4.22
|
||||
Kspace | 13.795 | 13.795 | 13.795 | 0.0 | 20.16
|
||||
Neigh | 1.0731 | 1.0731 | 1.0731 | 0.0 | 1.57
|
||||
Comm | 0.27067 | 0.27067 | 0.27067 | 0.0 | 0.40
|
||||
Output | 0.0031168 | 0.0031168 | 0.0031168 | 0.0 | 0.00
|
||||
Modify | 1.5207 | 1.5207 | 1.5207 | 0.0 | 2.22
|
||||
Other | | 0.04541 | | | 0.07
|
||||
|
||||
Nlocal: 5500 ave 5500 max 5500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 13157 ave 13157 max 13157 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.33822e+06 ave 1.33822e+06 max 1.33822e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1338215
|
||||
Ave neighs/atom = 243.312
|
||||
Ave special neighs/atom = 15.6364
|
||||
Neighbor list builds = 32
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:08
|
||||
254
examples/USER/drude/toluene/log.7Aug19.toluene.lang.g++.4
Normal file
254
examples/USER/drude/toluene/log.7Aug19.toluene.lang.g++.4
Normal file
@ -0,0 +1,254 @@
|
||||
LAMMPS (7 Aug 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 250 toluene system for drude polarizability example (Langevin)
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
improper_style fourier
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style lj/cut/thole/long 2.600 8.0 8.0
|
||||
pair_modify mix geometric tail yes
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
read_data data.toluene extra/special/per/atom 1
|
||||
orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
5500 atoms
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
8 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
2 = max impropers/atom
|
||||
reading bonds ...
|
||||
5500 bonds
|
||||
reading angles ...
|
||||
6000 angles
|
||||
reading dihedrals ...
|
||||
6000 dihedrals
|
||||
reading impropers ...
|
||||
1500 impropers
|
||||
5 = max # of 1-2 neighbors
|
||||
10 = max # of 1-3 neighbors
|
||||
16 = max # of 1-4 neighbors
|
||||
20 = max # of special neighbors
|
||||
special bonds CPU = 0.000747919 secs
|
||||
read_data CPU = 0.0168228 secs
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
group gTOLUENE molecule 1:250
|
||||
5500 atoms in group gTOLUENE
|
||||
group gCORES type 1 2 3 4 5 6 7
|
||||
3750 atoms in group gCORES
|
||||
group gDRUDES type 8 9 10 11 12
|
||||
1750 atoms in group gDRUDES
|
||||
|
||||
pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT
|
||||
pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO
|
||||
pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM
|
||||
pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP
|
||||
pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT
|
||||
pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT
|
||||
pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT
|
||||
pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO
|
||||
pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM
|
||||
pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP
|
||||
pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT
|
||||
pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT
|
||||
pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT
|
||||
pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM
|
||||
pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP
|
||||
pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT
|
||||
pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT
|
||||
pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT
|
||||
pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP
|
||||
pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT
|
||||
pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT
|
||||
pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT
|
||||
pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT
|
||||
pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT
|
||||
pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT
|
||||
pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT
|
||||
pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT
|
||||
pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT
|
||||
pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT
|
||||
pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO
|
||||
pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM
|
||||
pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP
|
||||
pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT
|
||||
pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT
|
||||
pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO
|
||||
pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM
|
||||
pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP
|
||||
pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT
|
||||
pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT
|
||||
pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO
|
||||
pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM
|
||||
pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP
|
||||
pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT
|
||||
pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT
|
||||
pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO
|
||||
pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM
|
||||
pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP
|
||||
pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT
|
||||
pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT
|
||||
pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO
|
||||
pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM
|
||||
pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP
|
||||
pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT
|
||||
pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT
|
||||
pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO
|
||||
pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM
|
||||
pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP
|
||||
pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT
|
||||
pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO
|
||||
pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM
|
||||
pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP
|
||||
pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT
|
||||
pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM
|
||||
pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP
|
||||
pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT
|
||||
pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP
|
||||
pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT
|
||||
pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 260.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gCORES create ${vTEMP} 12345
|
||||
velocity gCORES create 260 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C C C C N N D D D D D
|
||||
|
||||
fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
|
||||
1250 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
250 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
find clusters CPU = 0.000355244 secs
|
||||
|
||||
fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
|
||||
fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
|
||||
fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
|
||||
fix fNPH all nve
|
||||
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo 50
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:323)
|
||||
G vector (1/distance) = 0.382011
|
||||
grid = 40 40 40
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0325934
|
||||
estimated relative force accuracy = 9.8154e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 34263 16000
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 19
|
||||
New max number of 1-2 to 1-4 neighbors: 20 (+1)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/thole/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes
|
||||
Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2]
|
||||
0 11086.347 2910.7282 202.07402 8175.6191 6565.4851 20.333365 1.0706727e-06 -3299.85 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821
|
||||
50 4712.9507 4669.1606 324.15119 43.790082 1798.561 670.61319 690.16967 -3276.9493 811.643 1305983.2 -1306633.5 17164.771 48631.318 442.24313 116.13094
|
||||
100 2865.9139 3726.4166 258.70226 -860.50272 968.87546 749.70761 860.70151 -3270.7784 427.14745 1306104.7 -1306700.9 15017.273 48631.318 385.10628 35.845353
|
||||
150 1982.6673 3535.974 245.481 -1553.3068 764.86116 768.15837 658.70182 -3278.7906 108.49859 1306136.5 -1306711.2 16495.352 48631.318 378.64023 10.723986
|
||||
200 1440.0277 3240.5932 224.97452 -1800.5656 687.71813 791.29356 643.82915 -3276.9293 -99.549986 1306172.9 -1306719.8 13234.476 48631.318 350.46321 3.7468464
|
||||
250 1103.2915 3018.496 209.55567 -1915.2045 677.97905 825.32748 642.78891 -3278.0801 -226.1853 1306168.5 -1306725.5 8774.9103 48631.318 327.36313 1.8722119
|
||||
300 789.07159 2827.1716 196.27319 -2038.1 735.96101 852.72545 589.14167 -3280.0357 -374.66018 1306169 -1306730.2 2259.1028 48631.318 306.85585 1.3262598
|
||||
350 599.10023 2732.3739 189.69197 -2133.2737 677.67006 863.22888 565.41674 -3280.5231 -403.28794 1306177.4 -1306733.2 7989.222 48631.318 296.64126 1.1534418
|
||||
400 428.26436 2591.2884 179.89727 -2163.0241 676.18745 849.24505 612.34065 -3277.4703 -457.85799 1306173.6 -1306739.1 7282.1438 48631.318 281.34719 1.0502762
|
||||
450 307.26859 2534.2468 175.93722 -2226.9782 712.17636 853.98862 578.01327 -3279.7731 -533.87422 1306179.7 -1306737.2 1897.9643 48631.318 275.11317 1.0980929
|
||||
500 234.60959 2495.1082 173.22007 -2260.4987 707.43541 878.25753 547.08402 -3281.2756 -549.04991 1306176.5 -1306739.5 2683.0639 48631.318 270.85452 1.0984718
|
||||
550 203.34751 2445.6535 169.78673 -2242.306 669.03724 892.85034 599.20664 -3279.0757 -559.81157 1306175.9 -1306740.4 4512.9992 48631.318 265.49465 1.0628812
|
||||
600 205.63573 2526.5892 175.4056 -2320.9535 685.64073 887.97693 557.42296 -3280.0332 -597.34755 1306167.8 -1306742.5 2999.5823 48631.318 274.29935 1.064682
|
||||
650 176.23031 2526.3124 175.38638 -2350.0821 714.15285 895.42115 540.39191 -3280.8567 -636.27783 1306165.7 -1306748.6 871.68316 48631.318 274.2807 1.0442089
|
||||
700 106.97524 2441.1059 169.47101 -2334.1306 697.16018 905.51407 564.71847 -3279.6208 -631.62324 1306159.4 -1306749.6 1953.8241 48631.318 264.98935 1.0771037
|
||||
750 76.695104 2435.6635 169.09318 -2358.9684 672.01039 934.63351 545.64024 -3281.1075 -629.89722 1306152.4 -1306752.6 3044.0155 48631.318 264.39002 1.0932471
|
||||
800 57.614075 2456.928 170.56945 -2399.3139 720.76364 898.68013 534.10051 -3281.5897 -659.64354 1306145.5 -1306757.1 1691.9503 48631.318 266.72089 1.0622697
|
||||
850 -44.931126 2390.0608 165.92727 -2434.9919 708.70192 888.26851 537.13087 -3281.355 -665.17283 1306137.8 -1306760.3 123.07165 48631.318 259.45151 1.0516426
|
||||
900 -96.878205 2358.862 163.76133 -2455.7403 672.98976 868.41571 546.69492 -3280.6939 -636.80102 1306134.5 -1306760.9 1955.7005 48631.318 256.05598 1.05337
|
||||
950 -80.012575 2374.4497 164.84349 -2454.4623 679.59722 880.35157 548.35372 -3280.6061 -643.44517 1306125.8 -1306764.5 1510.9809 48631.318 257.72442 1.1017392
|
||||
1000 -21.440874 2440.6729 169.44096 -2462.1138 718.56593 868.65109 555.54643 -3279.8516 -686.71673 1306126.6 -1306765 -1148.6212 48631.318 264.92977 1.1019339
|
||||
1050 16.46903 2382.6961 165.41598 -2366.2271 712.51245 913.35848 579.81678 -3280.0559 -657.12122 1306129.3 -1306764 1004.5778 48631.318 258.64076 1.0684155
|
||||
1100 35.847247 2483.1985 172.39325 -2447.3513 685.05704 889.42278 553.73166 -3280.0177 -663.67201 1306134.3 -1306766.2 699.1824 48631.318 269.56773 1.0838094
|
||||
1150 -4.9817843 2431.4725 168.80223 -2436.4543 720.51056 868.17547 569.09902 -3280.5829 -677.99865 1306133.1 -1306768.7 435.19118 48631.318 263.96966 1.0303202
|
||||
1200 -23.907197 2443.6035 169.64441 -2467.5107 684.96437 887.58483 549.43666 -3280.3144 -679.46182 1306137.2 -1306766.9 367.11148 48631.318 265.28645 1.0344036
|
||||
1250 -16.904671 2389.9447 165.91921 -2406.8494 722.06959 902.90076 568.35616 -3280.6829 -683.32029 1306132.9 -1306769.1 76.759445 48631.318 259.41697 1.0908431
|
||||
1300 -1.7822102 2410.2768 167.33074 -2412.0591 706.98675 904.31941 551.23506 -3280.7552 -651.51211 1306127.3 -1306769.6 1659.1113 48631.318 261.64093 1.0701648
|
||||
1350 -3.569473 2446.3901 169.83786 -2449.9595 686.13971 894.85839 558.36242 -3279.9941 -664.59508 1306129 -1306773.7 783.32881 48631.318 265.5696 1.0709072
|
||||
1400 -33.385576 2400.262 166.63547 -2433.6476 709.5808 890.68408 571.13105 -3280.1428 -674.51247 1306123.4 -1306773.8 -751.38571 48631.318 260.54522 1.080234
|
||||
1450 -11.215152 2405.5409 167.00196 -2416.756 703.72038 913.21131 552.64196 -3280.9831 -649.19774 1306120.3 -1306776.4 1817.2174 48631.318 261.14741 1.031193
|
||||
1500 -25.974102 2435.8375 169.10527 -2461.8116 689.93174 900.70619 552.63711 -3280.1497 -671.17989 1306124 -1306777.8 -98.941796 48631.318 264.45069 1.0190784
|
||||
1550 -76.496407 2394.8126 166.25716 -2471.309 706.96953 886.06919 549.9101 -3280.8434 -659.57745 1306105.9 -1306779.7 -7.0989994 48631.318 259.95403 1.0772144
|
||||
1600 -79.549932 2395.1114 166.2779 -2474.6614 684.11692 888.93332 562.94522 -3280.1665 -665.21744 1306114.4 -1306779.6 320.58515 48631.318 260.00641 1.0425978
|
||||
1650 -99.702003 2360.5652 163.87957 -2460.2672 706.21244 900.9253 540.36599 -3280.2308 -655.96077 1306109.7 -1306781.3 307.35487 48631.318 256.23383 1.0666637
|
||||
1700 -69.422658 2372.1727 164.68541 -2441.5954 676.79347 913.90473 581.60658 -3279.997 -670.33218 1306115.7 -1306779.3 -204.22848 48631.318 257.50963 1.0434075
|
||||
1750 -80.889897 2425.3592 168.37782 -2506.2491 672.88937 911.52373 523.74733 -3280.4796 -673.90027 1306122 -1306782 965.12568 48631.318 263.26491 1.1001595
|
||||
1800 -82.419368 2361.798 163.96515 -2444.2173 716.51571 882.9729 577.92505 -3278.9279 -671.67438 1306111.6 -1306782.6 -44.954517 48631.318 256.36957 1.0636692
|
||||
1850 -93.715705 2373.3359 164.76616 -2467.0516 713.02466 907.03621 563.38626 -3280.2576 -693.30963 1306104.6 -1306781.5 -979.95945 48631.318 257.62543 1.0628288
|
||||
1900 -73.60945 2449.5873 170.05983 -2523.1967 683.65116 893.94251 539.90847 -3281.4318 -680.16358 1306108 -1306787.1 598.18213 48631.318 265.91405 1.0766352
|
||||
1950 -66.068291 2437.3691 169.21159 -2503.4374 672.5168 877.42934 573.56499 -3279.885 -668.54185 1306109.2 -1306787.7 733.05074 48631.318 264.61409 1.0224258
|
||||
2000 -91.043979 2374.4077 164.84057 -2465.4516 692.13299 909.46192 574.60109 -3279.837 -672.33599 1306102.4 -1306791.8 -665.61581 48631.318 257.76275 1.0263294
|
||||
Loop time of 23.7656 on 4 procs for 2000 steps with 5500 atoms
|
||||
|
||||
Performance: 3.636 ns/day, 6.602 hours/ns, 84.155 timesteps/s
|
||||
94.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 11.918 | 13.096 | 14.137 | 27.0 | 55.10
|
||||
Bond | 0.74012 | 0.76511 | 0.79225 | 2.9 | 3.22
|
||||
Kspace | 6.7821 | 7.8285 | 9.0172 | 35.4 | 32.94
|
||||
Neigh | 0.37249 | 0.37262 | 0.37278 | 0.0 | 1.57
|
||||
Comm | 0.70503 | 0.7188 | 0.72807 | 1.1 | 3.02
|
||||
Output | 0.0018752 | 0.0047592 | 0.013386 | 7.2 | 0.02
|
||||
Modify | 0.91164 | 0.91644 | 0.92123 | 0.5 | 3.86
|
||||
Other | | 0.06335 | | | 0.27
|
||||
|
||||
Nlocal: 1375 ave 1381 max 1368 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Nghost: 7803.75 ave 7856 max 7755 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 334465 ave 349504 max 315867 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 1337859
|
||||
Ave neighs/atom = 243.247
|
||||
Ave special neighs/atom = 15.6364
|
||||
Neighbor list builds = 32
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:23
|
||||
262
examples/USER/drude/toluene/log.7Aug19.toluene.nh.g++.1
Normal file
262
examples/USER/drude/toluene/log.7Aug19.toluene.nh.g++.1
Normal file
@ -0,0 +1,262 @@
|
||||
LAMMPS (7 Aug 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 250 toluene system for drude polarizability example (Nose-Hoover)
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
improper_style fourier
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style lj/cut/thole/long 2.600 8.0 8.0
|
||||
pair_modify mix geometric tail yes
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
read_data data.toluene extra/special/per/atom 1
|
||||
orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
5500 atoms
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
8 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
2 = max impropers/atom
|
||||
reading bonds ...
|
||||
5500 bonds
|
||||
reading angles ...
|
||||
6000 angles
|
||||
reading dihedrals ...
|
||||
6000 dihedrals
|
||||
reading impropers ...
|
||||
1500 impropers
|
||||
5 = max # of 1-2 neighbors
|
||||
10 = max # of 1-3 neighbors
|
||||
16 = max # of 1-4 neighbors
|
||||
20 = max # of special neighbors
|
||||
special bonds CPU = 0.0019815 secs
|
||||
read_data CPU = 0.0168803 secs
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
group gTOLUENE molecule 1:250
|
||||
5500 atoms in group gTOLUENE
|
||||
group gCORES type 1 2 3 4 5 6 7
|
||||
3750 atoms in group gCORES
|
||||
group gDRUDES type 8 9 10 11 12
|
||||
1750 atoms in group gDRUDES
|
||||
|
||||
pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT
|
||||
pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO
|
||||
pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM
|
||||
pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP
|
||||
pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT
|
||||
pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT
|
||||
pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT
|
||||
pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO
|
||||
pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM
|
||||
pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP
|
||||
pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT
|
||||
pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT
|
||||
pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT
|
||||
pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM
|
||||
pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP
|
||||
pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT
|
||||
pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT
|
||||
pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT
|
||||
pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP
|
||||
pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT
|
||||
pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT
|
||||
pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT
|
||||
pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT
|
||||
pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT
|
||||
pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT
|
||||
pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT
|
||||
pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT
|
||||
pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT
|
||||
pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT
|
||||
pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO
|
||||
pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM
|
||||
pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP
|
||||
pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT
|
||||
pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT
|
||||
pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO
|
||||
pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM
|
||||
pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP
|
||||
pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT
|
||||
pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT
|
||||
pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO
|
||||
pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM
|
||||
pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP
|
||||
pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT
|
||||
pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT
|
||||
pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO
|
||||
pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM
|
||||
pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP
|
||||
pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT
|
||||
pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT
|
||||
pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO
|
||||
pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM
|
||||
pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP
|
||||
pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT
|
||||
pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT
|
||||
pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO
|
||||
pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM
|
||||
pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP
|
||||
pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT
|
||||
pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO
|
||||
pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM
|
||||
pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP
|
||||
pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT
|
||||
pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM
|
||||
pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP
|
||||
pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT
|
||||
pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP
|
||||
pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT
|
||||
pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT
|
||||
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 260.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gCORES create ${vTEMP} 12345
|
||||
velocity gCORES create 260 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C C C C N N D D D D D
|
||||
|
||||
fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
|
||||
1250 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
250 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
find clusters CPU = 0.000715256 secs
|
||||
|
||||
compute cTEMP_CORE gCORES temp/com
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
fix fDIRECT all drude/transform/direct
|
||||
fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
|
||||
fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
|
||||
fix fNVT1 gCORES nvt temp 260 260 100.0
|
||||
fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
|
||||
fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
|
||||
fix fNVT2 gDRUDES nvt temp 1 1 20.0
|
||||
fix fINVERSE all drude/transform/inverse
|
||||
|
||||
fix fMOMENTUM all momentum 100 linear 1 1 1
|
||||
|
||||
thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo 50
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:323)
|
||||
G vector (1/distance) = 0.382011
|
||||
grid = 40 40 40
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0325934
|
||||
estimated relative force accuracy = 9.8154e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 103823 64000
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 19
|
||||
New max number of 1-2 to 1-4 neighbors: 20 (+1)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/thole/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 42.06 | 42.06 | 42.06 Mbytes
|
||||
Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2]
|
||||
0 11086.347 2910.7282 202.07402 8175.6191 6565.4851 20.333365 1.0706727e-06 -3299.85 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821
|
||||
50 3563.3755 4630.6343 321.47655 -1067.2588 735.72049 604.78665 689.14827 -3277.411 815.58183 1306088.7 -1306723.8 17813.424 48631.318 503.827 0.0087118192
|
||||
100 3327.4724 4395.1107 305.12559 -1067.6382 597.93176 651.62645 945.4151 -3267.2851 584.58833 1306135.9 -1306715.8 17407.337 48631.318 478.20171 0.0075985539
|
||||
150 3036.9065 4740.2304 329.08513 -1703.3239 558.64983 619.91284 658.80687 -3278.7837 285.12462 1306173 -1306720 18448.248 48631.318 515.75286 0.0063215188
|
||||
200 2697.958 4559.3445 316.52733 -1861.3864 522.09334 593.89129 754.61446 -3273.49 87.660461 1306183.9 -1306730 17888.936 48631.318 496.07143 0.0068706164
|
||||
250 2348.7568 4410.585 306.19988 -2061.8283 506.05007 575.35171 715.55054 -3276.3261 -18.364473 1306177.3 -1306741.4 11592.05 48631.318 479.88562 0.0071741032
|
||||
300 2019.8258 4040.1415 280.48226 -2020.3157 604.3077 641.66689 693.93801 -3278.5312 -115.73641 1306183.2 -1306749.1 3631.3628 48631.318 439.57995 0.0069886387
|
||||
350 1699.5166 3944.9851 273.87613 -2245.4685 452.07416 638.0653 658.79117 -3279.6053 -157.07584 1306196.9 -1306754.6 13544.368 48631.318 429.22694 0.0062868111
|
||||
400 1399.2929 3726.098 258.68014 -2326.8051 457.91943 621.44726 639.39903 -3279.2395 -188.85914 1306185.4 -1306762.8 10792.274 48631.318 405.41134 0.0059340078
|
||||
450 1120.5249 3518.345 244.25712 -2397.8201 519.48856 584.65789 646.36689 -3278.6685 -289.59913 1306184.1 -1306764.2 2755.5598 48631.318 382.80716 0.0055707485
|
||||
500 868.0166 3359.8794 233.25583 -2491.8628 460.7393 581.49563 581.01731 -3281.5544 -252.20169 1306184.3 -1306765.7 6120.3639 48631.318 365.56528 0.0058756154
|
||||
550 637.01567 3214.9521 223.19441 -2577.9364 431.81483 578.87411 540.94047 -3281.5337 -266.36075 1306182.8 -1306764.5 8622.4334 48631.318 349.79661 0.0058589653
|
||||
600 418.04086 3113.4064 216.14472 -2695.3655 430.45935 538.68157 522.24598 -3283.456 -311.87901 1306174.3 -1306765.8 7068.9273 48631.318 338.74797 0.0059567598
|
||||
650 218.5966 2930.8439 203.47052 -2712.2473 514.47294 514.28379 551.52551 -3282.0904 -405.37401 1306164.5 -1306769.5 -13.553736 48631.318 318.88482 0.0052667842
|
||||
700 45.22721 2830.1443 196.47956 -2784.917 451.11156 498.26423 541.18835 -3282.1427 -375.95313 1306157.1 -1306774.4 3947.6276 48631.318 307.92741 0.0068019029
|
||||
750 -114.28621 2798.3153 194.26988 -2912.6016 412.753 503.2878 481.32173 -3284.3411 -393.53984 1306147 -1306779.1 7143.3414 48631.318 304.46466 0.0061596717
|
||||
800 -263.63817 2694.8084 187.08403 -2958.4466 455.67914 487.49754 476.8659 -3284.3133 -451.9578 1306145 -1306787.2 1185.9502 48631.318 293.20288 0.0058203332
|
||||
850 -397.71592 2559.1921 177.66902 -2956.9081 458.83317 481.2262 478.31241 -3284.068 -437.26503 1306138.6 -1306792.6 346.80209 48631.318 278.44745 0.0054921692
|
||||
900 -515.1823 2544.8753 176.67509 -3060.0576 395.00163 457.58988 446.68352 -3285.485 -423.56221 1306145 -1306795.3 3712.8598 48631.318 276.88864 0.0074054008
|
||||
950 -617.28259 2451.1723 170.16987 -3068.4549 383.64277 446.59877 434.4624 -3285.1348 -391.59344 1306142.3 -1306798.7 5429.2488 48631.318 266.69431 0.0057487316
|
||||
1000 -703.15534 2334.837 162.09342 -3037.9923 424.34948 462.21112 451.80809 -3284.3803 -426.53369 1306133.9 -1306799.3 1137.6145 48631.318 254.03675 0.0053914731
|
||||
1050 -771.1763 2303.837 159.94128 -3075.0133 426.21409 436.50718 435.09987 -3285.1939 -411.14054 1306125.6 -1306802.1 1636.9383 48631.318 250.66295 0.0069342505
|
||||
1100 -822.72236 2283.4196 158.52382 -3106.142 376.67684 447.77729 418.45768 -3286.5919 -377.48204 1306118.9 -1306803.8 4760.5163 48631.318 248.44119 0.0074025012
|
||||
1150 -857.06075 2259.0717 156.8335 -3116.1324 400.31523 431.65981 457.68066 -3285.1977 -430.47723 1306115.8 -1306805.9 3194.5161 48631.318 245.79223 0.007063589
|
||||
1200 -875.50848 2238.2637 155.38893 -3113.7722 445.38524 460.97125 432.10511 -3285.4238 -472.46606 1306114.7 -1306809 -653.49784 48631.318 243.52819 0.0071448738
|
||||
1250 -880.37572 2294.6889 159.30618 -3175.0646 411.35427 444.73793 420.06468 -3286.0366 -458.05371 1306104.4 -1306811.5 945.80793 48631.318 249.66481 0.011853487
|
||||
1300 -871.31064 2284.2298 158.58007 -3155.5405 404.97412 441.75285 426.34477 -3285.4859 -424.79609 1306094.9 -1306813.2 4406.6196 48631.318 248.48563 0.084424118
|
||||
1350 -816.70005 2325.9264 161.47481 -3142.6265 696.80296 442.50053 431.19923 -3285.7859 -450.2699 1305836.2 -1306813.3 593.8098 48631.318 251.40749 2.9297319
|
||||
1400 -794.25335 2263.5101 157.14163 -3057.7635 645.65165 466.22086 446.22268 -3285.1821 -420.65317 1305903.7 -1306813.8 1386.3633 48631.318 245.20554 1.8916154
|
||||
1450 -776.10866 2287.6575 158.81803 -3063.7661 427.03477 479.10627 439.67495 -3285.9537 -395.13186 1306087.6 -1306816.1 2936.7806 48631.318 248.87167 0.061343245
|
||||
1500 -725.48181 2371.413 164.63266 -3096.8948 390.03204 464.30903 446.91959 -3284.7809 -393.16613 1306095.4 -1306815.6 3544.25 48631.318 258.01286 0.011586563
|
||||
1550 -671.4904 2315.9297 160.7808 -2987.4201 457.04935 500.25282 464.76203 -3284.9311 -400.98103 1306091.7 -1306815.3 2052.6339 48631.318 251.97726 0.0094517862
|
||||
1600 -618.83633 2449.0918 170.02543 -3067.9281 425.47487 474.65876 471.99171 -3284.3677 -430.32107 1306091.3 -1306816.6 441.15682 48631.318 266.46311 0.014260935
|
||||
1650 -567.82245 2425.2238 168.36842 -2993.0462 421.01953 511.27133 463.22065 -3285.038 -377.24066 1306088.4 -1306814.7 5198.8565 48631.318 263.83185 0.074738268
|
||||
1700 -502.4486 2441.8554 169.52305 -2944.304 642.39962 512.90234 490.38297 -3283.9751 -417.39288 1305929.1 -1306817.7 1141.4411 48631.318 264.52393 2.043674
|
||||
1750 -459.52196 2499.0746 173.49543 -2958.5966 679.38259 505.31787 484.77659 -3284.6272 -384.27736 1305861.6 -1306820.8 1527.2046 48631.318 270.10074 3.1869342
|
||||
1800 -471.14403 2476.2266 171.90923 -2947.3706 442.47741 530.45656 474.03057 -3284.0954 -371.95117 1306084.3 -1306822.6 3392.2533 48631.318 269.36446 0.10416401
|
||||
1850 -462.80763 2536.7112 176.10831 -2999.5188 437.08241 525.07462 474.0838 -3283.7906 -422.23719 1306091.6 -1306821.3 1629.8629 48631.318 275.99502 0.016806806
|
||||
1900 -469.89289 2468.9765 171.4059 -2938.8694 446.77624 531.61059 496.01046 -3284.2338 -395.15325 1306085.7 -1306819.6 3119.5402 48631.318 268.62645 0.014601992
|
||||
1950 -491.08007 2445.5966 169.78278 -2936.6767 457.80452 527.23373 470.18125 -3283.9608 -391.86377 1306101.9 -1306818 1122.5275 48631.318 266.08018 0.018911601
|
||||
2000 -518.40811 2418.7208 167.91696 -2937.1289 415.93135 536.5973 480.44651 -3283.7881 -363.72783 1306096.2 -1306818.7 4475.7317 48631.318 263.09007 0.13504326
|
||||
Loop time of 70.696 on 1 procs for 2000 steps with 5500 atoms
|
||||
|
||||
Performance: 1.222 ns/day, 19.638 hours/ns, 28.290 timesteps/s
|
||||
97.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 48.367 | 48.367 | 48.367 | 0.0 | 68.42
|
||||
Bond | 2.9191 | 2.9191 | 2.9191 | 0.0 | 4.13
|
||||
Kspace | 14.266 | 14.266 | 14.266 | 0.0 | 20.18
|
||||
Neigh | 1.5262 | 1.5262 | 1.5262 | 0.0 | 2.16
|
||||
Comm | 0.27841 | 0.27841 | 0.27841 | 0.0 | 0.39
|
||||
Output | 0.0035572 | 0.0035572 | 0.0035572 | 0.0 | 0.01
|
||||
Modify | 3.2856 | 3.2856 | 3.2856 | 0.0 | 4.65
|
||||
Other | | 0.05018 | | | 0.07
|
||||
|
||||
Nlocal: 5500 ave 5500 max 5500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 15317 ave 15317 max 15317 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.30285e+06 ave 1.30285e+06 max 1.30285e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1302849
|
||||
Ave neighs/atom = 236.882
|
||||
Ave special neighs/atom = 15.6364
|
||||
Neighbor list builds = 44
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:10
|
||||
262
examples/USER/drude/toluene/log.7Aug19.toluene.nh.g++.4
Normal file
262
examples/USER/drude/toluene/log.7Aug19.toluene.nh.g++.4
Normal file
@ -0,0 +1,262 @@
|
||||
LAMMPS (7 Aug 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 250 toluene system for drude polarizability example (Nose-Hoover)
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
improper_style fourier
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style lj/cut/thole/long 2.600 8.0 8.0
|
||||
pair_modify mix geometric tail yes
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
read_data data.toluene extra/special/per/atom 1
|
||||
orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
5500 atoms
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
8 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
2 = max impropers/atom
|
||||
reading bonds ...
|
||||
5500 bonds
|
||||
reading angles ...
|
||||
6000 angles
|
||||
reading dihedrals ...
|
||||
6000 dihedrals
|
||||
reading impropers ...
|
||||
1500 impropers
|
||||
5 = max # of 1-2 neighbors
|
||||
10 = max # of 1-3 neighbors
|
||||
16 = max # of 1-4 neighbors
|
||||
20 = max # of special neighbors
|
||||
special bonds CPU = 0.000718355 secs
|
||||
read_data CPU = 0.0167146 secs
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
group gTOLUENE molecule 1:250
|
||||
5500 atoms in group gTOLUENE
|
||||
group gCORES type 1 2 3 4 5 6 7
|
||||
3750 atoms in group gCORES
|
||||
group gDRUDES type 8 9 10 11 12
|
||||
1750 atoms in group gDRUDES
|
||||
|
||||
pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT
|
||||
pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO
|
||||
pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM
|
||||
pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP
|
||||
pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT
|
||||
pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT
|
||||
pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT
|
||||
pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO
|
||||
pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM
|
||||
pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP
|
||||
pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT
|
||||
pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT
|
||||
pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT
|
||||
pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM
|
||||
pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP
|
||||
pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT
|
||||
pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT
|
||||
pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT
|
||||
pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP
|
||||
pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT
|
||||
pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT
|
||||
pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT
|
||||
pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT
|
||||
pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT
|
||||
pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT
|
||||
pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT
|
||||
pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT
|
||||
pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT
|
||||
pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT
|
||||
pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO
|
||||
pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM
|
||||
pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP
|
||||
pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT
|
||||
pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT
|
||||
pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO
|
||||
pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM
|
||||
pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP
|
||||
pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT
|
||||
pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT
|
||||
pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO
|
||||
pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM
|
||||
pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP
|
||||
pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT
|
||||
pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT
|
||||
pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO
|
||||
pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM
|
||||
pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP
|
||||
pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT
|
||||
pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT
|
||||
pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO
|
||||
pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM
|
||||
pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP
|
||||
pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT
|
||||
pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT
|
||||
pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO
|
||||
pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM
|
||||
pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP
|
||||
pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT
|
||||
pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO
|
||||
pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM
|
||||
pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP
|
||||
pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT
|
||||
pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM
|
||||
pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP
|
||||
pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT
|
||||
pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP
|
||||
pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT
|
||||
pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT
|
||||
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 260.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gCORES create ${vTEMP} 12345
|
||||
velocity gCORES create 260 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C C C C N N D D D D D
|
||||
|
||||
fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
|
||||
1250 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
250 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
find clusters CPU = 0.000344038 secs
|
||||
|
||||
compute cTEMP_CORE gCORES temp/com
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
fix fDIRECT all drude/transform/direct
|
||||
fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
|
||||
fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
|
||||
fix fNVT1 gCORES nvt temp 260 260 100.0
|
||||
fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
|
||||
fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
|
||||
fix fNVT2 gDRUDES nvt temp 1 1 20.0
|
||||
fix fINVERSE all drude/transform/inverse
|
||||
|
||||
fix fMOMENTUM all momentum 100 linear 1 1 1
|
||||
|
||||
thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo 50
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:323)
|
||||
G vector (1/distance) = 0.382011
|
||||
grid = 40 40 40
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0325934
|
||||
estimated relative force accuracy = 9.8154e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 34263 16000
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 19
|
||||
New max number of 1-2 to 1-4 neighbors: 20 (+1)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/thole/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes
|
||||
Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2]
|
||||
0 11086.347 2910.7282 202.07402 8175.6191 6565.4851 20.333365 1.0706727e-06 -3299.85 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821
|
||||
50 3563.376 4630.6343 321.47655 -1067.2583 735.72048 604.78665 689.14826 -3277.411 815.58183 1306088.7 -1306723.8 17813.425 48631.318 503.827 0.0087118179
|
||||
100 3327.4722 4395.1107 305.12559 -1067.6385 597.93175 651.62645 945.4151 -3267.2851 584.58833 1306135.9 -1306715.8 17407.335 48631.318 478.2017 0.0075985638
|
||||
150 3036.9065 4740.2304 329.08513 -1703.3238 558.64983 619.91284 658.80686 -3278.7837 285.12462 1306173 -1306720 18448.248 48631.318 515.75286 0.0063215227
|
||||
200 2697.9581 4559.3445 316.52734 -1861.3864 522.09335 593.8913 754.61446 -3273.49 87.660464 1306183.9 -1306730 17888.937 48631.318 496.07143 0.006870622
|
||||
250 2348.7563 4410.585 306.19988 -2061.8288 506.05006 575.35172 715.55055 -3276.3261 -18.364482 1306177.3 -1306741.4 11592.049 48631.318 479.88562 0.0071741023
|
||||
300 2019.8256 4040.1415 280.48225 -2020.3159 604.30771 641.66688 693.93802 -3278.5312 -115.73639 1306183.2 -1306749.1 3631.3625 48631.318 439.57995 0.0069886424
|
||||
350 1699.5169 3944.9851 273.87613 -2245.4682 452.07416 638.06529 658.79116 -3279.6053 -157.07584 1306196.9 -1306754.6 13544.368 48631.318 429.22695 0.0062868216
|
||||
400 1399.2927 3726.098 258.68014 -2326.8053 457.91943 621.44727 639.39905 -3279.2395 -188.85912 1306185.4 -1306762.8 10792.273 48631.318 405.41133 0.0059340084
|
||||
450 1120.5246 3518.345 244.25712 -2397.8204 519.48859 584.6579 646.36688 -3278.6685 -289.59912 1306184.1 -1306764.2 2755.5597 48631.318 382.80717 0.005570751
|
||||
500 868.01643 3359.8794 233.25583 -2491.863 460.73928 581.49568 581.01732 -3281.5544 -252.20168 1306184.3 -1306765.7 6120.364 48631.318 365.56528 0.0058756204
|
||||
550 637.01646 3214.9521 223.19441 -2577.9356 431.81484 578.87415 540.94046 -3281.5337 -266.36074 1306182.8 -1306764.5 8622.4353 48631.318 349.79661 0.0058589476
|
||||
600 418.04028 3113.4063 216.14471 -2695.3661 430.45936 538.68158 522.24597 -3283.456 -311.87897 1306174.3 -1306765.8 7068.9275 48631.318 338.74796 0.0059567639
|
||||
650 218.59562 2930.8439 203.47052 -2712.2482 514.47296 514.2838 551.52551 -3282.0904 -405.37401 1306164.5 -1306769.5 -13.554086 48631.318 318.88481 0.0052667849
|
||||
700 45.227739 2830.1443 196.47957 -2784.9165 451.11157 498.26426 541.18833 -3282.1427 -375.95321 1306157.1 -1306774.4 3947.6268 48631.318 307.92741 0.0068018884
|
||||
750 -114.28676 2798.3154 194.26988 -2912.6022 412.75298 503.28782 481.32167 -3284.3411 -393.53987 1306147 -1306779.1 7143.3424 48631.318 304.46466 0.0061596613
|
||||
800 -263.63827 2694.8085 187.08403 -2958.4468 455.67916 487.49754 476.86576 -3284.3133 -451.95784 1306145 -1306787.2 1185.9474 48631.318 293.20289 0.0058203323
|
||||
850 -397.71592 2559.1922 177.66903 -2956.9082 458.83313 481.22619 478.31233 -3284.068 -437.26509 1306138.6 -1306792.6 346.80221 48631.318 278.44747 0.0054921238
|
||||
900 -515.18134 2544.8753 176.67509 -3060.0567 395.0016 457.5898 446.68361 -3285.485 -423.56234 1306145.1 -1306795.3 3712.8594 48631.318 276.88864 0.0074054726
|
||||
950 -617.28607 2451.1721 170.16985 -3068.4582 383.6428 446.59872 434.46241 -3285.1348 -391.59326 1306142.3 -1306798.7 5429.2191 48631.318 266.69429 0.0057487961
|
||||
1000 -703.15541 2334.8366 162.09339 -3037.992 424.34957 462.21115 451.80811 -3284.3803 -426.53346 1306133.9 -1306799.3 1137.6144 48631.318 254.03671 0.0053915025
|
||||
1050 -771.17572 2303.8364 159.94123 -3075.0121 426.21406 436.50744 435.10013 -3285.1938 -411.13999 1306125.6 -1306802.1 1636.9467 48631.318 250.66288 0.0069341736
|
||||
1100 -822.72317 2283.421 158.52392 -3106.1442 376.67703 447.77728 418.45763 -3286.5919 -377.48075 1306118.9 -1306803.8 4760.4718 48631.318 248.44134 0.0074024122
|
||||
1150 -857.06061 2259.0725 156.83355 -3116.1331 400.31517 431.65949 457.68078 -3285.1977 -430.47775 1306115.8 -1306805.9 3194.5159 48631.318 245.79231 0.007063706
|
||||
1200 -875.50971 2238.2632 155.38889 -3113.7729 445.38534 460.97161 432.10511 -3285.4238 -472.46582 1306114.7 -1306809 -653.49627 48631.318 243.52813 0.0071446561
|
||||
1250 -880.37609 2294.689 159.30619 -3175.0651 411.35498 444.73774 420.06429 -3286.0366 -458.05353 1306104.4 -1306811.5 945.79687 48631.318 249.66483 0.011854196
|
||||
1300 -871.31122 2284.2295 158.58005 -3155.5407 404.97869 441.75305 426.34479 -3285.4859 -424.79602 1306094.8 -1306813.2 4406.6128 48631.318 248.4856 0.084411062
|
||||
1350 -816.69657 2325.9211 161.47444 -3142.6176 696.85542 442.50059 431.19981 -3285.7859 -450.27129 1305836.1 -1306813.3 593.86622 48631.318 251.40736 2.9289249
|
||||
1400 -794.25213 2263.5122 157.14177 -3057.7643 645.6531 466.2204 446.22253 -3285.1821 -420.65316 1305903.7 -1306813.8 1386.3481 48631.318 245.20568 1.8917548
|
||||
1450 -776.1076 2287.6591 158.81814 -3063.7667 427.0331 479.10417 439.67675 -3285.9536 -395.13308 1306087.6 -1306816.1 2936.7117 48631.318 248.87185 0.061341392
|
||||
1500 -725.48032 2371.4108 164.63251 -3096.8911 390.03135 464.30817 446.91941 -3284.7808 -393.16302 1306095.4 -1306815.6 3544.3635 48631.318 258.01262 0.011585228
|
||||
1550 -671.48696 2315.9233 160.78035 -2987.4102 457.04771 500.26018 464.7623 -3284.931 -400.98142 1306091.7 -1306815.3 2052.6204 48631.318 251.97656 0.0094518433
|
||||
1600 -618.82679 2449.0893 170.02525 -3067.9161 425.47171 474.66369 471.99137 -3284.3677 -430.3224 1306091.3 -1306816.6 441.31257 48631.318 266.46283 0.014263201
|
||||
1650 -567.82233 2425.2281 168.36872 -2993.0504 421.02008 511.26686 463.22202 -3285.0378 -377.24205 1306088.4 -1306814.7 5198.6214 48631.318 263.83232 0.074728934
|
||||
1700 -502.46013 2441.8437 169.52224 -2944.3039 642.39863 512.90005 490.39655 -3283.975 -417.39351 1305929.1 -1306817.7 1141.2401 48631.318 264.52268 2.0436397
|
||||
1750 -459.52135 2499.0847 173.49613 -2958.606 679.34078 505.30943 484.78276 -3284.6269 -384.28217 1305861.7 -1306820.8 1527.0852 48631.318 270.10144 3.1876179
|
||||
1800 -471.14322 2476.2445 171.91047 -2947.3877 442.48278 530.4566 474.0343 -3284.0957 -371.97492 1306084.3 -1306822.6 3392.0306 48631.318 269.36641 0.1041603
|
||||
1850 -462.80151 2536.7173 176.10873 -2999.5188 437.07855 525.05914 474.07725 -3283.7908 -422.22641 1306091.6 -1306821.3 1630.1204 48631.318 275.99568 0.016808725
|
||||
1900 -469.8785 2468.9596 171.40473 -2938.8381 446.7879 531.6128 496.02681 -3284.2335 -395.17163 1306085.7 -1306819.6 3119.2384 48631.318 268.62462 0.014603394
|
||||
1950 -491.07182 2445.6794 169.78853 -2936.7512 457.80204 527.21208 470.1608 -3283.9622 -391.90163 1306101.9 -1306818 1122.0978 48631.318 266.08919 0.018903661
|
||||
2000 -518.41243 2418.604 167.90885 -2937.0165 415.92605 536.62844 480.48912 -3283.7876 -363.72641 1306096.2 -1306818.7 4474.8778 48631.318 263.07743 0.13492637
|
||||
Loop time of 22.3198 on 4 procs for 2000 steps with 5500 atoms
|
||||
|
||||
Performance: 3.871 ns/day, 6.200 hours/ns, 89.606 timesteps/s
|
||||
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 11.452 | 12.249 | 12.556 | 13.2 | 54.88
|
||||
Bond | 0.71352 | 0.72923 | 0.74557 | 1.3 | 3.27
|
||||
Kspace | 5.7189 | 6.0293 | 6.8195 | 18.6 | 27.01
|
||||
Neigh | 0.44028 | 0.44044 | 0.44065 | 0.0 | 1.97
|
||||
Comm | 0.39667 | 0.40817 | 0.41558 | 1.1 | 1.83
|
||||
Output | 0.0019479 | 0.0032187 | 0.0068657 | 3.7 | 0.01
|
||||
Modify | 2.413 | 2.4256 | 2.4347 | 0.5 | 10.87
|
||||
Other | | 0.0349 | | | 0.16
|
||||
|
||||
Nlocal: 1375 ave 1407 max 1349 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Nghost: 8082.5 ave 8114 max 8047 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 325715 ave 343636 max 314954 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1302860
|
||||
Ave neighs/atom = 236.884
|
||||
Ave special neighs/atom = 15.6364
|
||||
Neighbor list builds = 44
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:22
|
||||
1406
examples/USER/misc/local_density/benzene_water/benzene_water.data
Normal file
1406
examples/USER/misc/local_density/benzene_water/benzene_water.data
Normal file
File diff suppressed because it is too large
Load Diff
@ -0,0 +1,62 @@
|
||||
# LAMMPS input file for 26.5% benzene mole fraction solution
|
||||
# with 380 benzene and 1000 water molecules,
|
||||
# using all possible local density potentials
|
||||
# between benzene and water
|
||||
#
|
||||
# Author: Tanmoy Sanyal, Shell Group, UC Santa Barbara
|
||||
#
|
||||
# Refer: Sanyal and Shell, JPC-B, 2018, 122 (21), 5678-5693
|
||||
|
||||
|
||||
|
||||
# Initialize simulation box
|
||||
dimension 3
|
||||
boundary p p p
|
||||
units real
|
||||
atom_style molecular
|
||||
|
||||
# Set potential styles
|
||||
pair_style hybrid/overlay table spline 500 local/density
|
||||
|
||||
# Read molecule data and set initial velocities
|
||||
read_data benzene_water.data
|
||||
velocity all create 3.0000e+02 16611 rot yes dist gaussian
|
||||
|
||||
# Assign potentials
|
||||
pair_coeff 1 1 table benzene_water.pair.table PairBB
|
||||
pair_coeff 1 2 table benzene_water.pair.table PairWW
|
||||
pair_coeff 2 2 table benzene_water.pair.table PairBW
|
||||
pair_coeff * * local/density benzene_water.localdensity.table
|
||||
|
||||
# Recentering during minimization and equilibration
|
||||
fix recentering all recenter 0.0 0.0 0.0 units box
|
||||
|
||||
# Thermostat & time integration
|
||||
timestep 2.0
|
||||
thermo 100
|
||||
thermo_style custom temp ke pe etotal ebond eangle edihed evdwl
|
||||
|
||||
# Minimization
|
||||
minimize 1.e-4 0.0 10000 10000
|
||||
|
||||
# Set up integration parameters
|
||||
fix timeintegration all nve
|
||||
fix thermostat all langevin 3.0000e+02 3.0000e+02 1.0000e+02 81890
|
||||
|
||||
# Equilibration (for realistic results, run for 5000000 steps)
|
||||
reset_timestep 0
|
||||
run 5000
|
||||
|
||||
# Turn off recentering during production phase
|
||||
unfix recentering
|
||||
|
||||
# Setup trajectory output
|
||||
dump myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element
|
||||
dump_modify myDump element B W
|
||||
dump_modify myDump sort id
|
||||
|
||||
# Production (for realistic results, run for 10000000 steps)
|
||||
reset_timestep 0
|
||||
run 1000
|
||||
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
267
examples/USER/misc/local_density/benzene_water/log.04Sep19.g++.1
Normal file
267
examples/USER/misc/local_density/benzene_water/log.04Sep19.g++.1
Normal file
@ -0,0 +1,267 @@
|
||||
LAMMPS (7 Aug 2019)
|
||||
# LAMMPS input file for 26.5% benzene mole fraction solution
|
||||
# with 380 benzene and 1000 water molecules,
|
||||
# using all possible local density potentials
|
||||
# between benzene and water
|
||||
#
|
||||
# Author: Tanmoy Sanyal, Shell Group, UC Santa Barbara
|
||||
#
|
||||
# Refer: Sanyal and Shell, JPC-B, 2018, 122 (21), 5678-5693
|
||||
|
||||
|
||||
|
||||
# Initialize simulation box
|
||||
dimension 3
|
||||
boundary p p p
|
||||
units real
|
||||
atom_style molecular
|
||||
|
||||
# Set potential styles
|
||||
pair_style hybrid/overlay table spline 500 local/density
|
||||
|
||||
# Read molecule data and set initial velocities
|
||||
read_data benzene_water.data
|
||||
orthogonal box = (-12.865 -12.865 -64.829) to (12.865 12.865 64.829)
|
||||
1 by 1 by 8 MPI processor grid
|
||||
reading atoms ...
|
||||
1380 atoms
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000566959 secs
|
||||
read_data CPU = 0.00661397 secs
|
||||
velocity all create 3.0000e+02 16611 rot yes dist gaussian
|
||||
|
||||
# Assign potentials
|
||||
pair_coeff 1 1 table benzene_water.pair.table PairBB
|
||||
WARNING: 33 of 500 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (../pair_table.cpp:483)
|
||||
WARNING: 150 of 500 distance values in table with relative error
|
||||
over 1e-06 to re-computed values (../pair_table.cpp:492)
|
||||
pair_coeff 1 2 table benzene_water.pair.table PairWW
|
||||
WARNING: 61 of 500 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (../pair_table.cpp:483)
|
||||
WARNING: 90 of 500 distance values in table with relative error
|
||||
over 1e-06 to re-computed values (../pair_table.cpp:492)
|
||||
pair_coeff 2 2 table benzene_water.pair.table PairBW
|
||||
WARNING: 108 of 500 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (../pair_table.cpp:483)
|
||||
WARNING: 135 of 500 distance values in table with relative error
|
||||
over 1e-06 to re-computed values (../pair_table.cpp:492)
|
||||
pair_coeff * * local/density benzene_water.localdensity.table
|
||||
|
||||
# Recentering during minimization and equilibration
|
||||
fix recentering all recenter 0.0 0.0 0.0 units box
|
||||
|
||||
# Thermostat & time integration
|
||||
timestep 2.0
|
||||
thermo 100
|
||||
thermo_style custom temp ke pe etotal ebond eangle edihed evdwl
|
||||
|
||||
# Minimization
|
||||
minimize 1.e-4 0.0 10000 10000
|
||||
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 15.25
|
||||
ghost atom cutoff = 15.25
|
||||
binsize = 7.625, bins = 4 4 18
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair local/density, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.061 | 8.32 | 8.674 Mbytes
|
||||
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl
|
||||
300 1233.1611 4162.3053 5395.4665 0 0 0 4162.3053
|
||||
300 1233.1611 2275.526 3508.6871 0 0 0 2275.526
|
||||
Loop time of 0.352822 on 8 procs for 40 steps with 1380 atoms
|
||||
|
||||
71.3% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = linesearch alpha is zero
|
||||
Energy initial, next-to-last, final =
|
||||
4162.30533361 2208.86525108 2275.52597861
|
||||
Force two-norm initial, final = 259.364 69.3915
|
||||
Force max component initial, final = 22.2077 8.31436
|
||||
Final line search alpha, max atom move = 2.90022e-12 2.41135e-11
|
||||
Iterations, force evaluations = 40 110
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.053192 | 0.23903 | 0.32779 | 17.2 | 67.75
|
||||
Bond | 9.0599e-06 | 1.6302e-05 | 2.5272e-05 | 0.0 | 0.00
|
||||
Neigh | 0.00044513 | 0.0023614 | 0.0063851 | 5.1 | 0.67
|
||||
Comm | 0.015469 | 0.090432 | 0.20295 | 20.0 | 25.63
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.02098 | | | 5.95
|
||||
|
||||
Nlocal: 172.5 ave 348 max 72 min
|
||||
Histogram: 5 0 0 0 0 0 0 0 1 2
|
||||
Nghost: 2193.62 ave 4352 max 932 min
|
||||
Histogram: 3 0 0 2 0 0 2 0 0 1
|
||||
Neighs: 9700.5 ave 20535 max 3685 min
|
||||
Histogram: 5 0 0 0 0 0 0 1 0 2
|
||||
|
||||
Total # of neighbors = 77604
|
||||
Ave neighs/atom = 56.2348
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
# Set up integration parameters
|
||||
fix timeintegration all nve
|
||||
fix thermostat all langevin 3.0000e+02 3.0000e+02 1.0000e+02 81890
|
||||
|
||||
# Equilibration (for realistic results, run for 5000000 steps)
|
||||
reset_timestep 0
|
||||
run 5000
|
||||
WARNING: Fix recenter should come after all other integration fixes (../fix_recenter.cpp:131)
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.936 | 7.195 | 7.552 Mbytes
|
||||
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl
|
||||
300 1233.1611 2866.9109 4100.0721 0 0 0 2866.9109
|
||||
273.33541 1123.5553 3983.2007 5106.756 0 0 0 3983.2007
|
||||
293.68078 1207.1857 3319.6601 4526.8458 0 0 0 3319.6601
|
||||
314.21462 1291.5908 3389.2178 4680.8086 0 0 0 3389.2178
|
||||
323.77563 1330.8917 3332.9828 4663.8745 0 0 0 3332.9828
|
||||
302.5902 1243.8082 3461.7692 4705.5774 0 0 0 3461.7692
|
||||
295.39324 1214.2249 3411.5727 4625.7976 0 0 0 3411.5727
|
||||
320.52341 1317.5234 3453.1931 4770.7164 0 0 0 3453.1931
|
||||
312.00777 1282.5195 3403.3443 4685.8638 0 0 0 3403.3443
|
||||
307.96774 1265.9128 3429.7809 4695.6937 0 0 0 3429.7809
|
||||
294.75922 1211.6187 3388.8404 4600.4591 0 0 0 3388.8404
|
||||
311.24567 1279.3869 3514.9603 4794.3472 0 0 0 3514.9603
|
||||
306.6152 1260.3531 3447.2011 4707.5542 0 0 0 3447.2011
|
||||
305.23306 1254.6718 3375.5092 4630.181 0 0 0 3375.5092
|
||||
321.62889 1322.0675 3460.2581 4782.3256 0 0 0 3460.2581
|
||||
316.37725 1300.4804 3437.0312 4737.5116 0 0 0 3437.0312
|
||||
322.90522 1327.3139 3389.1262 4716.44 0 0 0 3389.1262
|
||||
307.57893 1264.3146 3359.8491 4624.1637 0 0 0 3359.8491
|
||||
302.22607 1242.3115 3406.1711 4648.4826 0 0 0 3406.1711
|
||||
302.73997 1244.4239 3220.2582 4464.6821 0 0 0 3220.2582
|
||||
303.66194 1248.2137 3318.4629 4566.6765 0 0 0 3318.4629
|
||||
308.73862 1269.0815 3369.5894 4638.671 0 0 0 3369.5894
|
||||
315.60294 1297.2976 3411.2405 4708.5381 0 0 0 3411.2405
|
||||
310.0113 1274.3129 3360.1054 4634.4183 0 0 0 3360.1054
|
||||
302.36229 1242.8714 3326.9845 4569.8559 0 0 0 3326.9845
|
||||
317.78659 1306.2735 3355.4976 4661.7711 0 0 0 3355.4976
|
||||
302.50479 1243.4571 3317.6846 4561.1417 0 0 0 3317.6846
|
||||
304.29249 1250.8056 3423.5068 4674.3124 0 0 0 3423.5068
|
||||
305.99948 1257.8222 3432.9395 4690.7617 0 0 0 3432.9395
|
||||
309.93363 1273.9937 3393.657 4667.6506 0 0 0 3393.657
|
||||
316.14884 1299.5415 3463.0636 4762.6051 0 0 0 3463.0636
|
||||
300.38817 1234.7567 3309.2495 4544.0062 0 0 0 3309.2495
|
||||
311.05735 1278.6128 3304.4418 4583.0546 0 0 0 3304.4418
|
||||
311.11872 1278.865 3291.1891 4570.0542 0 0 0 3291.1891
|
||||
315.74338 1297.8749 3341.3063 4639.1812 0 0 0 3341.3063
|
||||
297.5658 1223.1552 3316.3862 4539.5414 0 0 0 3316.3862
|
||||
311.79033 1281.6257 3357.4556 4639.0813 0 0 0 3357.4556
|
||||
310.93666 1278.1167 3414.7694 4692.8861 0 0 0 3414.7694
|
||||
307.37298 1263.468 3337.3889 4600.8569 0 0 0 3337.3889
|
||||
298.84185 1228.4005 3329.6173 4558.0178 0 0 0 3329.6173
|
||||
310.54684 1276.5143 3351.0852 4627.5995 0 0 0 3351.0852
|
||||
300.0871 1233.5191 3302.2315 4535.7506 0 0 0 3302.2315
|
||||
304.69078 1252.4427 3324.2508 4576.6935 0 0 0 3324.2508
|
||||
313.50714 1288.6827 3330.4088 4619.0915 0 0 0 3330.4088
|
||||
329.80018 1355.6559 3301.86 4657.5159 0 0 0 3301.86
|
||||
304.57609 1251.9713 3365.2938 4617.2652 0 0 0 3365.2938
|
||||
308.73584 1269.0701 3344.4155 4613.4856 0 0 0 3344.4155
|
||||
306.90951 1261.5629 3304.4698 4566.0327 0 0 0 3304.4698
|
||||
308.85761 1269.5707 3392.1511 4661.7218 0 0 0 3392.1511
|
||||
302.78788 1244.6208 3317.0849 4561.7057 0 0 0 3317.0849
|
||||
321.68092 1322.2813 3321.5755 4643.8568 0 0 0 3321.5755
|
||||
Loop time of 16.3061 on 8 procs for 5000 steps with 1380 atoms
|
||||
|
||||
Performance: 52.986 ns/day, 0.453 hours/ns, 306.634 timesteps/s
|
||||
69.6% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.1872 | 10.542 | 14.607 | 116.7 | 64.65
|
||||
Bond | 0.00044084 | 0.00069669 | 0.00095081 | 0.0 | 0.00
|
||||
Neigh | 0.026948 | 0.15225 | 0.44344 | 42.0 | 0.93
|
||||
Comm | 0.63452 | 4.2953 | 9.49 | 133.9 | 26.34
|
||||
Output | 0.0016391 | 0.012378 | 0.050919 | 13.9 | 0.08
|
||||
Modify | 0.45894 | 1.2107 | 4.4629 | 116.4 | 7.42
|
||||
Other | | 0.09292 | | | 0.57
|
||||
|
||||
Nlocal: 172.5 ave 380 max 70 min
|
||||
Histogram: 5 0 0 0 0 0 0 1 1 1
|
||||
Nghost: 2213 ave 4440 max 903 min
|
||||
Histogram: 3 0 0 2 0 0 2 0 0 1
|
||||
Neighs: 10042.5 ave 24051 max 3500 min
|
||||
Histogram: 5 0 0 0 0 0 0 1 1 1
|
||||
|
||||
Total # of neighbors = 80340
|
||||
Ave neighs/atom = 58.2174
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 123
|
||||
Dangerous builds = 1
|
||||
|
||||
# Turn off recentering during production phase
|
||||
unfix recentering
|
||||
|
||||
# Setup trajectory output
|
||||
dump myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element
|
||||
dump_modify myDump element B W
|
||||
dump_modify myDump sort id
|
||||
|
||||
# Production (for realistic results, run for 10000000 steps)
|
||||
reset_timestep 0
|
||||
run 1000
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.232 | 8.492 | 8.851 Mbytes
|
||||
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl
|
||||
321.68092 1322.2813 3784.0834 5106.3647 0 0 0 3784.0834
|
||||
310.59763 1276.7231 3318.3283 4595.0513 0 0 0 3318.3283
|
||||
303.39445 1247.1141 3324.1191 4571.2332 0 0 0 3324.1191
|
||||
311.37275 1279.9092 3305.0901 4584.9993 0 0 0 3305.0901
|
||||
311.29071 1279.572 3248.216 4527.788 0 0 0 3248.216
|
||||
314.53456 1292.906 3283.4563 4576.3623 0 0 0 3283.4563
|
||||
316.52595 1301.0916 3258.9171 4560.0087 0 0 0 3258.9171
|
||||
318.92447 1310.9509 3235.6256 4546.5765 0 0 0 3235.6256
|
||||
311.79212 1281.6331 3308.099 4589.7321 0 0 0 3308.099
|
||||
305.52477 1255.8709 3267.6907 4523.5616 0 0 0 3267.6907
|
||||
301.07457 1237.5782 3206.3997 4443.9779 0 0 0 3206.3997
|
||||
Loop time of 4.44139 on 8 procs for 1000 steps with 1380 atoms
|
||||
|
||||
Performance: 38.907 ns/day, 0.617 hours/ns, 225.155 timesteps/s
|
||||
60.8% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.656 | 2.5078 | 3.5775 | 57.7 | 56.46
|
||||
Bond | 0.00013375 | 0.0001854 | 0.0002377 | 0.0 | 0.00
|
||||
Neigh | 0.0048757 | 0.029188 | 0.090432 | 18.9 | 0.66
|
||||
Comm | 0.51836 | 1.4427 | 2.6285 | 56.9 | 32.48
|
||||
Output | 0.083084 | 0.089199 | 0.10333 | 2.3 | 2.01
|
||||
Modify | 0.0087376 | 0.019705 | 0.038437 | 8.4 | 0.44
|
||||
Other | | 0.3526 | | | 7.94
|
||||
|
||||
Nlocal: 172.5 ave 388 max 69 min
|
||||
Histogram: 5 0 0 0 0 0 0 2 0 1
|
||||
Nghost: 2207.88 ave 4429 max 896 min
|
||||
Histogram: 3 0 0 2 0 0 2 0 0 1
|
||||
Neighs: 10094.1 ave 24847 max 3403 min
|
||||
Histogram: 5 0 0 0 0 0 1 1 0 1
|
||||
|
||||
Total # of neighbors = 80753
|
||||
Ave neighs/atom = 58.5167
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 23
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Total wall time: 0:00:21
|
||||
@ -0,0 +1,226 @@
|
||||
LAMMPS (7 Aug 2019)
|
||||
# LAMMPS input file for 50.0% methanol mole fraction solution
|
||||
# with 2500 methanol molecules in implicit water.
|
||||
#
|
||||
#
|
||||
# Author: David Rosenberger, van der Vegt Group, TU Darmstadt
|
||||
#
|
||||
# Refer: Rosenberger, Sanyal, Shell, van der Vegt, J. Chem. Theory Comput. 15, 2881-2895 (2019)
|
||||
|
||||
|
||||
# Initialize simulation box
|
||||
dimension 3
|
||||
boundary p p p
|
||||
units real
|
||||
atom_style molecular
|
||||
|
||||
# Set potential styles
|
||||
pair_style hybrid/overlay table spline 500 local/density
|
||||
|
||||
# Read molecule data and set initial velocities
|
||||
read_data methanol_implicit_water.data
|
||||
orthogonal box = (-31.123 -31.123 -31.123) to (31.123 31.123 31.123)
|
||||
2 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2500 atoms
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.00063014 secs
|
||||
read_data CPU = 0.00599909 secs
|
||||
velocity all create 3.0000e+02 12142 rot yes dist gaussian
|
||||
|
||||
# Assign potentials
|
||||
pair_coeff 1 1 table methanol_implicit_water.pair.table PairMM
|
||||
WARNING: 93 of 500 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (../pair_table.cpp:483)
|
||||
WARNING: 254 of 500 distance values in table with relative error
|
||||
over 1e-06 to re-computed values (../pair_table.cpp:492)
|
||||
pair_coeff * * local/density methanol_implicit_water.localdensity.table
|
||||
|
||||
|
||||
|
||||
|
||||
#Recentering during minimization and equilibration
|
||||
fix recentering all recenter 0.0 0.0 0.0 units box
|
||||
|
||||
#Thermostat & time integration
|
||||
timestep 1.0
|
||||
thermo 100
|
||||
thermo_style custom etotal ke pe temp evdwl
|
||||
|
||||
#minimization
|
||||
minimize 1.e-4 0.0 1000 1000
|
||||
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 17
|
||||
ghost atom cutoff = 17
|
||||
binsize = 8.5, bins = 8 8 8
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair local/density, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.411 | 7.411 | 7.412 Mbytes
|
||||
TotEng KinEng PotEng Temp E_vdwl
|
||||
1470.3564 2234.7133 -764.35689 300 -764.35689
|
||||
46.496766 2234.7133 -2188.2165 300 -2188.2165
|
||||
7.9030246 2234.7133 -2226.8103 300 -2226.8103
|
||||
Loop time of 0.463996 on 8 procs for 121 steps with 2500 atoms
|
||||
|
||||
91.4% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = linesearch alpha is zero
|
||||
Energy initial, next-to-last, final =
|
||||
-764.356892369 -2227.85589084 -2226.81026984
|
||||
Force two-norm initial, final = 134.911 3.83896
|
||||
Force max component initial, final = 14.1117 1.07422
|
||||
Final line search alpha, max atom move = 5.06747e-10 5.44356e-10
|
||||
Iterations, force evaluations = 121 154
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.41442 | 0.41976 | 0.42434 | 0.5 | 90.47
|
||||
Bond | 1.1683e-05 | 2.0713e-05 | 3.5048e-05 | 0.0 | 0.00
|
||||
Neigh | 0.0084722 | 0.0090862 | 0.010038 | 0.5 | 1.96
|
||||
Comm | 0.022712 | 0.028157 | 0.034072 | 1.9 | 6.07
|
||||
Output | 3.1948e-05 | 3.6925e-05 | 6.6996e-05 | 0.0 | 0.01
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.006937 | | | 1.50
|
||||
|
||||
Nlocal: 312.5 ave 333 max 299 min
|
||||
Histogram: 2 2 0 0 1 0 2 0 0 1
|
||||
Nghost: 2546 ave 2580 max 2517 min
|
||||
Histogram: 1 1 0 3 0 1 0 0 0 2
|
||||
Neighs: 33215.4 ave 37251 max 29183 min
|
||||
Histogram: 1 0 0 1 2 2 0 1 0 1
|
||||
|
||||
Total # of neighbors = 265723
|
||||
Ave neighs/atom = 106.289
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
|
||||
#set up integration parameters
|
||||
fix timeintegration all nve
|
||||
fix thermostat all langevin 3.0000e+02 3.0000e+02 1.0000e+02 59915
|
||||
|
||||
#Equilibration (for realistic results, run for 2000000 steps)
|
||||
reset_timestep 0
|
||||
thermo 200
|
||||
thermo_style custom etotal ke pe temp evdwl
|
||||
|
||||
#run equilibration
|
||||
run 2000
|
||||
WARNING: Fix recenter should come after all other integration fixes (../fix_recenter.cpp:131)
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.286 | 6.286 | 6.287 Mbytes
|
||||
TotEng KinEng PotEng Temp E_vdwl
|
||||
177.26822 2234.7133 -2057.4451 300 -2057.4451
|
||||
736.24287 2151.2608 -1415.0179 288.79688 -1415.0179
|
||||
963.07617 2090.6433 -1127.5671 280.65926 -1127.5671
|
||||
1148.9049 2173.1327 -1024.2279 291.73309 -1024.2279
|
||||
1303.6409 2279.8586 -976.21767 306.06055 -976.21767
|
||||
1355.42 2281.0383 -925.61826 306.21892 -925.61826
|
||||
1394.5206 2276.2093 -881.68863 305.57064 -881.68863
|
||||
1346.9764 2215.2973 -868.32091 297.3935 -868.32091
|
||||
1381.3654 2248.8061 -867.44063 301.89189 -867.44063
|
||||
1315.8059 2189.3193 -873.51332 293.90606 -873.51332
|
||||
1314.4456 2209.7431 -895.29752 296.64787 -895.29752
|
||||
Loop time of 6.38989 on 8 procs for 2000 steps with 2500 atoms
|
||||
|
||||
Performance: 27.043 ns/day, 0.887 hours/ns, 312.994 timesteps/s
|
||||
80.5% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.2693 | 5.3572 | 5.457 | 2.1 | 83.84
|
||||
Bond | 0.00028825 | 0.00033835 | 0.00039148 | 0.0 | 0.01
|
||||
Neigh | 0.0296 | 0.032337 | 0.035071 | 0.9 | 0.51
|
||||
Comm | 0.64679 | 0.73397 | 0.80847 | 5.2 | 11.49
|
||||
Output | 0.00033498 | 0.00051582 | 0.0015228 | 0.0 | 0.01
|
||||
Modify | 0.16395 | 0.18919 | 0.21056 | 3.9 | 2.96
|
||||
Other | | 0.07636 | | | 1.19
|
||||
|
||||
Nlocal: 312.5 ave 337 max 295 min
|
||||
Histogram: 2 2 0 1 0 0 0 1 1 1
|
||||
Nghost: 2551.62 ave 2582 max 2525 min
|
||||
Histogram: 2 1 0 0 1 1 1 0 1 1
|
||||
Neighs: 33241.8 ave 37659 max 29705 min
|
||||
Histogram: 2 0 0 2 2 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 265934
|
||||
Ave neighs/atom = 106.374
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 21
|
||||
Dangerous builds = 0
|
||||
|
||||
#turn off recentering during production run
|
||||
unfix recentering
|
||||
|
||||
|
||||
#setup trajectory output
|
||||
dump myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element
|
||||
dump_modify myDump element M
|
||||
dump_modify myDump sort id
|
||||
|
||||
#run production (for realistic results, run for 10000000 steps)
|
||||
reset_timestep 0
|
||||
thermo 1000
|
||||
thermo_style custom etotal ke pe temp evdwl
|
||||
run 10000
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.588 | 7.589 | 7.589 Mbytes
|
||||
TotEng KinEng PotEng Temp E_vdwl
|
||||
1442.5428 2209.7431 -767.20027 296.64787 -767.20027
|
||||
1391.8624 2262.6889 -870.82656 303.7556 -870.82656
|
||||
1375.914 2244.6176 -868.7036 301.3296 -868.7036
|
||||
1345.9064 2227.2324 -881.32599 298.99573 -881.32599
|
||||
1379.2334 2278.1156 -898.88222 305.82657 -898.88222
|
||||
1389.7928 2255.8062 -866.01341 302.83163 -866.01341
|
||||
1380.4549 2258.2108 -877.75582 303.15443 -877.75582
|
||||
1380.8489 2256.9432 -876.09428 302.98426 -876.09428
|
||||
1326.5151 2225.7408 -899.22577 298.79549 -899.22577
|
||||
1376.6025 2253.0128 -876.41028 302.45662 -876.41028
|
||||
1331.0008 2218.1033 -887.10258 297.77019 -887.10258
|
||||
Loop time of 25.4591 on 8 procs for 10000 steps with 2500 atoms
|
||||
|
||||
Performance: 33.937 ns/day, 0.707 hours/ns, 392.787 timesteps/s
|
||||
89.3% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 21.635 | 21.916 | 22.237 | 3.9 | 86.08
|
||||
Bond | 0.0011308 | 0.0013149 | 0.0016932 | 0.5 | 0.01
|
||||
Neigh | 0.14593 | 0.15675 | 0.16667 | 1.9 | 0.62
|
||||
Comm | 1.3789 | 1.7502 | 1.9558 | 13.7 | 6.87
|
||||
Output | 0.34664 | 0.82927 | 1.2013 | 32.8 | 3.26
|
||||
Modify | 0.24904 | 0.25842 | 0.26907 | 1.2 | 1.02
|
||||
Other | | 0.5475 | | | 2.15
|
||||
|
||||
Nlocal: 312.5 ave 327 max 298 min
|
||||
Histogram: 2 0 0 1 1 0 1 1 1 1
|
||||
Nghost: 2575 ave 2601 max 2559 min
|
||||
Histogram: 2 0 3 1 0 0 0 0 1 1
|
||||
Neighs: 33223.2 ave 35920 max 30303 min
|
||||
Histogram: 1 1 1 1 0 1 0 0 0 3
|
||||
|
||||
Total # of neighbors = 265786
|
||||
Ave neighs/atom = 106.314
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 103
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Total wall time: 0:00:32
|
||||
File diff suppressed because it is too large
Load Diff
@ -0,0 +1,68 @@
|
||||
# LAMMPS input file for 50.0% methanol mole fraction solution
|
||||
# with 2500 methanol molecules in implicit water.
|
||||
#
|
||||
#
|
||||
# Author: David Rosenberger, van der Vegt Group, TU Darmstadt
|
||||
#
|
||||
# Refer: Rosenberger, Sanyal, Shell, van der Vegt, J. Chem. Theory Comput. 15, 2881-2895 (2019)
|
||||
|
||||
|
||||
# Initialize simulation box
|
||||
dimension 3
|
||||
boundary p p p
|
||||
units real
|
||||
atom_style molecular
|
||||
|
||||
# Set potential styles
|
||||
pair_style hybrid/overlay table spline 500 local/density
|
||||
|
||||
# Read molecule data and set initial velocities
|
||||
read_data methanol_implicit_water.data
|
||||
velocity all create 3.0000e+02 12142 rot yes dist gaussian
|
||||
|
||||
# Assign potentials
|
||||
pair_coeff 1 1 table methanol_implicit_water.pair.table PairMM
|
||||
pair_coeff * * local/density methanol_implicit_water.localdensity.table
|
||||
|
||||
|
||||
|
||||
|
||||
#Recentering during minimization and equilibration
|
||||
fix recentering all recenter 0.0 0.0 0.0 units box
|
||||
|
||||
#Thermostat & time integration
|
||||
timestep 1.0
|
||||
thermo 100
|
||||
thermo_style custom etotal ke pe temp evdwl
|
||||
|
||||
#minimization
|
||||
minimize 1.e-4 0.0 1000 1000
|
||||
|
||||
#set up integration parameters
|
||||
fix timeintegration all nve
|
||||
fix thermostat all langevin 3.0000e+02 3.0000e+02 1.0000e+02 59915
|
||||
|
||||
#Equilibration (for realistic results, run for 2000000 steps)
|
||||
reset_timestep 0
|
||||
thermo 200
|
||||
thermo_style custom etotal ke pe temp evdwl
|
||||
|
||||
#run equilibration
|
||||
run 2000
|
||||
|
||||
#turn off recentering during production run
|
||||
unfix recentering
|
||||
|
||||
|
||||
#setup trajectory output
|
||||
dump myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element
|
||||
dump_modify myDump element M
|
||||
dump_modify myDump sort id
|
||||
|
||||
#run production (for realistic results, run for 10000000 steps)
|
||||
reset_timestep 0
|
||||
thermo 1000
|
||||
thermo_style custom etotal ke pe temp evdwl
|
||||
run 10000
|
||||
|
||||
|
||||
@ -0,0 +1,509 @@
|
||||
#LOCAL DENSITY POTENTIALS
|
||||
|
||||
1 500
|
||||
|
||||
5.3000000e+00 6.3000000e+00
|
||||
1
|
||||
1
|
||||
0.0000000e+00 2.6000000e+01 5.2104208e-02
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4810000e-01
|
||||
1.4807157e-01
|
||||
1.4782582e-01
|
||||
1.4711763e-01
|
||||
1.4570179e-01
|
||||
1.4333312e-01
|
||||
1.3976643e-01
|
||||
1.3478059e-01
|
||||
1.2856173e-01
|
||||
1.2163552e-01
|
||||
1.1453802e-01
|
||||
1.0780525e-01
|
||||
1.0197328e-01
|
||||
9.7575837e-02
|
||||
9.4875548e-02
|
||||
9.3613063e-02
|
||||
9.3469690e-02
|
||||
9.4126738e-02
|
||||
9.5265515e-02
|
||||
9.6567329e-02
|
||||
9.7735007e-02
|
||||
9.8575495e-02
|
||||
9.8927186e-02
|
||||
9.8628481e-02
|
||||
9.7517779e-02
|
||||
9.5433481e-02
|
||||
9.2235018e-02
|
||||
8.8072568e-02
|
||||
8.3308496e-02
|
||||
7.8309990e-02
|
||||
7.3444241e-02
|
||||
6.9078438e-02
|
||||
6.5577180e-02
|
||||
6.3110699e-02
|
||||
6.1523109e-02
|
||||
6.0627357e-02
|
||||
6.0236386e-02
|
||||
6.0163144e-02
|
||||
6.0220573e-02
|
||||
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|
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|
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|
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|
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|
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2.4405000e-02
|
||||
2.4405000e-02
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user