Commit e79cd6c6 authored by Stefan Paquay's avatar Stefan Paquay
Browse files

Moved some stuff around.

parent 0448bc9c
......@@ -37,6 +37,10 @@ enable_language(CXX)
#####################################################################
include(CheckCCompilerFlag)
if (${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
endif()
########################################################################
# User input options #
########################################################################
......@@ -76,7 +80,7 @@ add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
if(LAMMPS_EXCEPTIONS)
add_definitions(-DLAMMPS_EXCEPTIONS)
set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES -DLAMMPS_EXCEPTIONS")
set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_EXCEPTIONS")
endif()
set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary and liblammps (WON'T enable any features automatically")
......@@ -101,7 +105,7 @@ set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE
USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
USER-SMTBQ USER-SPH USER-TALLY USER-VTK USER-QUIP USER-QMMM)
USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
foreach(PKG ${DEFAULT_PACKAGES})
option(ENABLE_${PKG} "Build ${PKG} Package" ${ENABLE_ALL})
......@@ -665,7 +669,9 @@ include_directories(${LAMMPS_STYLE_HEADERS_DIR})
############################################
add_library(lammps ${LIB_SOURCES})
target_link_libraries(lammps ${LAMMPS_LINK_LIBS})
add_dependencies(lammps ${LAMMPS_DEPS})
if(LAMMPS_DEPS)
add_dependencies(lammps ${LAMMPS_DEPS})
endif()
set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
if(BUILD_SHARED_LIBS)
set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
......
\documentclass[12pt]{article}
\pagestyle{empty}
\begin{document}
$$
E = K (r^2 - r_0^2)^2
$$
\end{document}
\documentclass[12pt]{article}
\begin{document}
\begin{eqnarray*}
U &=& \frac{1}{2} K (|\rho_{\vec{k}}| - a)^2 \\
\rho_{\vec{k}} &=& \sum_j^N \exp(-i\vec{k} \cdot \vec{r}_j )/\sqrt{N} \\
\vec{k} &=& (2\pi n_x /L_x , 2\pi n_y /L_y , 2\pi n_z/L_z )
\end{eqnarray*}
\end{document}
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doc/src/JPG/user_intel.png
doc/src/JPG/user_intel.png
doc/src/JPG/user_intel.png
doc/src/JPG/user_intel.png
  • 2-up
  • Swipe
  • Onion skin
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="22 Sep 2017 version">
<META NAME="docnumber" CONTENT="23 Oct 2017 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 @@
<H1></H1>
LAMMPS Documentation :c,h3
22 Sep 2017 version :c,h4
23 Oct 2017 version :c,h4
Version info: :h4
......
......@@ -720,6 +720,8 @@ package"_Section_start.html#start_3.
"nve/eff"_fix_nve_eff.html,
"nvt/eff"_fix_nh_eff.html,
"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
"npt/uef"_fix_nh_uef.html,
"nvt/uef"_fix_nh_uef.html,
"phonon"_fix_phonon.html,
"pimd"_fix_pimd.html,
"qbmsst"_fix_qbmsst.html,
......@@ -728,6 +730,7 @@ package"_Section_start.html#start_3.
"qtb"_fix_qtb.html,
"reax/c/bonds"_fix_reax_bonds.html,
"reax/c/species"_fix_reaxc_species.html,
"rhok"_fix_rhok.html,
"rx"_fix_rx.html,
"saed/vtk"_fix_saed_vtk.html,
"shardlow"_fix_shardlow.html,
......@@ -856,6 +859,7 @@ package"_Section_start.html#start_3.
"meso/t/atom"_compute_meso_t_atom.html,
"pe/tally"_compute_tally.html,
"pe/mol/tally"_compute_tally.html,
"pressure/uef"_compute_pressure_uef.html,
"saed"_compute_saed.html,
"smd/contact/radius"_compute_smd_contact_radius.html,
"smd/damage"_compute_smd_damage.html,
......@@ -884,6 +888,7 @@ package"_Section_start.html#start_3.
"temp/deform/eff"_compute_temp_deform_eff.html,
"temp/region/eff"_compute_temp_region_eff.html,
"temp/rotate"_compute_temp_rotate.html,
"temp/uef"_compute_temp_uef.html,
"xrd"_compute_xrd.html :tb(c=6,ea=c)
:line
......@@ -915,11 +920,12 @@ KOKKOS, o = USER-OMP, t = OPT.
"born/coul/long/cs"_pair_born.html,
"born/coul/msm (o)"_pair_born.html,
"born/coul/wolf (go)"_pair_born.html,
"born/coul/wolf/cs"_pair_born.html,
"brownian (o)"_pair_brownian.html,
"brownian/poly (o)"_pair_brownian.html,
"buck (gkio)"_pair_buck.html,
"buck/coul/cut (gkio)"_pair_buck.html,
"buck/coul/long (gkio)"_pair_buck.html,
"buck (giko)"_pair_buck.html,
"buck/coul/cut (giko)"_pair_buck.html,
"buck/coul/long (giko)"_pair_buck.html,
"buck/coul/long/cs"_pair_buck.html,
"buck/coul/msm (o)"_pair_buck.html,
"buck/long/coul/long (o)"_pair_buck_long.html,
......@@ -934,12 +940,13 @@ KOKKOS, o = USER-OMP, t = OPT.
"coul/msm"_pair_coul.html,
"coul/streitz"_pair_coul.html,
"coul/wolf (ko)"_pair_coul.html,
"dpd (go)"_pair_dpd.html,
"coul/wolf/cs"_pair_coul.html,
"dpd (gio)"_pair_dpd.html,
"dpd/tstat (go)"_pair_dpd.html,
"dsmc"_pair_dsmc.html,
"eam (gkiot)"_pair_eam.html,
"eam/alloy (gkiot)"_pair_eam.html,
"eam/fs (gkiot)"_pair_eam.html,
"eam (gikot)"_pair_eam.html,
"eam/alloy (gikot)"_pair_eam.html,
"eam/fs (gikot)"_pair_eam.html,
"eim (o)"_pair_eim.html,
"gauss (go)"_pair_gauss.html,
"gayberne (gio)"_pair_gayberne.html,
......@@ -953,9 +960,9 @@ KOKKOS, o = USER-OMP, t = OPT.
"kim"_pair_kim.html,
"lcbop"_pair_lcbop.html,
"line/lj"_pair_line_lj.html,
"lj/charmm/coul/charmm (kio)"_pair_charmm.html,
"lj/charmm/coul/charmm (iko)"_pair_charmm.html,
"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
"lj/charmm/coul/long (gkio)"_pair_charmm.html,
"lj/charmm/coul/long (giko)"_pair_charmm.html,
"lj/charmm/coul/msm"_pair_charmm.html,
"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
"lj/charmmfsw/coul/long"_pair_charmm.html,
......@@ -1005,9 +1012,9 @@ KOKKOS, o = USER-OMP, t = OPT.
"resquared (go)"_pair_resquared.html,
"snap"_pair_snap.html,
"soft (go)"_pair_soft.html,
"sw (gkio)"_pair_sw.html,
"sw (giko)"_pair_sw.html,
"table (gko)"_pair_table.html,
"tersoff (gkio)"_pair_tersoff.html,
"tersoff (giko)"_pair_tersoff.html,
"tersoff/mod (gko)"_pair_tersoff_mod.html,
"tersoff/mod/c (o)"_pair_tersoff_mod.html,
"tersoff/zbl (gko)"_pair_tersoff_zbl.html,
......@@ -1111,6 +1118,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"class2 (ko)"_bond_class2.html,
"fene (iko)"_bond_fene.html,
"fene/expand (o)"_bond_fene_expand.html,
"gromos (o)"_bond_gromos.html,
"harmonic (ko)"_bond_harmonic.html,
"morse (o)"_bond_morse.html,
"nonlinear (o)"_bond_nonlinear.html,
......@@ -1177,7 +1185,7 @@ USER-OMP, t = OPT.
"none"_dihedral_none.html,
"zero"_dihedral_zero.html,
"hybrid"_dihedral_hybrid.html,
"charmm (ko)"_dihedral_charmm.html,
"charmm (iko)"_dihedral_charmm.html,
"charmmfsw"_dihedral_charmm.html,
"class2 (ko)"_dihedral_class2.html,
"harmonic (io)"_dihedral_harmonic.html,
......@@ -1190,7 +1198,7 @@ used if "LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
"fourier (o)"_dihedral_fourier.html,
"fourier (io)"_dihedral_fourier.html,
"nharmonic (o)"_dihedral_nharmonic.html,
"quadratic (o)"_dihedral_quadratic.html,
"spherical (o)"_dihedral_spherical.html,
......@@ -1213,7 +1221,7 @@ USER-OMP, t = OPT.
"hybrid"_improper_hybrid.html,
"class2 (ko)"_improper_class2.html,
"cvff (io)"_improper_cvff.html,
"harmonic (ko)"_improper_harmonic.html,
"harmonic (iko)"_improper_harmonic.html,
"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
These are additional improper styles in USER packages, which can be
......
......@@ -150,6 +150,7 @@ Package, Description, Doc page, Example, Library
"USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
"USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
"USER-TALLY"_#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
"USER-UEF"_#USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, -
"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)
:line
......@@ -705,7 +706,7 @@ dynamics can be run with LAMMPS using density-functional tight-binding
quantum forces calculated by LATTE.
More information on LATTE can be found at this web site:
"https://github.com/lanl/LATTE"_#latte_home. A brief technical
"https://github.com/lanl/LATTE"_latte_home. A brief technical
description is given with the "fix latte"_fix_latte.html command.
:link(latte_home,https://github.com/lanl/LATTE)
......@@ -728,6 +729,7 @@ make lib-latte args="-b" # download and build in lib/latte/LATTE-
make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
make lib-latte args="-b -m gfortran" # download and build in lib/latte and
# copy Makefile.lammps.gfortran to Makefile.lammps
:pre
Note that 3 symbolic (soft) links, "includelink" and "liblink" and
"filelink", are created in lib/latte to point into the LATTE home dir.
......@@ -2770,13 +2772,44 @@ examples/USER/tally :ul
:line
USER-UEF package :link(USER-UEF),h4
[Contents:]
A fix style for the integration of the equations of motion under
extensional flow with proper boundary conditions, as well as several
supporting compute styles and an output option.
[Author:] David Nicholson (MIT).
[Install or un-install:]
make yes-user-uef
make machine :pre
make no-user-uef
make machine :pre
[Supporting info:]
src/USER-UEF: filenames -> commands
src/USER-UEF/README
"fix nvt/uef"_fix_nh_uef.html
"fix npt/uef"_fix_nh_uef.html
"compute pressure/uef"_compute_pressure_uef.html
"compute temp/uef"_compute_temp_uef.html
"dump cfg/uef"_dump_cfg_uef.html
examples/uef :ul
:line
USER-VTK package :link(USER-VTK),h4
[Contents:]
A "dump vtk"_dump_vtk.html command which outputs
snapshot info in the "VTK format"_vtk, enabling visualization by
"Paraview"_paraview or other visuzlization packages.
A "dump vtk"_dump_vtk.html command which outputs snapshot info in the
"VTK format"_vtk, enabling visualization by "Paraview"_paraview or
other visuzlization packages.
:link(vtk,http://www.vtk.org)
:link(paraview,http://www.paraview.org)
......
......@@ -25,14 +25,14 @@ LAMMPS to run on the CPU cores and coprocessor cores simultaneously.
[Currently Available USER-INTEL Styles:]
Angle Styles: charmm, harmonic :ulb,l
Bond Styles: fene, harmonic :l
Bond Styles: fene, fourier, harmonic :l
Dihedral Styles: charmm, harmonic, opls :l
Fixes: nve, npt, nvt, nvt/sllod :l
Fixes: nve, npt, nvt, nvt/sllod, nve/asphere :l
Improper Styles: cvff, harmonic :l
Pair Styles: airebo, airebo/morse, buck/coul/cut, buck/coul/long,
buck, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm,
lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, rebo,
sw, tersoff :l
buck, dpd, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm,
lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long,
rebo, sw, tersoff :l
K-Space Styles: pppm, pppm/disp :l
:ule
......@@ -54,11 +54,12 @@ warmup run (for use with offload benchmarks).
:c,image(JPG/user_intel.png)
Results are speedups obtained on Intel Xeon E5-2697v4 processors
(code-named Broadwell) and Intel Xeon Phi 7250 processors
(code-named Knights Landing) with "June 2017" LAMMPS built with
Intel Parallel Studio 2017 update 2. Results are with 1 MPI task
per physical core. See {src/USER-INTEL/TEST/README} for the raw
simulation rates and instructions to reproduce.
(code-named Broadwell), Intel Xeon Phi 7250 processors (code-named
Knights Landing), and Intel Xeon Gold 6148 processors (code-named
Skylake) with "June 2017" LAMMPS built with Intel Parallel Studio
2017 update 2. Results are with 1 MPI task per physical core. See
{src/USER-INTEL/TEST/README} for the raw simulation rates and
instructions to reproduce.
:line
......@@ -82,6 +83,11 @@ this order :l
The {newton} setting applies to all atoms, not just atoms shared
between MPI tasks :l
Vectorization can change the order for adding pairwise forces :l
When using the -DLMP_USE_MKL_RNG define (all included intel optimized
makefiles do) at build time, the random number generator for
dissipative particle dynamics (pair style dpd/intel) uses the Mersenne
Twister generator included in the Intel MKL library (that should be
more robust than the default Masaglia random number generator) :l
:ule
The precision mode (described below) used with the USER-INTEL
......@@ -108,7 +114,7 @@ $t should be 2 for Intel Xeon CPUs and 2 or 4 for Intel Xeon Phi :l
For some of the simple 2-body potentials without long-range
electrostatics, performance and scalability can be better with
the "newton off" setting added to the input script :l
For simulations on higher node counts, add "processors * * * grid
For simulations on higher node counts, add "processors * * * grid
numa" to the beginning of the input script for better scalability :l
If using {kspace_style pppm} in the input script, add
"kspace_modify diff ad" for better performance :l
......@@ -119,8 +125,8 @@ For Intel Xeon Phi CPUs:
Runs should be performed using MCDRAM. :ulb,l
:ule
For simulations using {kspace_style pppm} on Intel CPUs
supporting AVX-512:
For simulations using {kspace_style pppm} on Intel CPUs supporting
AVX-512:
Add "kspace_modify diff ad" to the input script :ulb,l
The command-line option should be changed to
......@@ -237,14 +243,17 @@ However, if you do not have coprocessors on your system, building
without offload support will produce a smaller binary.
The general requirements for Makefiles with the USER-INTEL package
are as follows. "-DLAMMPS_MEMALIGN=64" is required for CCFLAGS. When
using Intel compilers, "-restrict" is required and "-qopenmp" is
highly recommended for CCFLAGS and LINKFLAGS. LIB should include
"-ltbbmalloc". For builds supporting offload, "-DLMP_INTEL_OFFLOAD"
is required for CCFLAGS and "-qoffload" is required for LINKFLAGS.
Other recommended CCFLAG options for best performance are
"-O2 -fno-alias -ansi-alias -qoverride-limits fp-model fast=2
-no-prec-div".
are as follows. When using Intel compilers, "-restrict" is required
and "-qopenmp" is highly recommended for CCFLAGS and LINKFLAGS.
CCFLAGS should include "-DLMP_INTEL_USELRT" (unless POSIX Threads
are not supported in the build environment) and "-DLMP_USE_MKL_RNG"
(unless Intel Math Kernel Library (MKL) is not available in the build
environment). For Intel compilers, LIB should include "-ltbbmalloc"
or if the library is not available, "-DLMP_INTEL_NO_TBB" can be added
to CCFLAGS. For builds supporting offload, "-DLMP_INTEL_OFFLOAD" is
required for CCFLAGS and "-qoffload" is required for LINKFLAGS. Other
recommended CCFLAG options for best performance are "-O2 -fno-alias
-ansi-alias -qoverride-limits fp-model fast=2 -no-prec-div".
NOTE: The vectorization and math capabilities can differ depending on
the CPU. For Intel compilers, the "-x" flag specifies the type of
......
......@@ -16,7 +16,7 @@ atom_modify keyword values ... :pre
one or more keyword/value pairs may be appended :ulb,l
keyword = {id} or {map} or {first} or {sort} :l
{id} value = {yes} or {no}
{map} value = {array} or {hash}
{map} value = {yes} or {array} or {hash}
{first} value = group-ID = group whose atoms will appear first in internal atom lists
{sort} values = Nfreq binsize
Nfreq = sort atoms spatially every this many time steps
......@@ -25,8 +25,8 @@ keyword = {id} or {map} or {first} or {sort} :l
[Examples:]
atom_modify map hash
atom_modify map array sort 10000 2.0
atom_modify map yes
atom_modify map hash sort 10000 2.0
atom_modify first colloid :pre
[Description:]
......@@ -62,29 +62,33 @@ switch. This is described in "Section 2.2"_Section_start.html#start_2
of the manual. If atom IDs are not used, they must be specified as 0
for all atoms, e.g. in a data or restart file.
The {map} keyword determines how atom ID lookup is done for molecular
atom styles. Lookups are performed by bond (angle, etc) routines in
LAMMPS to find the local atom index associated with a global atom ID.
When the {array} value is used, each processor stores a lookup table
of length N, where N is the largest atom ID in the system. This is a
The {map} keyword determines how atoms with specific IDs are found
when required. An example are the bond (angle, etc) methods which
need to find the local index of an atom with a specific global ID
which is a bond (angle, etc) partner. LAMMPS performs this operation
efficiently by creating a "map", which is either an {array} or {hash}
table, as descibed below.
When the {map} keyword is not specified in your input script, LAMMPS
only creates a map for "atom_styles"_atom_style.html for molecular
systems which have permanent bonds (angles, etc). No map is created
for atomic systems, since it is normally not needed. However some
LAMMPS commands require a map, even for atomic systems, and will
generate an error if one does not exist. The {map} keyword thus
allows you to force the creation of a map. The {yes} value will
create either an {array} or {hash} style map, as explained in the next
paragraph. The {array} and {hash} values create an atom-style or
hash-style map respectively.
For an {array}-style map, each processor stores a lookup table of
length N, where N is the largest atom ID in the system. This is a
fast, simple method for many simulations, but requires too much memory
for large simulations. The {hash} value uses a hash table to perform
the lookups. This can be slightly slower than the {array} method, but
its memory cost is proportional to the number of atoms owned by a
processor, i.e. N/P when N is the total number of atoms in the system
and P is the number of processors.
When this setting is not specified in your input script, LAMMPS
creates a map, if one is needed, as an array or hash. See the
discussion of default values below for how LAMMPS chooses which kind
of map to build. Note that atomic systems do not normally need to
create a map. However, even in this case some LAMMPS commands will
create a map to find atoms (and then destroy it), or require a
permanent map. An example of the former is the "velocity loop
all"_velocity.html command, which uses a map when looping over all
atoms and insuring the same velocity values are assigned to an atom
ID, no matter which processor owns it.
for large simulations. For a {hash}-style map, a hash table is
created on each processor, which finds an atom ID in constant time
(independent of the global number of atom IDs). It can be slightly
slower than the {array} map, but its memory cost is proportional to
the number of atoms owned by a processor, i.e. N/P when N is the total
number of atoms in the system and P is the number of processors.
The {first} keyword allows a "group"_group.html to be specified whose
atoms will be maintained as the first atoms in each processor's list
......
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
bond_style gromos command :h3
bond_style gromos/omp command :h3
[Syntax:]
bond_style gromos :pre
[Examples:]
bond_style gromos
bond_coeff 5 80.0 1.2 :pre
[Description:]
The {gromos} bond style uses the potential
:c,image(Eqs/bond_gromos.jpg)
where r0 is the equilibrium bond distance. Note that the usual 1/4
factor is included in K.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy/distance^4)
r0 (distance) :ul
: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 in "Section 5"_Section_accelerate.html
of the manual. 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 "Making
LAMMPS"_Section_start.html#start_3 section 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"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
MOLECULE package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none
......@@ -8,6 +8,7 @@ Bond Styles :h1
bond_class2
bond_fene
bond_fene_expand
bond_gromos
bond_harmonic
bond_harmonic_shift
bond_harmonic_shift_cut
......
......@@ -32,6 +32,7 @@ Commands :h1
dimension
displace_atoms
dump
dump_cfg_uef
dump_h5md
dump_image
dump_modify
......
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute pressure/uef command :h3
[Syntax:]
compute ID group-ID pressure/uef temp-ID keyword ... :pre
ID, group-ID are documented in "compute"_compute.html command
pressure/uef = style name of this compute command
temp-ID = ID of compute that calculates temperature, can be NULL if not needed
zero or more keywords may be appended
keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} :ul
[Examples:]
compute 1 all pressure/uef my_temp_uef
compute 2 all pressure/uef my_temp_uef virial :pre
[Description:]
This command is used to compute the pressure tensor in
the reference frame of the applied flow field when
"fix nvt/uef"_fix_nh_uef.html" or
"fix npt/uef"_fix_nh_uef.html" is used.
It is not necessary to use this command to compute the scalar
value of the pressure. A "compute pressure"_compute_pressure.html
may be used for that purpose.
The keywords and output information are documented in
"compute_pressure"_compute_pressure.html.
[Restrictions:]
This fix is part of the USER-UEF package. It is only enabled if
LAMMPS was built with that package. See the
"Making LAMMPS"_Section_start.html#start_3 section for more info.
This command can only be used when "fix nvt/uef"_fix_nh_uef.html
or "fix npt/uef"_fix_nh_uef.html is active.
The kinetic contribution to the pressure tensor
will be accurate only when
the compute specificed by {temp-ID} is a
"compute temp/uef"_compute_temp_uef.html.
[Related commands:]
"compute pressure"_compute_pressure.html,
"fix nvt/uef"_fix_nh_uef.html,
"compute temp/uef"_compute_temp_uef.html
[Default:] none
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute temp/uef command :h3
[Syntax:]
compute ID group-ID temp/uef :pre
ID, group-ID are documented in "compute"_compute.html command
temp/uef = style name of this compute command :ul
[Examples:]
compute 1 all temp/uef
compute 2 sel temp/uef :pre
[Description:]
This command is used to compute the kinetic energy tensor in
the reference frame of the applied flow field when
"fix nvt/uef"_fix_nh_uef.html" or
"fix npt/uef"_fix_nh_uef.html" is used.
It is not necessary to use this command to compute the scalar
value of the temperature. A "compute temp"_compute_temp.html
may be used for that purpose.
Output information for this command can be found in the
documentation for "compute temp"_compute_temp.html.