forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14535 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
8e9f616a2e
commit
216f83d10d
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@ -436,8 +436,8 @@ performance.</p>
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files for doing particle dumps in XTC format. This is only necessary
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if your platform does have its own XDR files available. See the
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Restrictions section of the <a class="reference internal" href="dump.html"><em>dump</em></a> command for details.</p>
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<p>Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG, -D-
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DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG. These
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<p>Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG,
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-DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG. These
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settings refer to use of 4-byte (small) vs 8-byte (big) integers
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within LAMMPS, as specified in src/lmptype.h. The only reason to use
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the BIGBIG setting is to enable simulation of huge molecular systems
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@ -1288,7 +1288,7 @@ use this executable to run on a single processor by typing something
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like: “lmp_win_mpi -in in.lj”.</li>
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</ul>
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<hr class="docutils" />
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<p>The screen output from LAMMPS is described in the next section. As it
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<p>The screen output from LAMMPS is described in a section below. As it
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runs, LAMMPS also writes a log.lammps file with the same information.</p>
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<p>Note that this sequence of commands copies the LAMMPS executable
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(lmp_linux) to the directory with the input files. This may not be
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@ -13,10 +13,10 @@ atom_style command :h3
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atom_style style args :pre
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style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
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{electron} or {ellipsoid} or {full} or {line} or {meso} or \
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{dpd} or {electron} or {ellipsoid} or {full} or {line} or {meso} or \
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{molecular} or {peri} or {smd} or {sphere} or {tri} or \
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{template} or {hybrid} :ulb,l
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args = none for any style except {body} and {hybrid}
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args = none for any style except the following
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{body} args = bstyle bstyle-args
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bstyle = style of body particles
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bstyle-args = additional arguments specific to the bstyle
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@ -47,6 +47,10 @@ used before a simulation is setup via a "read_data"_read_data.html,
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"read_restart"_read_restart.html, or "create_box"_create_box.html
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command.
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NOTE: Many of the atom styles discussed here are only enabled if
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LAMMPS was built with a specific package, as listed below in the
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Restrictions section.
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Once a style is assigned, it cannot be changed, so use a style general
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enough to encompass all attributes. E.g. with style {bond}, angular
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terms cannot be used or added later to the model. It is OK to use a
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@ -70,6 +74,7 @@ quantities.
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{bond} | bonds | bead-spring polymers |
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{charge} | charge | atomic system with charges |
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{dipole} | charge and dipole moment | system with dipolar particles |
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{dpd} | internal temperature and internal energies | DPD particles |
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{electron} | charge and spin and eradius | electronic force field |
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{ellipsoid} | shape, quaternion, angular momentum | aspherical particles |
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{full} | molecular + charge | bio-molecules |
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@ -128,6 +133,10 @@ position, which is represented by the eradius = electron size.
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For the {peri} style, the particles are spherical and each stores a
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per-particle mass and volume.
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The {dpd} style is for dissipative particle dynamics (DPD) particles
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which store the particle internal temperature (dpdTheta), internal
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conductive energy (uCond) and internal mechanical energy (uMech).
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The {meso} style is for smoothed particle hydrodynamics (SPH)
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particles which store a density (rho), energy (e), and heat capacity
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(cv).
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@ -247,20 +256,34 @@ more instructions on how to use the accelerated styles effectively.
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This command cannot be used after the simulation box is defined by a
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"read_data"_read_data.html or "create_box"_create_box.html command.
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The {angle}, {bond}, {full}, {molecular}, and {template} styles are
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part of the MOLECULE package. The {line} and {tri} styles are part
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of the ASPHERE pacakge. The {body} style is part of the BODY package.
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The {dipole} style is part of the DIPOLE package. The {peri} style is
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part of the PERI package for Peridynamics. The {electron} style is
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part of the USER-EFF package for "electronic force
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fields"_pair_eff.html. The {meso} style is part of the USER-SPH
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package for smoothed particle hydrodyanmics (SPH). See "this PDF
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guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. The
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{wavepacket} style is part of the USER-AWPMD package for the
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"antisymmetrized wave packet MD method"_pair_awpmd.html. They are
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only enabled if LAMMPS was built with that package. See the "Making
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Many of the styles listed above are only enabled if LAMMPS was built
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with a specific package, as listed below. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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The {angle}, {bond}, {full}, {molecular}, and {template} styles are
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part of the MOLECULE package.
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The {line} and {tri} styles are part of the ASPHERE pacakge.
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The {body} style is part of the BODY package.
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The {dipole} style is part of the DIPOLE package.
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The {peri} style is part of the PERI package for Peridynamics.
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The {electron} style is part of the USER-EFF package for "electronic
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force fields"_pair_eff.html.
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The {dpd} style is part of the USER-DPD package for dissipative
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particle dynamics (DPD).
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The {meso} style is part of the USER-SPH package for smoothed particle
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hydrodyanmics (SPH). See "this PDF
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guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS.
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The {wavepacket} style is part of the USER-AWPMD package for the
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"antisymmetrized wave packet MD method"_pair_awpmd.html.
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[Related commands:]
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"read_data"_read_data.html, "pair_style"_pair_style.html
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@ -0,0 +1,67 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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compute dpd command :h3
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[Syntax:]
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compute ID group-ID dpd :pre
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ID, group-ID are documented in "compute"_compute.html command
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dpd = style name of this compute command :ul
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[Examples:]
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compute 1 all dpd :pre
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[Description:]
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Define a computation that accumulates the total internal conductive
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energy (U_cond), the total internal mechanical energy (U_mech), the
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total internal energy (U) and the {harmonic} average of the internal
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temperature (dpdTheta) for the entire system of particles. See the
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"compute dpd/atom"_compute_dpd_atom.html command if you want
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per-particle internal energies and internal temperatures.
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The system internal properties are computed according to the following
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relations:
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:c,image(Eqs/compute_dpd.jpg)
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where N is the number of particles in the system
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:line
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[Output info:]
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This compute calculates a global vector of length 5 (U_cond, U_mech,
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U, dpdTheta, N_particles), which can be accessed by indices 1-5. See
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"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
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output options.
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The vector values will be in energy and temperature "units"_units.html.
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[Restrictions:]
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The compute {dpd} is only available if LAMMPS is built with the
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USER-DPD package and requires the "atom_style dpd"_atom_style.html.
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[Related commands:]
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"compute dpd/atom"_compute_dpd_atom.html,
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"thermo_style"_thermo_style.html
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[Default:] none
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:line
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:link(Larentzos)
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[(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and
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W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
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Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
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Laboratory, Aberdeen Proving Ground, MD (2014).
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@ -0,0 +1,60 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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compute dpd/atom command :h3
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[Syntax:]
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compute ID group-ID dpd/atom :pre
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ID, group-ID are documented in "compute"_compute.html command
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dpd/atom = style name of this compute command :ul
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[Examples:]
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compute 1 all dpd/atom
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[Description:]
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Define a computation that accesses the per-particle internal
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conductive energy (u_cond), internal mechanical energy (u_mech) and
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internal temperatures (dpdTheta) for each particle in a group. See
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the "compute dpd"_compute_dpd.html command if you want the total
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internal conductive energy, the total internal mechanical energy, and
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average internal temperature of the entire system or group of dpd
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particles.
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[Output info:]
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This compute calculates a per-particle array with 3 columns (u_cond,
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u_mech, dpdTheta), which can be accessed by indices 1-3 by any command
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that uses per-particle values from a compute as input. See
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"Section_howto15"_Section_howto.html#howto_15 for an overview of
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LAMMPS output options.
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The per-particle array values will be in energy (u_cond, u_mech) and
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temperature (dpdTheta) "units"_units.html.
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[Restrictions:]
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The compute {dpd/atom} is only available if LAMMPS is built with the
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USER-DPD package.
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[Related commands:]
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"dump custom"_dump.html, "compute dpd"_compute_dpd.html
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[Default:] none
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:line
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:link(Larentzos)
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[(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and
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W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
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Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
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Laboratory, Aberdeen Proving Ground, MD (2014).
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|
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@ -0,0 +1,131 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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compute temp/body command :h3
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[Syntax:]
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compute ID group-ID temp/body keyword value ... :pre
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ID, group-ID are documented in "compute"_compute.html command :ulb,l
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temp/body = style name of this compute command :l
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zero or more keyword/value pairs may be appended :l
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keyword = {bias} or {dof} :l
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{bias} value = bias-ID
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bias-ID = ID of a temperature compute that removes a velocity bias
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{dof} value = {all} or {rotate}
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all = compute temperature of translational and rotational degrees of freedom
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rotate = compute temperature of just rotational degrees of freedom :pre
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:ule
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[Examples:]
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compute 1 all temp/body
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compute myTemp mobile temp/body bias tempCOM
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compute myTemp mobile temp/body dof rotate :pre
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[Description:]
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Define a computation that calculates the temperature of a group of
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body particles, including a contribution from both their
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translational and rotational kinetic energy. This differs from the
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usual "compute temp"_compute_temp.html command, which assumes point
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particles with only translational kinetic energy.
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Only body particles can be included in the group. For 3d particles,
|
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each has 6 degrees of freedom (3 translational, 3 rotational). For 2d
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body particles, each has 3 degrees of freedom (2 translational, 1
|
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rotational).
|
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|
||||
NOTE: This choice for degrees of freedom (dof) assumes that all body
|
||||
particles in your model will freely rotate, sampling all their
|
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rotational dof. It is possible to use a combination of interaction
|
||||
potentials and fixes that induce no torque or otherwise constrain some
|
||||
of all of your particles so that this is not the case. Then there are
|
||||
less dof and you should use the "compute_modify
|
||||
extra"_compute_modify.html command to adjust the dof accordingly.
|
||||
|
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The translational kinetic energy is computed the same as is described
|
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by the "compute temp"_compute_temp.html command. The rotational
|
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kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor
|
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for the aspherical particle and w is its angular velocity, which is
|
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computed from its angular momentum.
|
||||
|
||||
A kinetic energy tensor, stored as a 6-element vector, is also
|
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calculated by this compute. The formula for the components of the
|
||||
tensor is the same as the above formula, except that v^2 and w^2 are
|
||||
replaced by vx*vy and wx*wy for the xy component, and the appropriate
|
||||
elements of the inertia tensor are used. The 6 components of the
|
||||
vector are ordered xx, yy, zz, xy, xz, yz.
|
||||
|
||||
The number of atoms contributing to the temperature is assumed to be
|
||||
constant for the duration of the run; use the {dynamic} option of the
|
||||
"compute_modify"_compute_modify.html command if this is not the case.
|
||||
|
||||
This compute subtracts out translational degrees-of-freedom due to
|
||||
fixes that constrain molecular motion, such as "fix
|
||||
shake"_fix_shake.html and "fix rigid"_fix_rigid.html. This means the
|
||||
temperature of groups of atoms that include these constraints will be
|
||||
computed correctly. If needed, the subtracted degrees-of-freedom can
|
||||
be altered using the {extra} option of the
|
||||
"compute_modify"_compute_modify.html command.
|
||||
|
||||
See "this howto section"_Section_howto.html#howto_16 of the manual for
|
||||
a discussion of different ways to compute temperature and perform
|
||||
thermostatting.
|
||||
|
||||
:line
|
||||
|
||||
The keyword/value option pairs are used in the following ways.
|
||||
|
||||
For the {bias} keyword, {bias-ID} refers to the ID of a temperature
|
||||
compute that removes a "bias" velocity from each atom. This allows
|
||||
compute temp/sphere to compute its thermal temperature after the
|
||||
translational kinetic energy components have been altered in a
|
||||
prescribed way, e.g. to remove a flow velocity profile. Thermostats
|
||||
that use this compute will work with this bias term. See the doc
|
||||
pages for individual computes that calculate a temperature and the doc
|
||||
pages for fixes that perform thermostatting for more details.
|
||||
|
||||
For the {dof} keyword, a setting of {all} calculates a temperature
|
||||
that includes both translational and rotational degrees of freedom. A
|
||||
setting of {rotate} calculates a temperature that includes only
|
||||
rotational degrees of freedom.
|
||||
|
||||
:line
|
||||
|
||||
[Output info:]
|
||||
|
||||
This compute calculates a global scalar (the temperature) and a global
|
||||
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
|
||||
These values can be used by any command that uses global scalar or
|
||||
vector values from a compute as input. See "this
|
||||
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature "units"_units.html. The
|
||||
vector values will be in energy "units"_units.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This compute is part of the BODY 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 compute requires that atoms store angular momementum and a
|
||||
quaternion as defined by the "atom_style body"_atom_style.html
|
||||
command.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"compute temp"_compute_temp.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -695,7 +695,7 @@ support. These settings are made automatically if the “-sf intel”
|
|||
not used, you must invoke the package intel command in your input
|
||||
script or or via the “-pk intel” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>.</p>
|
||||
<p>For the KOKKOS package, the option defaults neigh = full, newton =
|
||||
off, binsize = 0.0, and comm = host. These settings are made
|
||||
off, binsize = 0.0, and comm = device. These settings are made
|
||||
automatically by the required “-k on” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>. You can change them bu using the
|
||||
package kokkos command in your input script or via the “-pk kokkos”
|
||||
<a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>.</p>
|
||||
|
|
|
|||
|
|
@ -0,0 +1,107 @@
|
|||
"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
|
||||
|
||||
pair_style body/rounded/polygon command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style body/rounded/polygon cutoff_global cutoff_inner delta_ua c_n :pre
|
||||
|
||||
cutoff_global = global cutoff for COM interactions (distance units)
|
||||
cutoff_inner = cutoff for vertex-vertex and vertex-edge interactions (distance units)
|
||||
delta_ua = characteristic contact length (distance units)
|
||||
c_n = normal friction coefficient (energy time/distance^2) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style body/rounded/polygon 6.0 0.5 0.5 0.1
|
||||
pair_coeff 1 1 1.0 100.0 12.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {body/rounded/polygon} implements the pairwise body/body
|
||||
interactions between 2D convex polygons, as described
|
||||
in "Fraige"_#Fraige. This pair style is designed for use with
|
||||
the "rounded/polygon" body style, which is specified as
|
||||
an argument to the "atom-style body/rounded/polygon" command.
|
||||
See the "body"_body.html doc page for more details about the body
|
||||
styles LAMMPS supports.
|
||||
|
||||
The "rounded/polygon" style treats a body particle as a discrete
|
||||
element model (DEM) polygon composed of N vertices.
|
||||
The coordinates of a body particle are its center-of-mass (COM).
|
||||
The initial position of the vertices are specified the data file.
|
||||
The current implementation follows the multiple contact points model as
|
||||
described in "Fraige"_#Fraige, but neglects and the contact history
|
||||
the tangential contact forces for now.
|
||||
|
||||
The parameters {delta_ua} and {c_n} are the characteristic contact length
|
||||
and the normal friction coefficient, respectively. See Eqs. (1) and (5)
|
||||
in "Fraige"_#Fraige for more details.
|
||||
|
||||
For style {body/rounded/polygon}, the following coefficients
|
||||
must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html
|
||||
command as in the examples above:
|
||||
|
||||
sigma = vertex rounded diameter (distance units)
|
||||
k_n = normal repulsion strength (energy/distance^2)
|
||||
k_na = normal attraction strength (energy/distance^2)
|
||||
cutoff = cutoff for COM interactions (distance units) :ul
|
||||
|
||||
The last parameter is optional. If not specified, the global
|
||||
cutoff specified in the pair_style command is used.
|
||||
|
||||
Note that the current implementation assumes that the edge length
|
||||
of the polygons (L) should be at least twice greater than
|
||||
the vertex rounded radius (sigma) so as to distinguish vertex-vertex from
|
||||
vertex-edge contacts.
|
||||
|
||||
NOTE: Because this pair style requires the body velocities to compute
|
||||
the friction component of the forces, users should specify
|
||||
{comm_modify vel yes} in the input script with this pair style.
|
||||
|
||||
:line
|
||||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
|
||||
and cutoff distance for all of this pair style can be mixed. The
|
||||
default mix value is {geometric}. See the "pair_modify" command for
|
||||
details.
|
||||
|
||||
This pair style does not support the "pair_modify"_pair_modify.html
|
||||
shift, table, and tail options.
|
||||
|
||||
This pair style does not write its information to "binary restart
|
||||
files"_restart.html.
|
||||
|
||||
This pair style can only be used via the {pair} keyword of the
|
||||
"run_style respa"_run_style.html command. It does not support the
|
||||
{inner}, {middle}, {outer} keywords.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This style is part of the BODY package. It is only enabled if LAMMPS
|
||||
was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
||||
|
||||
Defining particles to be bodies so they participate in body/body or
|
||||
body/particle interactions requires the use of the "atom_style
|
||||
body"_atom_style.html command.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:link(Fraige)
|
||||
[(Fraige)] F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds,
|
||||
Particuology, 6, 455 (2008).
|
||||
|
|
@ -0,0 +1,72 @@
|
|||
"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
|
||||
|
||||
pair_style dpd/conservative command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style dpd/conservative cutoff :pre
|
||||
|
||||
cutoff = global cutoff for DPD interactions (distance units) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style dpd/conservative 2.5
|
||||
pair_coeff * * 3.0 2.5
|
||||
pair_coeff 1 1 3.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {dpd/conservative} computes the conservative force for
|
||||
dissipative particle dynamics (DPD). The conservative force on atom I
|
||||
due to atom J is given by
|
||||
|
||||
:c,image(Eqs/pair_dpd_conservative.jpg)
|
||||
|
||||
where the weighting factor, omega_ij, varies between 0 and 1, and is
|
||||
chosen to have the following functional form:
|
||||
|
||||
:c,image(Eqs/pair_dpd_omega.jpg)
|
||||
|
||||
where Rij is a unit vector in the direction Ri - Rj, and Rc is the
|
||||
cutoff. Note that alternative definitions of the weighting function
|
||||
exist, but would have to be implemented as a separate pair style
|
||||
command.
|
||||
|
||||
Style {dpd/conservative} differs from the other dpd styles in that the
|
||||
dissipative and random forces are not computed within the pair style.
|
||||
|
||||
For style {dpd/conservative}, the pairwise energy is due only to the
|
||||
conservative force term Fc, and is shifted to be zero at the cutoff
|
||||
distance Rc. The pairwise virial is calculated using only the
|
||||
conservative term.
|
||||
|
||||
Style {dpd/conservative} requires the following coefficients to be
|
||||
defined for each pair of atoms types via the
|
||||
"pair_coeff"_pair_coeff.html command as in the examples above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
A (force units)
|
||||
cutoff (distance units) :ul
|
||||
|
||||
The last coefficient is optional. If not specified, the global DPD
|
||||
cutoff is used.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The pair style {dpd/conservative} is only available if LAMMPS is built
|
||||
with the USER-DPD package.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html, "pair_dpd"_pair_dpd.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -0,0 +1,136 @@
|
|||
"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
|
||||
|
||||
pair_style dpd/fdt command :h3
|
||||
pair_style dpd/fdt/energy command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style style args :pre
|
||||
|
||||
style = {dpd/fdt} or {dpd/fdt/energy}
|
||||
args = list of arguments for a particular style :ul
|
||||
{dpd/fdt} args = T cutoff seed
|
||||
T = temperature (temperature units)
|
||||
cutoff = global cutoff for DPD interactions (distance units)
|
||||
seed = random # seed (positive integer)
|
||||
{dpd/fdt/energy} args = cutoff seed
|
||||
cutoff = global cutoff for DPD interactions (distance units)
|
||||
seed = random # seed (positive integer) :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style dpd/fdt 300.0 2.5 34387
|
||||
pair_coeff * * 3.0 1.0 2.5 :pre
|
||||
|
||||
pair_style dpd/fdt/energy 2.5 34387
|
||||
pair_coeff * * 3.0 1.0 0.1 2.5 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Styles {dpd/fdt} and {dpd/fdt/energy} set the fluctuation-dissipation
|
||||
theorem parameters and compute the conservative force for dissipative
|
||||
particle dynamics (DPD). The conservative force on atom I due to atom
|
||||
J is given by
|
||||
|
||||
:c,image(Eqs/pair_dpd_conservative.jpg)
|
||||
|
||||
where the weighting factor, omega_ij, varies between 0 and 1, and is
|
||||
chosen to have the following functional form:
|
||||
|
||||
:c,image(Eqs/pair_dpd_omega.jpg)
|
||||
|
||||
where Rij is a unit vector in the direction Ri - Rj, and Rc is the
|
||||
cutoff. Note that alternative definitions of the weighting function
|
||||
exist, but would have to be implemented as a separate pair style
|
||||
command.
|
||||
|
||||
These pair style differ from the other dpd styles in that the
|
||||
dissipative and random forces are not computed within the pair style.
|
||||
This style can be combined with the "fix shardlow"_fix_shardlow.html
|
||||
to perform the stochastic integration of the dissipative and random
|
||||
forces through the Shardlow splitting algorithm approach.
|
||||
|
||||
The pairwise energy associated with styles {dpd/fdt} and
|
||||
{dpd/fdt/energy} is only due to the conservative force term Fc, and is
|
||||
shifted to be zero at the cutoff distance Rc. The pairwise virial is
|
||||
calculated using only the conservative term.
|
||||
|
||||
For style {dpd/fdt}, the fluctuation-dissipation theorem defines gamma
|
||||
to be set equal to sigma*sigma/(2 T), where T is the set point
|
||||
temperature specified as a pair style parameter in the above examples.
|
||||
This style can be combined with "fix shardlow"_fix_shardlow.html to
|
||||
perform DPD simulations under isothermal and isobaric conditions (see
|
||||
"(Lisal)"_#Lisal). The following coefficients must be defined for
|
||||
each pair of atoms types via the "pair_coeff"_pair_coeff.html command
|
||||
as in the examples above, or in the data file or restart files read by
|
||||
the "read_data"_read_data.html or "read_restart"_read_restart.html
|
||||
commands:
|
||||
|
||||
A (force units)
|
||||
sigma (force*time^(1/2) units)
|
||||
cutoff (distance units) :ul
|
||||
|
||||
The last coefficient is optional. If not specified, the global DPD
|
||||
cutoff is used.
|
||||
|
||||
For style {dpd/fdt/energy}, the fluctuation-dissipation theorem
|
||||
defines gamma to be set equal to sigma*sigma/(2 dpdTheta), where
|
||||
dpdTheta is the average internal temperature for the pair.
|
||||
Furthermore, the fluctuation-dissipation defines alpha*alpha to be set
|
||||
equal to 2*kB*kappa, where kappa is the mesoparticle thermal
|
||||
conductivity parameter. This style can be combined with "fix
|
||||
shardlow"_fix_shardlow.html to perform DPD simulations under
|
||||
isoenergetic and isoenthalpic conditions (see "(Lisal)"_#Lisal). The
|
||||
following coefficients must be defined for each pair of atoms types
|
||||
via the "pair_coeff"_pair_coeff.html command as in the examples above,
|
||||
or in the data file or restart files read by the
|
||||
"read_data"_read_data.html or "read_restart"_read_restart.html
|
||||
commands:
|
||||
|
||||
A (force units)
|
||||
sigma (force*time^(1/2) units)
|
||||
kappa (1/time units)
|
||||
cutoff (distance units) :ul
|
||||
|
||||
The last coefficient is optional. If not specified, the global DPD
|
||||
cutoff is used.
|
||||
|
||||
For style {dpd/fdt/energy}, the particle internal temperature is
|
||||
related to the particle internal energy through a mesoparticle
|
||||
equation of state. Thus, an an additional "fix eos"_fix.html must be
|
||||
specified.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
Pair styles {dpd/fdt} and {dpd/fdt/energy} are only available if
|
||||
LAMMPS is built with the USER-DPD package.
|
||||
|
||||
Pair styles {dpd/fdt} and {dpd/fdt/energy} require use of the
|
||||
"communicate vel yes"_communicate.html option so that velocites are
|
||||
stored by ghost atoms.
|
||||
|
||||
Pair style {dpd/fdt/energy} requires "atom_style dpd"_atom_style.html
|
||||
to be used in order to properly account for the particle internal
|
||||
energies and temperatures.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html, "fix shardlow"_fix_shardlow.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Lisal)
|
||||
[(Lisal)] M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative
|
||||
particle dynamics as isothermal, isobaric, isoenergetic, and
|
||||
isoenthalpic conditions using Shardlow-like splitting algorithms.",
|
||||
J. Chem. Phys., 135, 204105 (2011).
|
||||
|
|
@ -527,6 +527,7 @@ body: atom-ID atom-type bodyflag mass x y z
|
|||
bond: atom-ID molecule-ID atom-type x y z
|
||||
charge: atom-ID atom-type q x y z
|
||||
dipole: atom-ID atom-type q x y z mux muy muz
|
||||
dpd: atom-ID atom-type theta x y z
|
||||
electron: atom-ID atom-type q spin eradius x y z
|
||||
ellipsoid: atom-ID atom-type ellipsoidflag density x y z
|
||||
full: atom-ID molecule-ID atom-type q x y z
|
||||
|
|
@ -534,40 +535,41 @@ line: atom-ID molecule-ID atom-type lineflag density x y z
|
|||
meso: atom-ID atom-type rho e cv x y z
|
||||
molecular: atom-ID molecule-ID atom-type x y z
|
||||
peri: atom-ID atom-type volume density x y z
|
||||
smd: atom-ID atom-type molecule volume mass kernel_radius contact_radius x y z
|
||||
smd: atom-ID atom-type molecule volume mass kernel-radius contact-radius x y z
|
||||
sphere: atom-ID atom-type diameter density x y z
|
||||
template: atom-ID molecule-ID template-index template-atom atom-type x y z
|
||||
tri: atom-ID molecule-ID atom-type triangleflag density x y z
|
||||
wavepacket: atom-ID atom-type charge spin eradius etag cs_re cs_im x y z
|
||||
hybrid: atom-ID atom-type x y z sub-style1 sub-style2 ... :tb(s=:)
|
||||
|
||||
The keywords have these meanings:
|
||||
The per-atom values have these meanings and units, listed alphabetically:
|
||||
|
||||
atom-ID = integer ID of atom
|
||||
molecule-ID = integer ID of molecule the atom belongs to
|
||||
atom-type = type of atom (1-Ntype)
|
||||
q = charge on atom (charge units)
|
||||
diameter = diameter of spherical atom (distance units)
|
||||
ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
|
||||
lineflag = 1 for line segment particles, 0 for point particles
|
||||
triangleflag = 1 for triangular particles, 0 for point particles
|
||||
bodyflag = 1 for body particles, 0 for point particles
|
||||
template-index = which molecule within the molecule template the atom is part of
|
||||
template-atom = which atom within a template molecule the atom is
|
||||
density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
|
||||
mass = mass of particle (mass units)
|
||||
volume = volume of particle (distance^3 units)
|
||||
x,y,z = coordinates of atom
|
||||
mux,muy,muz = components of dipole moment of atom (dipole units)
|
||||
rho = density (need units) for SPH particles
|
||||
e = energy (need units) for SPH particles
|
||||
contact-radius = ??? (distance units)
|
||||
cs_re,cs_im = real/imaginary parts of wavepacket coefficients
|
||||
cv = heat capacity (need units) for SPH particles
|
||||
spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
|
||||
density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
|
||||
diameter = diameter of spherical atom (distance units)
|
||||
e = energy (need units) for SPH particles
|
||||
ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
|
||||
eradius = electron radius (or fixed-core radius)
|
||||
etag = integer ID of electron that each wavepacket belongs to
|
||||
cs_re,cs_im = real/imaginary parts of wavepacket coefficients
|
||||
kernel_radius = ??? (distance units)
|
||||
contact_radius = ??? (distance units) :ul
|
||||
kernel-radius = ??? (distance units)
|
||||
lineflag = 1 for line segment particles, 0 for point or spherical particles
|
||||
mass = mass of particle (mass units)
|
||||
molecule-ID = integer ID of molecule the atom belongs to
|
||||
mux,muy,muz = components of dipole moment of atom (dipole units)
|
||||
q = charge on atom (charge units)
|
||||
rho = density (need units) for SPH particles
|
||||
spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
|
||||
template-atom = which atom within a template molecule the atom is
|
||||
template-index = which molecule within the molecule template the atom is part of
|
||||
theta = internal temperature of a DPD particle
|
||||
triangleflag = 1 for triangular particles, 0 for point or sperhical particles
|
||||
volume = volume of Peridynamic particle (distance^3 units)
|
||||
x,y,z = coordinates of atom (distance units) :ul
|
||||
|
||||
The units for these quantities depend on the unit style; see the
|
||||
"units"_units.html command for details.
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
|
|||
{mass} or {density} or {volume} or {image} or \
|
||||
{bond} or {angle} or {dihedral} or {improper} or \
|
||||
{meso/e} or {meso/cv} or {meso/rho} or \
|
||||
{smd/contact/radius} or {smd/mass/density} or \
|
||||
{smd/contact/radius} or {smd/mass/density} or {dpd/theta} or \
|
||||
{i_name} or {d_name} :l
|
||||
{type} value = atom type
|
||||
value can be an atom-style variable (see below)
|
||||
|
|
@ -92,6 +92,7 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
|
|||
value can be an atom-style variable (see below)
|
||||
{smd/mass/density} = set particle mass based on volume by providing a mass density
|
||||
value can be an atom-style variable (see below)
|
||||
{dpd/theta} value = internal temperature of DPD particles (temperature units)
|
||||
{i_name} value = value for custom integer vector with name
|
||||
{d_name} value = value for custom floating-point vector with name :pre
|
||||
:ule
|
||||
|
|
@ -389,6 +390,9 @@ other. Note that the SPH smoothing kernel diameter used for computing
|
|||
long range, nonlocal interactions, is set using the {diameter}
|
||||
keyword.
|
||||
|
||||
Keyword {dpd/theta} sets the internal temperature of a DPD particle
|
||||
as defined by the USER-DPD package.
|
||||
|
||||
Keywords {i_name} and {d_name} refer to custom integer and
|
||||
floating-point properties that have been added to each atom via the
|
||||
"fix property/atom"_fix_property_atom.html command. When that command
|
||||
|
|
|
|||
Loading…
Reference in New Issue