clean up doc src
This commit is contained in:
Steve Plimpton
@ -109,7 +109,7 @@ it gives quick access to documentation for all LAMMPS commands.
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:caption: User Documentation
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:name: userdoc
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:includehidden:
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Section_intro
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Section_start
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Section_commands
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@ -144,7 +144,7 @@ Indices and tables
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* :ref:`genindex`
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* :ref:`search`
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END_RST -->
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<!-- HTML_ONLY -->
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@ -117,7 +117,7 @@ PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to
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achieve the same accuracy as 4-FFT PPPM. For problems where the FFT
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cost is the performance bottleneck (typically large problems running
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on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM.
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Staggered PPPM performs calculations using two different meshes, one
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shifted slightly with respect to the other. This can reduce force
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aliasing errors and increase the accuracy of the method, but also
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@ -37,14 +37,14 @@ simulation with all the settings. Rather, the input script is read
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one line at a time and each command takes effect when it is read.
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Thus this sequence of commands:
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timestep 0.5
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run 100
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timestep 0.5
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run 100
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run 100 :pre
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does something different than this sequence:
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run 100
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timestep 0.5
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run 100
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timestep 0.5
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run 100 :pre
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In the first case, the specified timestep (0.5 fmsec) is used for two
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@ -97,7 +97,7 @@ single leading "#" will comment out the entire command.
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(3) The line is searched repeatedly for $ characters, which indicate
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variables that are replaced with a text string. See an exception in
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(6).
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(6).
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If the $ is followed by curly brackets, then the variable name is the
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text inside the curly brackets. If no curly brackets follow the $,
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@ -123,7 +123,7 @@ variable X equal (xlo+xhi)/2+sqrt(v_area)
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region 1 block $X 2 INF INF EDGE EDGE
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variable X delete :pre
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can be replaced by
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can be replaced by
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region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
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@ -159,7 +159,7 @@ As a last resort, you can send an email directly to the
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These are two alphabetic lists of the "ERROR"_#error and
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"WARNING"_#warn messages LAMMPS prints out and the reason why. If the
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explanation here is not sufficient, the documentation for the
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offending command may help.
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offending command may help.
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Error and warning messages also list the source file and line number
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where the error was generated. For example, this message
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@ -120,7 +120,7 @@ browser.
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Uppercase directories :h4
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ASPHERE: various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc
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COUPLE: examples of how to use LAMMPS as a library
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COUPLE: examples of how to use LAMMPS as a library
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DIFFUSE: compute diffusion coefficients via several methods
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ELASTIC: compute elastic constants at zero temperature
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ELASTIC_T: compute elastic constants at finite temperature
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@ -37,7 +37,7 @@ pitfalls or alternatives.
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Please see some of the closed issues for examples of how to
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suggest code enhancements, submit proposed changes, or report
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elated issues and how they are resoved.
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elated issues and how they are resoved.
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As an alternative to using GitHub, you may e-mail the
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"core developers"_http://lammps.sandia.gov/authors.html or send
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@ -71,7 +71,7 @@ a parallel framework similar to LAMMPS. Most notably, these have
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included many-body potentials - Stillinger-Weber, Tersoff, ReaxFF -
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and the associated charge-equilibration routines needed for ReaxFF.
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The "History link"_http://lammps.sandia.gov/history.html on the
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The "History link"_http://lammps.sandia.gov/history.html on the
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LAMMPS WWW page gives a timeline of features added to the
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C++ open-source version of LAMMPS over the last several years.
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@ -80,7 +80,7 @@ site"_lws, except for Warp & GranFlow which were primarily used
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internally. A brief listing of their features is given here.
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LAMMPS 2001
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F90 + MPI
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dynamic memory
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spatial-decomposition parallelism
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@ -96,7 +96,7 @@ LAMMPS 2001
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user-defined diagnostics :ul
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LAMMPS 99
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F77 + MPI
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static memory allocation
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spatial-decomposition parallelism
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@ -4,7 +4,7 @@
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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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:line
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6. How-to discussions :h3
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@ -522,7 +522,7 @@ H mass = 1.008
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O charge = -1.040
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H charge = 0.520
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r0 of OH bond = 0.9572
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theta of HOH angle = 104.52
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theta of HOH angle = 104.52
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OM distance = 0.15
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LJ epsilon of O-O = 0.1550
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LJ sigma of O-O = 3.1536
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@ -629,7 +629,7 @@ the SPC and SPC/E models.
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Wikipedia also has a nice article on "water
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models"_http://en.wikipedia.org/wiki/Water_model.
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:line
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:line
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6.10 Coupling LAMMPS to other codes :link(howto_10),h4
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@ -729,7 +729,7 @@ LAMMPS and half to the other code and run both codes simultaneously
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before syncing them up periodically. Or it might instantiate multiple
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instances of LAMMPS to perform different calculations.
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:line
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:line
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6.11 Visualizing LAMMPS snapshots :link(howto_11),h4
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@ -832,7 +832,7 @@ rotation of [A], [B], and [C] and can be computed as follows:
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where A = | [A] | indicates the scalar length of [A]. The hat symbol (^)
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indicates the corresponding unit vector. {beta} and {gamma} are angles
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between the vectors described below. Note that by construction,
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between the vectors described below. Note that by construction,
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[a], [b], and [c] have strictly positive x, y, and z components, respectively.
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If it should happen that
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[A], [B], and [C] form a left-handed basis, then the above equations
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@ -841,17 +841,17 @@ to first apply an inversion. This can be achieved
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by interchanging two basis vectors or by changing the sign of one of them.
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For consistency, the same rotation/inversion applied to the basis vectors
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must also be applied to atom positions, velocities,
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must also be applied to atom positions, velocities,
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and any other vector quantities.
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This can be conveniently achieved by first converting to
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This can be conveniently achieved by first converting to
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fractional coordinates in the
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old basis and then converting to distance coordinates in the new basis.
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The transformation is given by the following equation:
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:c,image(Eqs/rotate.jpg)
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where {V} is the volume of the box, [X] is the original vector quantity and
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[x] is the vector in the LAMMPS basis.
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where {V} is the volume of the box, [X] is the original vector quantity and
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[x] is the vector in the LAMMPS basis.
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There is no requirement that a triclinic box be periodic in any
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dimension, though it typically should be in at least the 2nd dimension
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@ -938,17 +938,17 @@ defined above. The relationship between these 6 quantities
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(a,b,c,alpha,beta,gamma) and the LAMMPS box sizes (lx,ly,lz) =
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(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows:
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:c,image(Eqs/box.jpg)
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:c,image(Eqs/box.jpg)
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The inverse relationship can be written as follows:
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:c,image(Eqs/box_inverse.jpg)
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:c,image(Eqs/box_inverse.jpg)
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The values of {a}, {b}, {c} , {alpha}, {beta} , and {gamma} can be printed
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out or accessed by computes using the
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"thermo_style custom"_thermo_style.html keywords
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The values of {a}, {b}, {c} , {alpha}, {beta} , and {gamma} can be printed
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out or accessed by computes using the
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"thermo_style custom"_thermo_style.html keywords
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{cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, {cellgamma},
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respectively.
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respectively.
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As discussed on the "dump"_dump.html command doc page, when the BOX
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BOUNDS for a snapshot is written to a dump file for a triclinic box,
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@ -2130,7 +2130,7 @@ but uses the Einstein formulation, analogous to the Einstein
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mean-square-displacement formulation for self-diffusivity. The
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time-integrated momentum fluxes play the role of Cartesian
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coordinates, whose mean-square displacement increases linearly
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with time at sufficiently long times.
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with time at sufficiently long times.
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:line
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@ -2510,8 +2510,8 @@ the electrostatic environment inducing polarizability.
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Technically, shells are attached to the cores by a spring force f =
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k*r where k is a parametrized spring constant and r is the distance
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between the core and the shell. The charges of the core and the shell
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add up to the ion charge, thus q(ion) = q(core) + q(shell). This
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setup introduces the ion polarizability (alpha) given by
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add up to the ion charge, thus q(ion) = q(core) + q(shell). This
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setup introduces the ion polarizability (alpha) given by
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alpha = q(shell)^2 / k. In a
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similar fashion the mass of the ion is distributed on the core and the
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shell with the core having the larger mass.
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@ -2526,7 +2526,7 @@ for NaCl, as found in examples/coreshell, has this format:
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432 atoms # core and shell atoms
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216 bonds # number of core/shell springs :pre
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4 atom types # 2 cores and 2 shells for Na and Cl
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4 atom types # 2 cores and 2 shells for Na and Cl
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2 bond types :pre
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0.0 24.09597 xlo xhi
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@ -2545,19 +2545,19 @@ Atoms :pre
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1 1 2 1.5005 0.00000000 0.00000000 0.00000000 # core of core/shell pair 1
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2 1 4 -2.5005 0.00000000 0.00000000 0.00000000 # shell of core/shell pair 1
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3 2 1 1.5056 4.01599500 4.01599500 4.01599500 # core of core/shell pair 2
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4 2 3 -0.5056 4.01599500 4.01599500 4.01599500 # shell of core/shell pair 2
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4 2 3 -0.5056 4.01599500 4.01599500 4.01599500 # shell of core/shell pair 2
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(...) :pre
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Bonds # Bond topology for spring forces :pre
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1 2 1 2 # spring for core/shell pair 1
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2 2 3 4 # spring for core/shell pair 2
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2 2 3 4 # spring for core/shell pair 2
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(...) :pre
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Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only
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defined between the shells. Coulombic interactions are defined
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between all cores and shells. If desired, additional bonds can be
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specified between cores.
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specified between cores.
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The "special_bonds"_special_bonds.html command should be used to
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turn-off the Coulombic interaction within core/shell pairs, since that
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@ -2620,7 +2620,7 @@ Note that to perform thermostatting using this definition of
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temperature, the "fix modify temp"_fix_modify.html command should be
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used to assign the compute to the thermostat fix. Likewise the
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"thermo_modify temp"_thermo_modify.html command can be used to make
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this temperature be output for the overall system.
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this temperature be output for the overall system.
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For the NaCl example, this can be done as follows:
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@ -2632,13 +2632,13 @@ fix thermostatequ all nve # integrator as needed f
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fix_modify thermoberendsen temp CSequ
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thermo_modify temp CSequ # output of center-of-mass derived temperature :pre
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If "compute temp/cs"_compute_temp_cs.html is used, the decoupled
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relative motion of the core and the shell should in theory be
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If "compute temp/cs"_compute_temp_cs.html is used, the decoupled
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relative motion of the core and the shell should in theory be
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stable. However numerical fluctuation can introduce a small
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momentum to the system, which is noticable over long trajectories.
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Therefore it is recomendable to use the "fix
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momentum"_fix_momentum.html command in combination with "compute
|
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temp/cs"_compute_temp_cs.html when equilibrating the system to
|
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Therefore it is recomendable to use the "fix
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momentum"_fix_momentum.html command in combination with "compute
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temp/cs"_compute_temp_cs.html when equilibrating the system to
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prevent any drift.
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When intializing the velocities of a system with core/shell pairs, it
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@ -2661,17 +2661,17 @@ to the electrostatic environment. This fast movement also limits the
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timestep size that can be used.
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The primary literature of the adiabatic core/shell model suggests that
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the fast relative motion of the core/shell pairs only allows negligible
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the fast relative motion of the core/shell pairs only allows negligible
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energy transfer to the environment. Therefore it is not intended to
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decouple the core/shell degree of freedom from the physical system
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during production runs. In other words, the "compute
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temp/cs"_compute_temp_cs.html command should not be used during
|
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production runs and is only required during equilibration. This way one
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is consistent with literature (based on the code packages DL_POLY or
|
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production runs and is only required during equilibration. This way one
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is consistent with literature (based on the code packages DL_POLY or
|
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GULP for instance).
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The mentioned energy transfer will typically lead to a a small drift
|
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in total energy over time. This internal energy can be monitored
|
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The mentioned energy transfer will typically lead to a a small drift
|
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in total energy over time. This internal energy can be monitored
|
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using the "compute chunk/atom"_compute_chunk_atom.html and "compute
|
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temp/chunk"_compute_temp_chunk.html commands. The internal kinetic
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energies of each core/shell pair can then be summed using the sum()
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@ -2702,14 +2702,14 @@ The additional section in the date file would be formatted like this:
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|
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CS-Info # header of additional section :pre
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|
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1 1 # column 1 = atom ID, column 2 = core/shell ID
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2 1
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3 2
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4 2
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5 3
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6 3
|
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7 4
|
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8 4
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1 1 # column 1 = atom ID, column 2 = core/shell ID
|
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2 1
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3 2
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4 2
|
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5 3
|
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6 3
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7 4
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8 4
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(...) :pre
|
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|
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:line
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|
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@ -181,7 +181,7 @@ Atom creation :h5
|
||||
displace atoms :ul
|
||||
|
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Ensembles, constraints, and boundary conditions :h5
|
||||
("fix"_fix.html command)
|
||||
("fix"_fix.html command)
|
||||
|
||||
2d or 3d systems
|
||||
orthogonal or non-orthogonal (triclinic symmetry) simulation domains
|
||||
@ -199,7 +199,7 @@ Ensembles, constraints, and boundary conditions :h5
|
||||
variety of additional boundary conditions and constraints :ul
|
||||
|
||||
Integrators :h5
|
||||
("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands)
|
||||
("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands)
|
||||
|
||||
velocity-Verlet integrator
|
||||
Brownian dynamics
|
||||
@ -213,7 +213,7 @@ Diagnostics :h5
|
||||
see the various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul
|
||||
|
||||
Output :h5
|
||||
("dump"_dump.html, "restart"_restart.html commands)
|
||||
("dump"_dump.html, "restart"_restart.html commands)
|
||||
|
||||
log file of thermodynamic info
|
||||
text dump files of atom coords, velocities, other per-atom quantities
|
||||
|
||||
@ -182,7 +182,7 @@ Supporting info: "atom_style body"_atom_style.html, "body"_body.html,
|
||||
"pair_style body"_pair_body.html, examples/body
|
||||
|
||||
:line
|
||||
|
||||
|
||||
CLASS2 package :link(CLASS2),h5
|
||||
|
||||
Contents: Bond, angle, dihedral, improper, and pair styles for the
|
||||
@ -206,9 +206,9 @@ Supporting info: "bond_style class2"_bond_class2.html, "angle_style
|
||||
class2"_angle_class2.html, "dihedral_style
|
||||
class2"_dihedral_class2.html, "improper_style
|
||||
class2"_improper_class2.html, "pair_style lj/class2"_pair_class2.html
|
||||
|
||||
|
||||
:line
|
||||
|
||||
|
||||
COLLOID package :link(COLLOID),h5
|
||||
|
||||
Contents: Support for coarse-grained colloidal particles. Wall fix
|
||||
@ -239,9 +239,9 @@ lubricate"_pair_lubricate.html, "pair_style
|
||||
lubricateU"_pair_lubricateU.html, examples/colloid, examples/srd
|
||||
|
||||
:line
|
||||
|
||||
|
||||
COMPRESS package :link(COMPRESS),h5
|
||||
|
||||
|
||||
Contents: Support for compressed output of dump files via the zlib
|
||||
compression library, using dump styles with a "gz" in their style
|
||||
name.
|
||||
@ -271,7 +271,7 @@ atom/gz"_dump.html, "dump cfg/gz"_dump.html, "dump
|
||||
custom/gz"_dump.html, "dump xyz/gz"_dump.html
|
||||
|
||||
:line
|
||||
|
||||
|
||||
CORESHELL package :link(CORESHELL),h5
|
||||
|
||||
Contents: Compute and pair styles that implement the adiabatic
|
||||
@ -302,7 +302,7 @@ buck/coul/long/cs"_pair_cs.html, pair_style
|
||||
lj/cut/coul/long/cs"_pair_lj.html, examples/coreshell
|
||||
|
||||
:line
|
||||
|
||||
|
||||
DIPOLE package :link(DIPOLE),h5
|
||||
|
||||
Contents: An atom style and several pair styles to support point
|
||||
@ -326,9 +326,9 @@ Supporting info: "atom_style dipole"_atom_style.html, "pair_style
|
||||
lj/cut/dipole/cut"_pair_dipole.html, "pair_style
|
||||
lj/cut/dipole/long"_pair_dipole.html, "pair_style
|
||||
lj/long/dipole/long"_pair_dipole.html, examples/dipole
|
||||
|
||||
|
||||
:line
|
||||
|
||||
|
||||
GPU package :link(GPU),h5
|
||||
|
||||
Contents: Dozens of pair styles and a version of the PPPM long-range
|
||||
@ -385,9 +385,9 @@ Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5
|
||||
for any pair style listed with a (g),
|
||||
"kspace_style"_kspace_style.html, "package gpu"_package.html,
|
||||
examples/accelerate, bench/FERMI, bench/KEPLER
|
||||
|
||||
|
||||
:line
|
||||
|
||||
|
||||
GRANULAR package :link(GRANULAR),h5
|
||||
|
||||
Contents: Fixes and pair styles that support models of finite-size
|
||||
@ -412,9 +412,9 @@ Supporting info: "Section 6.6"_Section_howto.html#howto_6, "fix
|
||||
pour"_fix_pour.html, "fix wall/gran"_fix_wall_gran.html, "pair_style
|
||||
gran/hooke"_pair_gran.html, "pair_style
|
||||
gran/hertz/history"_pair_gran.html, examples/pour, bench/in.chute
|
||||
|
||||
|
||||
:line
|
||||
|
||||
|
||||
KIM package :link(KIM),h5
|
||||
|
||||
Contents: A pair style that interfaces to the Knowledge Base for
|
||||
@ -443,9 +443,9 @@ Make.py -p ^kim -a machine :pre
|
||||
|
||||
Supporting info: src/KIM/README, lib/kim/README, "pair_style
|
||||
kim"_pair_kim.html, examples/kim
|
||||
|
||||
|
||||
:line
|
||||
|
||||
|
||||
KOKKOS package :link(KOKKOS),h5
|
||||
|
||||
Contents: Dozens of atom, pair, bond, angle, dihedral, improper styles
|
||||
@ -501,7 +501,7 @@ for any pair style listed with a (k), "package kokkos"_package.html,
|
||||
examples/accelerate, bench/FERMI, bench/KEPLER
|
||||
|
||||
:line
|
||||
|
||||
|
||||
KSPACE package :link(KSPACE),h5
|
||||
|
||||
Contents: A variety of long-range Coulombic solvers, and pair styles
|
||||
@ -543,7 +543,7 @@ which have "long" or "msm" in their style name,
|
||||
examples/peptide, bench/in.rhodo
|
||||
|
||||
:line
|
||||
|
||||
|
||||
MANYBODY package :link(MANYBODY),h5
|
||||
|
||||
Contents: A variety of many-body and bond-order potentials. These
|
||||
@ -565,14 +565,14 @@ make machine :pre
|
||||
|
||||
Make.py -p ^manybody -a machine :pre
|
||||
|
||||
Supporting info:
|
||||
|
||||
Supporting info:
|
||||
|
||||
Examples: Pair Styles section of "Section
|
||||
3.5"_Section_commands.html#cmd_5, examples/comb, examples/eim,
|
||||
examples/nb3d, examples/vashishta
|
||||
|
||||
:line
|
||||
|
||||
|
||||
MC package :link(MC),h5
|
||||
|
||||
Contents: Several fixes and a pair style that have Monte Carlo (MC) or
|
||||
@ -598,9 +598,9 @@ Supporting info: "fix atom/swap"_fix_atom_swap.html, "fix
|
||||
bond/break"_fix_bond_break.html, "fix
|
||||
bond/create"_fix_bond_create.html, "fix bond/swap"_fix_bond_swap.html,
|
||||
"fix gcmc"_fix_gcmc.html, "pair_style dsmc"_pair_dsmc.html
|
||||
|
||||
|
||||
:line
|
||||
|
||||
|
||||
MEAM package :link(MEAM),h5
|
||||
|
||||
Contents: A pair style for the modified embedded atom (MEAM)
|
||||
@ -644,9 +644,9 @@ Make.py -p ^meam -a machine :pre
|
||||
|
||||
Supporting info: lib/meam/README, "pair_style meam"_pair_meam.html,
|
||||
examples/meam
|
||||
|
||||
|
||||
:line
|
||||
|
||||
|
||||
MISC package :link(MISC),h5
|
||||
|
||||
Contents: A variety of computes, fixes, and pair styles that are not
|
||||
@ -670,9 +670,9 @@ Make.py -p ^misc -a machine :pre
|
||||
Supporting info: "compute ti"_compute_ti.html, "fix
|
||||
evaporate"_fix_evaporate.html, "fix tmm"_fix_ttm.html, "fix
|
||||
viscosity"_fix_viscosity.html, examples/misc
|
||||
|
||||
|
||||
:line
|
||||
|
||||
|
||||
MOLECULE package :link(MOLECULE),h5
|
||||
|
||||
Contents: A large number of atom, pair, bond, angle, dihedral,
|
||||
@ -704,7 +704,7 @@ lj/charmm/coul/charmm"_pair_charmm.html,
|
||||
examples/micelle, examples/peptide, bench/in.chain, bench/in.rhodo
|
||||
|
||||
:line
|
||||
|
||||
|
||||
MPIIO package :link(MPIIO),h5
|
||||
|
||||
Contents: Support for parallel output/input of dump and restart files
|
||||
@ -729,9 +729,9 @@ Make.py -p ^mpiio -a machine :pre
|
||||
|
||||
Supporting info: "dump"_dump.html, "restart"_restart.html,
|
||||
"write_restart"_write_restart.html, "read_restart"_read_restart.html
|
||||
|
||||
|
||||
:line
|
||||
|
||||
|
||||
OPT package :link(OPT),h5
|
||||
|
||||
Contents: A handful of pair styles with an "opt" in their style name
|
||||
@ -768,7 +768,7 @@ Supporting info: "Section 5.3"_Section_accelerate.html#acc_3,
|
||||
listed with an (t), examples/accelerate, bench/KEPLER
|
||||
|
||||
:line
|
||||
|
||||
|
||||
PERI package :link(PERI),h5
|
||||
|
||||
Contents: Support for the Peridynamics method, a particle-based
|
||||
@ -796,9 +796,9 @@ Supporting info:
|
||||
"doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf, "atom_style
|
||||
peri"_atom_style.html, "compute damage/atom"_compute_damage_atom.html,
|
||||
"pair_style peri/pmb"_pair_peri.html, examples/peri
|
||||
|
||||
|
||||
:line
|
||||
|
||||
|
||||
POEMS package :link(POEMS),h5
|
||||
|
||||
Contents: A fix that wraps the Parallelizable Open source Efficient
|
||||
@ -839,7 +839,7 @@ Supporting info: src/POEMS/README, lib/poems/README,
|
||||
"fix poems"_fix_poems.html, examples/rigid
|
||||
|
||||
:line
|
||||
|
||||
|
||||
PYTHON package :link(PYTHON),h5
|
||||
|
||||
Contents: A "python"_python.html command which allow you to execute
|
||||
@ -873,9 +873,9 @@ make machine :pre
|
||||
Make.py -p ^python -a machine :pre
|
||||
|
||||
Supporting info: examples/python
|
||||
|
||||
|
||||
:line
|
||||
|
||||
|
||||
QEQ package :link(QEQ),h5
|
||||
|
||||
Contents: Several fixes for performing charge equilibration (QEq) via
|
||||
@ -897,9 +897,9 @@ make machine :pre
|
||||
Make.py -p ^qeq -a machine :pre
|
||||
|
||||
Supporting info: "fix qeq/*"_fix_qeq.html, examples/qeq
|
||||
|
||||
|
||||
:line
|
||||
|
||||
|
||||
REAX package :link(REAX),h5
|
||||
|
||||
Contents: A pair style for the ReaxFF potential, a universal reactive
|
||||
@ -941,9 +941,9 @@ Make.py -p ^reax -a machine :pre
|
||||
|
||||
Supporting info: lib/reax/README, "pair_style reax"_pair_reax.html,
|
||||
"fix reax/bonds"_fix_reax_bonds.html, examples/reax
|
||||
|
||||
|
||||
:line
|
||||
|
||||
|
||||
REPLICA package :link(REPLICA),h5
|
||||
|
||||
Contents: A collection of multi-replica methods that are used by
|
||||
@ -978,7 +978,7 @@ Supporting info: "Section 6.5"_Section_howto.html#howto_5,
|
||||
examples/tad
|
||||
|
||||
:line
|
||||
|
||||
|
||||
RIGID package :link(RIGID),h5
|
||||
|
||||
Contents: A collection of computes and fixes which enforce rigid
|
||||
@ -1005,7 +1005,7 @@ Supporting info: "compute erotate/rigid"_compute_erotate_rigid.html,
|
||||
rigid/*"_fix_rigid.html, examples/ASPHERE, examples/rigid
|
||||
|
||||
:line
|
||||
|
||||
|
||||
SHOCK package :link(SHOCK),h5
|
||||
|
||||
Contents: A small number of fixes useful for running impact
|
||||
@ -1028,15 +1028,15 @@ Make.py -p ^shock -a machine :pre
|
||||
Supporting info: "fix append/atoms"_fix_append_atoms.html, "fix
|
||||
msst"_fix_msst.html, "fix nphug"_fix_nphug.html, "fix
|
||||
wall/piston"_fix_wall_piston.html, examples/hugoniostat, examples/msst
|
||||
|
||||
|
||||
:line
|
||||
|
||||
|
||||
SNAP package :link(SNAP),h5
|
||||
|
||||
Contents: A pair style for the spectral neighbor analysis potential
|
||||
(SNAP), which is an empirical potential which can be quantum accurate
|
||||
when fit to an archive of DFT data. Computes useful for analyzing
|
||||
properties of the potential are also included.
|
||||
when fit to an archive of DFT data. Computes useful for analyzing
|
||||
properties of the potential are also included.
|
||||
|
||||
To install via make or Make.py:
|
||||
|
||||
@ -1055,9 +1055,9 @@ Make.py -p ^snap -a machine :pre
|
||||
Supporting info: "pair snap"_pair_snap.html, "compute
|
||||
sna/atom"_compute_sna_atom.html, "compute snad/atom"_compute_sna_atom.html,
|
||||
"compute snav/atom"_compute_sna_atom.html, examples/snap
|
||||
|
||||
|
||||
:line
|
||||
|
||||
|
||||
SRD package :link(SRD),h5
|
||||
|
||||
Contents: Two fixes which implement the Stochastic Rotation Dynamics
|
||||
@ -1080,9 +1080,9 @@ Make.py -p ^srd -a machine :pre
|
||||
|
||||
Supporting info: "fix srd"_fix_srd.html, "fix
|
||||
wall/srd"_fix_wall_srd.html, examples/srd, examples/ASPHERE
|
||||
|
||||
|
||||
:line
|
||||
|
||||
|
||||
VORONOI package :link(VORONOI),h5
|
||||
|
||||
Contents: A "compute voronoi/atom"_compute_voronoi_atom.html command
|
||||
@ -1129,9 +1129,9 @@ Make.py -p ^voronoi -a machine :pre
|
||||
|
||||
Supporting info: src/VORONOI/README, lib/voronoi/README, "compute
|
||||
voronoi/atom"_compute_voronoi_atom.html, examples/voronoi
|
||||
|
||||
|
||||
:line
|
||||
|
||||
|
||||
4.2 User packages :h4,link(pkg_2)
|
||||
|
||||
The current list of user-contributed packages is as follows:
|
||||
@ -1302,7 +1302,7 @@ fix. The COLVARS library itself is written and maintained by Giacomo
|
||||
Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and Jerome
|
||||
Henin (LISM, CNRS, Marseille, France). Contact them directly if you
|
||||
have questions.
|
||||
|
||||
|
||||
:line
|
||||
|
||||
USER-DIFFRACTION package :link(USER-DIFFRACTION),h5
|
||||
@ -1380,7 +1380,7 @@ in 2007. See src/USER-EFF/README for more details. There are
|
||||
auxiliary tools for using this package in tools/eff; see its README
|
||||
file.
|
||||
|
||||
Supporting info:
|
||||
Supporting info:
|
||||
|
||||
Author: Andres Jaramillo-Botero at CalTech (ajaramil at
|
||||
wag.caltech.edu). Contact him directly if you have questions.
|
||||
@ -1456,21 +1456,21 @@ LINKFLAGS: add -fopenmp :ul
|
||||
|
||||
For Phi mode add the following in addition to the CPU mode flags:
|
||||
|
||||
CCFLAGS: add -DLMP_INTEL_OFFLOAD and
|
||||
CCFLAGS: add -DLMP_INTEL_OFFLOAD and
|
||||
LINKFLAGS: add -offload :ul
|
||||
|
||||
And also add this to CCFLAGS:
|
||||
|
||||
-offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\"" :pre
|
||||
|
||||
Examples:
|
||||
Examples:
|
||||
|
||||
:line
|
||||
|
||||
USER-LB package :link(USER-LB),h5
|
||||
|
||||
Supporting info:
|
||||
|
||||
Supporting info:
|
||||
|
||||
This package contains a LAMMPS implementation of a background
|
||||
Lattice-Boltzmann fluid, which can be used to model MD particles
|
||||
influenced by hydrodynamic forces.
|
||||
@ -1489,8 +1489,8 @@ Examples: examples/USER/lb
|
||||
|
||||
USER-MGPT package :link(USER-MGPT),h5
|
||||
|
||||
Supporting info:
|
||||
|
||||
Supporting info:
|
||||
|
||||
This package contains a fast implementation for LAMMPS of
|
||||
quantum-based MGPT multi-ion potentials. The MGPT or model GPT method
|
||||
derives from first-principles DFT-based generalized pseudopotential
|
||||
@ -1521,8 +1521,8 @@ Examples: examples/USER/mgpt
|
||||
|
||||
USER-MISC package :link(USER-MISC),h5
|
||||
|
||||
Supporting info:
|
||||
|
||||
Supporting info:
|
||||
|
||||
The files in this package are a potpourri of (mostly) unrelated
|
||||
features contributed to LAMMPS by users. Each feature is a single
|
||||
pair of files (*.cpp and *.h).
|
||||
@ -1548,8 +1548,8 @@ Examples: examples/USER/misc
|
||||
|
||||
USER-MANIFOLD package :link(USER-MANIFOLD),h5
|
||||
|
||||
Supporting info:
|
||||
|
||||
Supporting info:
|
||||
|
||||
This package contains a dump molfile command which uses molfile
|
||||
plugins that are bundled with the
|
||||
"VMD"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and
|
||||
@ -1574,8 +1574,8 @@ Contact him directly if you have questions.
|
||||
|
||||
USER-MOLFILE package :link(USER-MOLFILE),h5
|
||||
|
||||
Supporting info:
|
||||
|
||||
Supporting info:
|
||||
|
||||
This package contains a dump molfile command which uses molfile
|
||||
plugins that are bundled with the
|
||||
"VMD"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and
|
||||
@ -1600,12 +1600,12 @@ The person who created this package is Axel Kohlmeyer at Temple U
|
||||
|
||||
USER-OMP package :link(USER-OMP),h5
|
||||
|
||||
Supporting info:
|
||||
|
||||
Supporting info:
|
||||
|
||||
This package provides OpenMP multi-threading support and
|
||||
other optimizations of various LAMMPS pair styles, dihedral
|
||||
styles, and fix styles.
|
||||
|
||||
|
||||
See this section of the manual to get started:
|
||||
|
||||
"Section 5.3"_Section_accelerate.html#acc_3
|
||||
@ -1643,8 +1643,8 @@ Examples: examples/USER/phonon
|
||||
|
||||
USER-QMMM package :link(USER-QMMM),h5
|
||||
|
||||
Supporting info:
|
||||
|
||||
Supporting info:
|
||||
|
||||
This package provides a fix qmmm command which allows LAMMPS to be
|
||||
used in a QM/MM simulation, currently only in combination with pw.x
|
||||
code from the "Quantum ESPRESSO"_espresso package.
|
||||
@ -1667,11 +1667,11 @@ The person who created this package is Axel Kohlmeyer at Temple U
|
||||
(akohlmey at gmail.com). Contact him directly if you have questions.
|
||||
|
||||
:line
|
||||
|
||||
|
||||
USER-QTB package :link(USER-QTB),h5
|
||||
|
||||
Supporting info:
|
||||
|
||||
Supporting info:
|
||||
|
||||
This package provides a self-consistent quantum treatment of the
|
||||
vibrational modes in a classical molecular dynamics simulation. By
|
||||
coupling the MD simulation to a colored thermostat, it introduces zero
|
||||
@ -1701,16 +1701,16 @@ Examples: examples/USER/qtb
|
||||
|
||||
USER-QUIP package :link(USER-QUIP),h5
|
||||
|
||||
Supporting info:
|
||||
|
||||
Supporting info:
|
||||
|
||||
Examples: examples/USER/quip
|
||||
|
||||
:line
|
||||
|
||||
USER-REAXC package :link(USER-REAXC),h5
|
||||
|
||||
Supporting info:
|
||||
|
||||
Supporting info:
|
||||
|
||||
This package contains a implementation for LAMMPS of the ReaxFF force
|
||||
field. ReaxFF uses distance-dependent bond-order functions to
|
||||
represent the contributions of chemical bonding to the potential
|
||||
@ -1748,24 +1748,24 @@ Examples: examples/reax
|
||||
|
||||
USER-SMD package :link(USER-SMD),h5
|
||||
|
||||
Supporting info:
|
||||
|
||||
Supporting info:
|
||||
|
||||
This package implements smoothed Mach dynamics (SMD) in
|
||||
LAMMPS. Currently, the package has the following features:
|
||||
|
||||
* Does liquids via traditional Smooth Particle Hydrodynamics (SPH)
|
||||
|
||||
* Also solves solids mechanics problems via a state of the art
|
||||
* Also solves solids mechanics problems via a state of the art
|
||||
stabilized meshless method with hourglass control.
|
||||
|
||||
* Can specify hydrostatic interactions independently from material
|
||||
* Can specify hydrostatic interactions independently from material
|
||||
strength models, i.e. pressure and deviatoric stresses are separated.
|
||||
|
||||
* Many material models available (Johnson-Cook, plasticity with
|
||||
hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new
|
||||
* Many material models available (Johnson-Cook, plasticity with
|
||||
hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new
|
||||
material models.
|
||||
|
||||
* Rigid boundary conditions (walls) can be loaded as surface geometries
|
||||
* Rigid boundary conditions (walls) can be loaded as surface geometries
|
||||
from *.STL files.
|
||||
|
||||
See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started.
|
||||
@ -1783,8 +1783,8 @@ Examples: examples/USER/smd
|
||||
|
||||
USER-SMTBQ package :link(USER-SMTBQ),h5
|
||||
|
||||
Supporting info:
|
||||
|
||||
Supporting info:
|
||||
|
||||
This package implements the Second Moment Tight Binding - QEq (SMTB-Q)
|
||||
potential for the description of ionocovalent bonds in oxides.
|
||||
|
||||
@ -1806,22 +1806,22 @@ Examples: examples/USER/smtbq
|
||||
|
||||
USER-SPH package :link(USER-SPH),h5
|
||||
|
||||
Supporting info:
|
||||
Supporting info:
|
||||
|
||||
This package implements smoothed particle hydrodynamics (SPH) in
|
||||
LAMMPS. Currently, the package has the following features:
|
||||
|
||||
* Tait, ideal gas, Lennard-Jones equation of states, full support for
|
||||
* Tait, ideal gas, Lennard-Jones equation of states, full support for
|
||||
complete (i.e. internal-energy dependent) equations of state
|
||||
|
||||
* Plain or Monaghans XSPH integration of the equations of motion
|
||||
|
||||
* Density continuity or density summation to propagate the density field
|
||||
|
||||
* Commands to set internal energy and density of particles from the
|
||||
* Commands to set internal energy and density of particles from the
|
||||
input script
|
||||
|
||||
* Output commands to access internal energy and density for dumping and
|
||||
* Output commands to access internal energy and density for dumping and
|
||||
thermo output
|
||||
|
||||
See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started.
|
||||
@ -1839,7 +1839,7 @@ Examples: examples/USER/sph
|
||||
|
||||
USER-TALLY package :link(USER-TALLY),h5
|
||||
|
||||
Supporting info:
|
||||
Supporting info:
|
||||
|
||||
Examples: examples/USER/tally
|
||||
|
||||
|
||||
@ -23,7 +23,7 @@ In Python lingo, this is "embedding" Python in LAMMPS.
|
||||
This section describes how to do both.
|
||||
|
||||
11.1 "Overview of running LAMMPS from Python"_#py_1
|
||||
11.2 "Overview of using Python from a LAMMPS script"_#py_2
|
||||
11.2 "Overview of using Python from a LAMMPS script"_#py_2
|
||||
11.3 "Building LAMMPS as a shared library"_#py_3
|
||||
11.4 "Installing the Python wrapper into Python"_#py_4
|
||||
11.5 "Extending Python with MPI to run in parallel"_#py_5
|
||||
@ -503,7 +503,7 @@ one of several ways:
|
||||
The last command requires that the first line of the script be
|
||||
something like this:
|
||||
|
||||
#!/usr/local/bin/python
|
||||
#!/usr/local/bin/python
|
||||
#!/usr/local/bin/python -i :pre
|
||||
|
||||
where the path points to where you have Python installed, and that you
|
||||
@ -724,7 +724,7 @@ lmp.scatter_coords("x",1,3,x) :pre
|
||||
Alternatively, you can just change values in the vector returned by
|
||||
gather_atoms("x",1,3), since it is a ctypes vector of doubles.
|
||||
|
||||
:line
|
||||
:line
|
||||
|
||||
As noted above, these Python class methods correspond one-to-one with
|
||||
the functions in the LAMMPS library interface in src/library.cpp and
|
||||
@ -767,7 +767,7 @@ vizplotgui_tool.py, combination of viz_tool.py and plot.py and gui.py :tb(c=2)
|
||||
|
||||
For the viz_tool.py and vizplotgui_tool.py commands, replace "tool"
|
||||
with "gl" or "atomeye" or "pymol" or "vmd", depending on what
|
||||
visualization package you have installed.
|
||||
visualization package you have installed.
|
||||
|
||||
Note that for GL, you need to be able to run the Pizza.py GL tool,
|
||||
which is included in the pizza sub-directory. See the "Pizza.py doc
|
||||
|
||||
@ -33,7 +33,7 @@ tar -xzvf lammps*.tar.gz :pre
|
||||
|
||||
This will create a LAMMPS directory containing two files and several
|
||||
sub-directories:
|
||||
|
||||
|
||||
README: text file
|
||||
LICENSE: the GNU General Public License (GPL)
|
||||
bench: benchmark problems
|
||||
@ -600,10 +600,10 @@ LAMMPS will generate a run-time error. As far as we know, the
|
||||
settings defined in src/lmptype.h are portable and work on every
|
||||
current system.
|
||||
|
||||
In all cases, the size of problem that can be run on a per-processor
|
||||
basis is limited by 4-byte integer storage to 2^31 atoms per processor
|
||||
(about 2 billion). This should not normally be a limitation since such
|
||||
a problem would have a huge per-processor memory footprint due to
|
||||
In all cases, the size of problem that can be run on a per-processor
|
||||
basis is limited by 4-byte integer storage to 2^31 atoms per processor
|
||||
(about 2 billion). This should not normally be a limitation since such
|
||||
a problem would have a huge per-processor memory footprint due to
|
||||
neighbor lists and would run very slowly in terms of CPU secs/timestep.
|
||||
|
||||
:line
|
||||
@ -841,7 +841,7 @@ libpackage.a
|
||||
Makefile.lammps :pre
|
||||
|
||||
The Makefile.lammps file will typically be a copy of one of the
|
||||
Makefile.lammps.* files in the library directory.
|
||||
Makefile.lammps.* files in the library directory.
|
||||
|
||||
Note that you must insure that the settings in Makefile.lammps are
|
||||
appropriate for your system. If they are not, the LAMMPS build may
|
||||
@ -883,7 +883,7 @@ A few packages require specific settings in Makefile.machine, to
|
||||
either build or use the package effectively. These are the
|
||||
USER-INTEL, KOKKOS, USER-OMP, and OPT packages, used for accelerating
|
||||
code performance on CPUs or other hardware, as discussed in "Section
|
||||
5.3"_Section_accelerate.html#acc_3.
|
||||
5.3"_Section_accelerate.html#acc_3.
|
||||
|
||||
A summary of what Makefile.machine changes are needed for each of
|
||||
these packages is given in "Section 4"_Section_packages.html.
|
||||
@ -1199,7 +1199,7 @@ installer package from "here"_http://rpm.lammps.org/windows.html
|
||||
|
||||
For running the non-MPI executable, follow these steps:
|
||||
|
||||
Get a command prompt by going to Start->Run... ,
|
||||
Get a command prompt by going to Start->Run... ,
|
||||
then typing "cmd". :ulb,l
|
||||
|
||||
Move to the directory where you have your input, e.g. a copy of
|
||||
@ -1209,7 +1209,7 @@ At the command prompt, type "lmp_serial -in in.lj", replacing [in.lj]
|
||||
with the name of your LAMMPS input script. :l
|
||||
:ule
|
||||
|
||||
For the MPI version, which allows you to run LAMMPS under Windows on
|
||||
For the MPI version, which allows you to run LAMMPS under Windows on
|
||||
multiple processors, follow these steps:
|
||||
|
||||
Download and install
|
||||
@ -1224,7 +1224,7 @@ For this you need to start a Command Prompt in {Administrator Mode}
|
||||
installation directory, then into the subdirectory [bin] and execute
|
||||
[smpd.exe -install]. Exit the command window.
|
||||
|
||||
Get a new, regular command prompt by going to Start->Run... ,
|
||||
Get a new, regular command prompt by going to Start->Run... ,
|
||||
then typing "cmd". :l
|
||||
|
||||
Move to the directory where you have your input file
|
||||
@ -1488,7 +1488,7 @@ of the manual. World- and universe-style "variables"_variable.html
|
||||
are useful in this context.
|
||||
|
||||
-plog file :pre
|
||||
|
||||
|
||||
Specify the base name for the partition log files, so partition N
|
||||
writes log information to file.N. If file is none, then no partition
|
||||
log files are created. This overrides the filename specified in the
|
||||
@ -1499,7 +1499,7 @@ replica_files/log.lammps) If this option is not used the log file for
|
||||
partition N is log.lammps.N or whatever is specified by the -log
|
||||
command-line option.
|
||||
|
||||
-pscreen file :pre
|
||||
-pscreen file :pre
|
||||
|
||||
Specify the base name for the partition screen file, so partition N
|
||||
writes screen information to file.N. If file is none, then no
|
||||
@ -1511,7 +1511,7 @@ sub-directory (-pscreen replica_files/screen). If this option is not
|
||||
used the screen file for partition N is screen.N or whatever is
|
||||
specified by the -screen command-line option.
|
||||
|
||||
-restart restartfile {remap} datafile keyword value ... :pre
|
||||
-restart restartfile {remap} datafile keyword value ... :pre
|
||||
|
||||
Convert the restart file into a data file and immediately exit. This
|
||||
is the same operation as if the following 2-line input script were
|
||||
@ -1572,7 +1572,7 @@ to
|
||||
|
||||
so that the processors in each partition will be
|
||||
|
||||
0 1 2 4 5 6 8 9 10
|
||||
0 1 2 4 5 6 8 9 10
|
||||
3 7 11 :pre
|
||||
|
||||
See the "processors" command for how to insure processors from each
|
||||
@ -1663,12 +1663,12 @@ invokes the default USER-INTEL settings, as if the command "package
|
||||
intel 1" were used at the top of your input script. These settings
|
||||
can be changed by using the "-package intel" command-line switch or
|
||||
the "package intel"_package.html command in your script. If the
|
||||
USER-OMP package is also installed, the hybrid style with "intel omp"
|
||||
arguments can be used to make the omp suffix a second choice, if a
|
||||
requested style is not available in the USER-INTEL package. It will
|
||||
also invoke the default USER-OMP settings, as if the command "package
|
||||
omp 0" were used at the top of your input script. These settings can
|
||||
be changed by using the "-package omp" command-line switch or the
|
||||
USER-OMP package is also installed, the hybrid style with "intel omp"
|
||||
arguments can be used to make the omp suffix a second choice, if a
|
||||
requested style is not available in the USER-INTEL package. It will
|
||||
also invoke the default USER-OMP settings, as if the command "package
|
||||
omp 0" were used at the top of your input script. These settings can
|
||||
be changed by using the "-package omp" command-line switch or the
|
||||
"package omp"_package.html command in your script.
|
||||
|
||||
For the KOKKOS package, using this command-line switch also invokes
|
||||
@ -1833,7 +1833,7 @@ e.g.
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = linesearch alpha is zero
|
||||
Energy initial, next-to-last, final =
|
||||
Energy initial, next-to-last, final =
|
||||
-6372.3765206 -8328.46998942 -8328.46998942
|
||||
Force two-norm initial, final = 1059.36 5.36874
|
||||
Force max component initial, final = 58.6026 1.46872
|
||||
|
||||
@ -104,7 +104,7 @@ since binary files are not compatible across all platforms.
|
||||
ch2lmp tool :h4,link(charmm)
|
||||
|
||||
The ch2lmp sub-directory contains tools for converting files
|
||||
back-and-forth between the CHARMM MD code and LAMMPS.
|
||||
back-and-forth between the CHARMM MD code and LAMMPS.
|
||||
|
||||
They are intended to make it easy to use CHARMM as a builder and as a
|
||||
post-processor for LAMMPS. Using charmm2lammps.pl, you can convert a
|
||||
|
||||
@ -29,80 +29,80 @@ Bond Styles: fene, harmonic :l
|
||||
Dihedral Styles: charmm, harmonic, opls :l
|
||||
Fixes: nve, npt, nvt, nvt/sllod :l
|
||||
Improper Styles: cvff, harmonic :l
|
||||
Pair Styles: buck/coul/cut, buck/coul/long, buck, gayberne,
|
||||
Pair Styles: buck/coul/cut, buck/coul/long, buck, gayberne,
|
||||
charmm/coul/long, lj/cut, lj/cut/coul/long, sw, tersoff :l
|
||||
K-Space Styles: pppm :l
|
||||
:ule
|
||||
|
||||
[Speed-ups to expect:]
|
||||
|
||||
The speedups will depend on your simulation, the hardware, which
|
||||
styles are used, the number of atoms, and the floating-point
|
||||
precision mode. Performance improvements are shown compared to
|
||||
LAMMPS {without using other acceleration packages} as these are
|
||||
under active development (and subject to performance changes). The
|
||||
The speedups will depend on your simulation, the hardware, which
|
||||
styles are used, the number of atoms, and the floating-point
|
||||
precision mode. Performance improvements are shown compared to
|
||||
LAMMPS {without using other acceleration packages} as these are
|
||||
under active development (and subject to performance changes). The
|
||||
measurements were performed using the input files available in
|
||||
the src/USER-INTEL/TEST directory. These are scalable in size; the
|
||||
results given are with 512K particles (524K for Liquid Crystal).
|
||||
the src/USER-INTEL/TEST directory. These are scalable in size; the
|
||||
results given are with 512K particles (524K for Liquid Crystal).
|
||||
Most of the simulations are standard LAMMPS benchmarks (indicated
|
||||
by the filename extension in parenthesis) with modifications to the
|
||||
run length and to add a warmup run (for use with offload
|
||||
benchmarks).
|
||||
by the filename extension in parenthesis) with modifications to the
|
||||
run length and to add a 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
|
||||
Results are speedups obtained on Intel Xeon E5-2697v4 processors
|
||||
(code-named Broadwell) and Intel Xeon Phi 7250 processors
|
||||
(code-named Knights Landing) with "18 Jun 2016" LAMMPS built with
|
||||
Intel Parallel Studio 2016 update 3. Results are with 1 MPI task
|
||||
per physical core. See {src/USER-INTEL/TEST/README} for the raw
|
||||
Intel Parallel Studio 2016 update 3. 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
|
||||
|
||||
[Quick Start for Experienced Users:]
|
||||
|
||||
LAMMPS should be built with the USER-INTEL package installed.
|
||||
LAMMPS should be built with the USER-INTEL package installed.
|
||||
Simulations should be run with 1 MPI task per physical {core},
|
||||
not {hardware thread}.
|
||||
|
||||
For Intel Xeon CPUs:
|
||||
|
||||
Edit src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi as necessary. :ulb,l
|
||||
If using {kspace_style pppm} in the input script, add "neigh_modify binsize 3" and "kspace_modify diff ad" to the input script for better
|
||||
If using {kspace_style pppm} in the input script, add "neigh_modify binsize 3" and "kspace_modify diff ad" to the input script for better
|
||||
performance. :l
|
||||
"-pk intel 0 omp 2 -sf intel" added to LAMMPS command-line :l
|
||||
:ule
|
||||
|
||||
For Intel Xeon Phi CPUs for simulations without {kspace_style
|
||||
For Intel Xeon Phi CPUs for simulations without {kspace_style
|
||||
pppm} in the input script :
|
||||
|
||||
Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l
|
||||
Runs should be performed using MCDRAM. :l
|
||||
"-pk intel 0 omp 2 -sf intel" {or} "-pk intel 0 omp 4 -sf intel"
|
||||
should be added to the LAMMPS command-line. Choice for best
|
||||
"-pk intel 0 omp 2 -sf intel" {or} "-pk intel 0 omp 4 -sf intel"
|
||||
should be added to the LAMMPS command-line. Choice for best
|
||||
performance will depend on the simulation. :l
|
||||
:ule
|
||||
|
||||
For Intel Xeon Phi CPUs for simulations with {kspace_style
|
||||
For Intel Xeon Phi CPUs for simulations with {kspace_style
|
||||
pppm} in the input script:
|
||||
|
||||
Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l
|
||||
Runs should be performed using MCDRAM. :l
|
||||
Add "neigh_modify binsize 3" to the input script for better
|
||||
Add "neigh_modify binsize 3" to the input script for better
|
||||
performance. :l
|
||||
Add "kspace_modify diff ad" to the input script for better
|
||||
Add "kspace_modify diff ad" to the input script for better
|
||||
performance. :l
|
||||
export KMP_AFFINITY=none :l
|
||||
"-pk intel 0 omp 3 lrt yes -sf intel" or "-pk intel 0 omp 1 lrt yes
|
||||
-sf intel" added to LAMMPS command-line. Choice for best performance
|
||||
-sf intel" added to LAMMPS command-line. Choice for best performance
|
||||
will depend on the simulation. :l
|
||||
:ule
|
||||
|
||||
For Intel Xeon Phi coprocessors (Offload):
|
||||
For Intel Xeon Phi coprocessors (Offload):
|
||||
|
||||
Edit src/MAKE/OPTIONS/Makefile.intel_coprocessor as necessary :ulb,l
|
||||
"-pk intel N omp 1" added to command-line where N is the number of
|
||||
"-pk intel N omp 1" added to command-line where N is the number of
|
||||
coprocessors per node. :l
|
||||
:ule
|
||||
|
||||
@ -111,7 +111,7 @@ coprocessors per node. :l
|
||||
[Required hardware/software:]
|
||||
|
||||
In order to use offload to coprocessors, an Intel Xeon Phi
|
||||
coprocessor and an Intel compiler are required. For this, the
|
||||
coprocessor and an Intel compiler are required. For this, the
|
||||
recommended version of the Intel compiler is 14.0.1.106 or
|
||||
versions 15.0.2.044 and higher.
|
||||
|
||||
@ -133,7 +133,7 @@ slightly lower.
|
||||
|
||||
[Notes about Simultaneous Multithreading:]
|
||||
|
||||
Modern CPUs often support Simultaneous Multithreading (SMT). On
|
||||
Modern CPUs often support Simultaneous Multithreading (SMT). On
|
||||
Intel processors, this is called Hyper-Threading (HT) technology.
|
||||
SMT is hardware support for running multiple threads efficiently on
|
||||
a single core. {Hardware threads} or {logical cores} are often used
|
||||
@ -141,8 +141,8 @@ to refer to the number of threads that are supported in hardware.
|
||||
For example, the Intel Xeon E5-2697v4 processor is described
|
||||
as having 36 cores and 72 threads. This means that 36 MPI processes
|
||||
or OpenMP threads can run simultaneously on separate cores, but that
|
||||
up to 72 MPI processes or OpenMP threads can be running on the CPU
|
||||
without costly operating system context switches.
|
||||
up to 72 MPI processes or OpenMP threads can be running on the CPU
|
||||
without costly operating system context switches.
|
||||
|
||||
Molecular dynamics simulations will often run faster when making use
|
||||
of SMT. If a thread becomes stalled, for example because it is
|
||||
@ -150,7 +150,7 @@ waiting on data that has not yet arrived from memory, another thread
|
||||
can start running so that the CPU pipeline is still being used
|
||||
efficiently. Although benefits can be seen by launching a MPI task
|
||||
for every hardware thread, for multinode simulations, we recommend
|
||||
that OpenMP threads are used for SMT instead, either with the
|
||||
that OpenMP threads are used for SMT instead, either with the
|
||||
USER-INTEL package, "USER-OMP package"_accelerate_omp.html", or
|
||||
"KOKKOS package"_accelerate_kokkos.html. In the example above, up
|
||||
to 36X speedups can be observed by using all 36 physical cores with
|
||||
@ -158,10 +158,10 @@ LAMMPS. By using all 72 hardware threads, an additional 10-30%
|
||||
performance gain can be achieved.
|
||||
|
||||
The BIOS on many platforms allows SMT to be disabled, however, we do
|
||||
not recommend this on modern processors as there is little to no
|
||||
not recommend this on modern processors as there is little to no
|
||||
benefit for any software package in most cases. The operating system
|
||||
will report every hardware thread as a separate core allowing one to
|
||||
determine the number of hardware threads available. On Linux systems,
|
||||
will report every hardware thread as a separate core allowing one to
|
||||
determine the number of hardware threads available. On Linux systems,
|
||||
this information can normally be obtained with:
|
||||
|
||||
cat /proc/cpuinfo :pre
|
||||
@ -182,21 +182,21 @@ Makefile.intel_cpu_openpmi # Intel Compiler, OpenMPI, No Offload
|
||||
Makefile.intel_coprocessor # Intel Compiler, Intel MPI, Offload :pre
|
||||
|
||||
Makefile.knl is identical to Makefile.intel_cpu_intelmpi except that
|
||||
it explicitly specifies that vectorization should be for Intel
|
||||
Xeon Phi x200 processors making it easier to cross-compile. For
|
||||
users with recent installations of Intel Parallel Studio, the
|
||||
it explicitly specifies that vectorization should be for Intel
|
||||
Xeon Phi x200 processors making it easier to cross-compile. For
|
||||
users with recent installations of Intel Parallel Studio, the
|
||||
process can be as simple as:
|
||||
|
||||
make yes-user-intel
|
||||
source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
|
||||
source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
|
||||
# or psxevars.csh for C-shell
|
||||
make intel_cpu_intelmpi :pre
|
||||
|
||||
Alternatively, the build can be accomplished with the src/Make.py
|
||||
script, described in "Section 2.4"_Section_start.html#start_4 of the
|
||||
Alternatively, the build can be accomplished with the src/Make.py
|
||||
script, described in "Section 2.4"_Section_start.html#start_4 of the
|
||||
manual. Type "Make.py -h" for help. For an example:
|
||||
|
||||
Make.py -v -p intel omp -intel cpu -a file intel_cpu_intelmpi :pre
|
||||
Make.py -v -p intel omp -intel cpu -a file intel_cpu_intelmpi :pre
|
||||
|
||||
Note that if you build with support for a Phi coprocessor, the same
|
||||
binary can be used on nodes with or without coprocessors installed.
|
||||
@ -205,26 +205,26 @@ 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
|
||||
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". The Make.py command will add all of these
|
||||
Other recommended CCFLAG options for best performance are
|
||||
"-O2 -fno-alias -ansi-alias -qoverride-limits fp-model fast=2
|
||||
-no-prec-div". The Make.py command will add all of these
|
||||
automatically.
|
||||
|
||||
NOTE: The vectorization and math capabilities can differ depending on
|
||||
the CPU. For Intel compilers, the "-x" flag specifies the type of
|
||||
processor for which to optimize. "-xHost" specifies that the compiler
|
||||
should build for the processor used for compiling. For Intel Xeon Phi
|
||||
should build for the processor used for compiling. For Intel Xeon Phi
|
||||
x200 series processors, this option is "-xMIC-AVX512". For fourth
|
||||
generation Intel Xeon (v4/Broadwell) processors, "-xCORE-AVX2" should
|
||||
generation Intel Xeon (v4/Broadwell) processors, "-xCORE-AVX2" should
|
||||
be used. For older Intel Xeon processors, "-xAVX" will perform best
|
||||
in general for the different simulations in LAMMPS. The default
|
||||
in most of the example Makefiles is to use "-xHost", however this
|
||||
should not be used when cross-compiling.
|
||||
|
||||
|
||||
[Running LAMMPS with the USER-INTEL package:]
|
||||
|
||||
Running LAMMPS with the USER-INTEL package is similar to normal use
|
||||
@ -232,7 +232,7 @@ with the exceptions that one should 1) specify that LAMMPS should use
|
||||
the USER-INTEL package, 2) specify the number of OpenMP threads, and
|
||||
3) optionally specify the specific LAMMPS styles that should use the
|
||||
USER-INTEL package. 1) and 2) can be performed from the command-line
|
||||
or by editing the input script. 3) requires editing the input script.
|
||||
or by editing the input script. 3) requires editing the input script.
|
||||
Advanced performance tuning options are also described below to get
|
||||
the best performance.
|
||||
|
||||
@ -241,14 +241,14 @@ coprocessor), best performance is normally obtained by using 1 MPI
|
||||
task per physical core and additional OpenMP threads with SMT. For
|
||||
Intel Xeon processors, 2 OpenMP threads should be used for SMT.
|
||||
For Intel Xeon Phi CPUs, 2 or 4 OpenMP threads should be used
|
||||
(best choice depends on the simulation). In cases where the user
|
||||
specifies that LRT mode is used (described below), 1 or 3 OpenMP
|
||||
(best choice depends on the simulation). In cases where the user
|
||||
specifies that LRT mode is used (described below), 1 or 3 OpenMP
|
||||
threads should be used. For multi-node runs, using 1 MPI task per
|
||||
physical core will often perform best, however, depending on the
|
||||
machine and scale, users might get better performance by decreasing
|
||||
the number of MPI tasks and using more OpenMP threads. For
|
||||
performance, the product of the number of MPI tasks and OpenMP
|
||||
threads should not exceed the number of available hardware threads in
|
||||
the number of MPI tasks and using more OpenMP threads. For
|
||||
performance, the product of the number of MPI tasks and OpenMP
|
||||
threads should not exceed the number of available hardware threads in
|
||||
almost all cases.
|
||||
|
||||
NOTE: Setting core affinity is often used to pin MPI tasks and OpenMP
|
||||
@ -257,21 +257,21 @@ uniform. Unless disabled at build time, affinity for MPI tasks and
|
||||
OpenMP threads on the host (CPU) will be set by default on the host
|
||||
{when using offload to a coprocessor}. In this case, it is unnecessary
|
||||
to use other methods to control affinity (e.g. taskset, numactl,
|
||||
I_MPI_PIN_DOMAIN, etc.). This can be disabled with the {no_affinity}
|
||||
option to the "package intel"_package.html command or by disabling the
|
||||
option at build time (by adding -DINTEL_OFFLOAD_NOAFFINITY to the
|
||||
CCFLAGS line of your Makefile). Disabling this option is not
|
||||
recommended, especially when running on a machine with Intel
|
||||
I_MPI_PIN_DOMAIN, etc.). This can be disabled with the {no_affinity}
|
||||
option to the "package intel"_package.html command or by disabling the
|
||||
option at build time (by adding -DINTEL_OFFLOAD_NOAFFINITY to the
|
||||
CCFLAGS line of your Makefile). Disabling this option is not
|
||||
recommended, especially when running on a machine with Intel
|
||||
Hyper-Threading technology disabled.
|
||||
|
||||
[Run with the USER-INTEL package from the command line:]
|
||||
|
||||
To enable USER-INTEL optimizations for all available styles used in
|
||||
the input script, the "-sf intel"
|
||||
To enable USER-INTEL optimizations for all available styles used in
|
||||
the input script, the "-sf intel"
|
||||
"command-line switch"_Section_start.html#start_7 can be used without
|
||||
any requirement for editing the input script. This switch will
|
||||
automatically append "intel" to styles that support it. It also
|
||||
invokes a default command: "package intel 1"_package.html. This
|
||||
automatically append "intel" to styles that support it. It also
|
||||
invokes a default command: "package intel 1"_package.html. This
|
||||
package command is used to set options for the USER-INTEL package.
|
||||
The default package command will specify that USER-INTEL calculations
|
||||
are performed in mixed precision, that the number of OpenMP threads
|
||||
@ -281,16 +281,16 @@ support, that 1 coprocessor per node will be used with automatic
|
||||
balancing of work between the CPU and the coprocessor.
|
||||
|
||||
You can specify different options for the USER-INTEL package by using
|
||||
the "-pk intel Nphi" "command-line switch"_Section_start.html#start_7
|
||||
the "-pk intel Nphi" "command-line switch"_Section_start.html#start_7
|
||||
with keyword/value pairs as specified in the documentation. Here,
|
||||
Nphi = # of Xeon Phi coprocessors/node (ignored without offload
|
||||
support). Common options to the USER-INTEL package include {omp} to
|
||||
override any OMP_NUM_THREADS setting and specify the number of OpenMP
|
||||
threads, {mode} to set the floating-point precision mode, and
|
||||
{lrt} to enable Long-Range Thread mode as described below. See the
|
||||
"package intel"_package.html command for details, including the
|
||||
default values used for all its options if not specified, and how to
|
||||
set the number of OpenMP threads via the OMP_NUM_THREADS environment
|
||||
{lrt} to enable Long-Range Thread mode as described below. See the
|
||||
"package intel"_package.html command for details, including the
|
||||
default values used for all its options if not specified, and how to
|
||||
set the number of OpenMP threads via the OMP_NUM_THREADS environment
|
||||
variable if desired.
|
||||
|
||||
Examples (see documentation for your MPI/Machine for differences in
|
||||
@ -303,7 +303,7 @@ mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode
|
||||
|
||||
As an alternative to adding command-line arguments, the input script
|
||||
can be edited to enable the USER-INTEL package. This requires adding
|
||||
the "package intel"_package.html command to the top of the input
|
||||
the "package intel"_package.html command to the top of the input
|
||||
script. For the second example above, this would be:
|
||||
|
||||
package intel 0 omp 2 mode double :pre
|
||||
@ -314,46 +314,46 @@ add an "intel" suffix to the individual style, e.g.:
|
||||
pair_style lj/cut/intel 2.5 :pre
|
||||
|
||||
Alternatively, the "suffix intel"_suffix.html command can be added to
|
||||
the input script to enable USER-INTEL styles for the commands that
|
||||
the input script to enable USER-INTEL styles for the commands that
|
||||
follow in the input script.
|
||||
|
||||
[Tuning for Performance:]
|
||||
|
||||
NOTE: The USER-INTEL package will perform better with modifications
|
||||
to the input script when "PPPM"_kspace_style.html is used:
|
||||
"kspace_modify diff ad"_kspace_modify.html and "neigh_modify binsize
|
||||
NOTE: The USER-INTEL package will perform better with modifications
|
||||
to the input script when "PPPM"_kspace_style.html is used:
|
||||
"kspace_modify diff ad"_kspace_modify.html and "neigh_modify binsize
|
||||
3"_neigh_modify.html should be added to the input script.
|
||||
|
||||
Long-Range Thread (LRT) mode is an option to the "package
|
||||
Long-Range Thread (LRT) mode is an option to the "package
|
||||
intel"_package.html command that can improve performance when using
|
||||
"PPPM"_kspace_style.html for long-range electrostatics on processors
|
||||
with SMT. It generates an extra pthread for each MPI task. The thread
|
||||
is dedicated to performing some of the PPPM calculations and MPI
|
||||
with SMT. It generates an extra pthread for each MPI task. The thread
|
||||
is dedicated to performing some of the PPPM calculations and MPI
|
||||
communications. On Intel Xeon Phi x200 series CPUs, this will likely
|
||||
always improve performance, even on a single node. On Intel Xeon
|
||||
processors, using this mode might result in better performance when
|
||||
using multiple nodes, depending on the machine. To use this mode,
|
||||
specify that the number of OpenMP threads is one less than would
|
||||
specify that the number of OpenMP threads is one less than would
|
||||
normally be used for the run and add the "lrt yes" option to the "-pk"
|
||||
command-line suffix or "package intel" command. For example, if a run
|
||||
would normally perform best with "-pk intel 0 omp 4", instead use
|
||||
"-pk intel 0 omp 3 lrt yes". When using LRT, you should set the
|
||||
environment variable "KMP_AFFINITY=none". LRT mode is not supported
|
||||
"-pk intel 0 omp 3 lrt yes". When using LRT, you should set the
|
||||
environment variable "KMP_AFFINITY=none". LRT mode is not supported
|
||||
when using offload.
|
||||
|
||||
Not all styles are supported in the USER-INTEL package. You can mix
|
||||
the USER-INTEL package with styles from the "OPT"_accelerate_opt.html
|
||||
package or the "USER-OMP package"_accelerate_omp.html". Of course,
|
||||
the USER-INTEL package with styles from the "OPT"_accelerate_opt.html
|
||||
package or the "USER-OMP package"_accelerate_omp.html". Of course,
|
||||
this requires that these packages were installed at build time. This
|
||||
can performed automatically by using "-sf hybrid intel opt" or
|
||||
"-sf hybrid intel omp" command-line options. Alternatively, the "opt"
|
||||
and "omp" suffixes can be appended manually in the input script. For
|
||||
the latter, the "package omp"_package.html command must be in the
|
||||
input script or the "-pk omp Nt" "command-line
|
||||
switch"_Section_start.html#start_7 must be used where Nt is the
|
||||
input script or the "-pk omp Nt" "command-line
|
||||
switch"_Section_start.html#start_7 must be used where Nt is the
|
||||
number of OpenMP threads. The number of OpenMP threads should not be
|
||||
set differently for the different packages. Note that the "suffix
|
||||
hybrid intel omp"_suffix.html command can also be used within the
|
||||
set differently for the different packages. Note that the "suffix
|
||||
hybrid intel omp"_suffix.html command can also be used within the
|
||||
input script to automatically append the "omp" suffix to styles when
|
||||
USER-INTEL styles are not available.
|
||||
|
||||
@ -374,33 +374,33 @@ that MPI runs are performed in MCDRAM.
|
||||
|
||||
[Tuning for Offload Performance:]
|
||||
|
||||
The default settings for offload should give good performance.
|
||||
The default settings for offload should give good performance.
|
||||
|
||||
When using LAMMPS with offload to Intel coprocessors, best performance
|
||||
will typically be achieved with concurrent calculations performed on
|
||||
both the CPU and the coprocessor. This is achieved by offloading only
|
||||
a fraction of the neighbor and pair computations to the coprocessor or
|
||||
using "hybrid"_pair_hybrid.html pair styles where only one style uses
|
||||
the "intel" suffix. For simulations with long-range electrostatics or
|
||||
bond, angle, dihedral, improper calculations, computation and data
|
||||
transfer to the coprocessor will run concurrently with computations
|
||||
the "intel" suffix. For simulations with long-range electrostatics or
|
||||
bond, angle, dihedral, improper calculations, computation and data
|
||||
transfer to the coprocessor will run concurrently with computations
|
||||
and MPI communications for these calculations on the host CPU. This
|
||||
is illustrated in the figure below for the rhodopsin protein benchmark
|
||||
running on E5-2697v2 processors with a Intel Xeon Phi 7120p
|
||||
running on E5-2697v2 processors with a Intel Xeon Phi 7120p
|
||||
coprocessor. In this plot, the vertical access is time and routines
|
||||
running at the same time are running concurrently on both the host and
|
||||
the coprocessor.
|
||||
|
||||
:c,image(JPG/offload_knc.png)
|
||||
|
||||
The fraction of the offloaded work is controlled by the {balance}
|
||||
keyword in the "package intel"_package.html command. A balance of 0
|
||||
runs all calculations on the CPU. A balance of 1 runs all
|
||||
supported calculations on the coprocessor. A balance of 0.5 runs half
|
||||
of the calculations on the coprocessor. Setting the balance to -1
|
||||
(the default) will enable dynamic load balancing that continously
|
||||
adjusts the fraction of offloaded work throughout the simulation.
|
||||
Because data transfer cannot be timed, this option typically produces
|
||||
The fraction of the offloaded work is controlled by the {balance}
|
||||
keyword in the "package intel"_package.html command. A balance of 0
|
||||
runs all calculations on the CPU. A balance of 1 runs all
|
||||
supported calculations on the coprocessor. A balance of 0.5 runs half
|
||||
of the calculations on the coprocessor. Setting the balance to -1
|
||||
(the default) will enable dynamic load balancing that continously
|
||||
adjusts the fraction of offloaded work throughout the simulation.
|
||||
Because data transfer cannot be timed, this option typically produces
|
||||
results within 5 to 10 percent of the optimal fixed balance.
|
||||
|
||||
If running short benchmark runs with dynamic load balancing, adding a
|
||||
@ -418,15 +418,15 @@ with 60 cores available for offload and 4 hardware threads per core
|
||||
each MPI task to use a subset of 10 threads on the coprocessor. Fine
|
||||
tuning of the number of threads to use per MPI task or the number of
|
||||
threads to use per core can be accomplished with keyword settings of
|
||||
the "package intel"_package.html command.
|
||||
the "package intel"_package.html command.
|
||||
|
||||
The USER-INTEL package has two modes for deciding which atoms will be
|
||||
handled by the coprocessor. This choice is controlled with the {ghost}
|
||||
keyword of the "package intel"_package.html command. When set to 0,
|
||||
ghost atoms (atoms at the borders between MPI tasks) are not offloaded
|
||||
to the card. This allows for overlap of MPI communication of forces
|
||||
with computation on the coprocessor when the "newton"_newton.html
|
||||
setting is "on". The default is dependent on the style being used,
|
||||
The USER-INTEL package has two modes for deciding which atoms will be
|
||||
handled by the coprocessor. This choice is controlled with the {ghost}
|
||||
keyword of the "package intel"_package.html command. When set to 0,
|
||||
ghost atoms (atoms at the borders between MPI tasks) are not offloaded
|
||||
to the card. This allows for overlap of MPI communication of forces
|
||||
with computation on the coprocessor when the "newton"_newton.html
|
||||
setting is "on". The default is dependent on the style being used,
|
||||
however, better performance may be achieved by setting this option
|
||||
explictly.
|
||||
|
||||
@ -442,10 +442,10 @@ mode is being used and indicating the number of coprocessor threads
|
||||
per MPI task. Additionally, an offload timing summary is printed at
|
||||
the end of each run. When offloading, the frequency for "atom
|
||||
sorting"_atom_modify.html is changed to 1 so that the per-atom data is
|
||||
effectively sorted at every rebuild of the neighbor lists. All the
|
||||
available coprocessor threads on each Phi will be divided among MPI
|
||||
tasks, unless the {tptask} option of the "-pk intel" "command-line
|
||||
switch"_Section_start.html#start_7 is used to limit the coprocessor
|
||||
effectively sorted at every rebuild of the neighbor lists. All the
|
||||
available coprocessor threads on each Phi will be divided among MPI
|
||||
tasks, unless the {tptask} option of the "-pk intel" "command-line
|
||||
switch"_Section_start.html#start_7 is used to limit the coprocessor
|
||||
threads per MPI task.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
@ -65,7 +65,7 @@ Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi # or one-line build via Ma
|
||||
|
||||
mpirun -np 16 lmp_mpi -k on -sf kk -in in.lj # 1 node, 16 MPI tasks/node, no threads
|
||||
mpirun -np 2 -ppn 1 lmp_mpi -k on t 16 -sf kk -in in.lj # 2 nodes, 1 MPI task/node, 16 threads/task
|
||||
mpirun -np 2 lmp_mpi -k on t 8 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 8 threads/task
|
||||
mpirun -np 2 lmp_mpi -k on t 8 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 8 threads/task
|
||||
mpirun -np 32 -ppn 4 lmp_mpi -k on t 4 -sf kk -in in.lj # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre
|
||||
|
||||
specify variables and settings in your Makefile.machine that enable OpenMP, GPU, or Phi support
|
||||
@ -178,7 +178,7 @@ make kokkos_cuda_mpich :pre
|
||||
|
||||
These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
|
||||
make command line which requires a GNU-compatible make command. Try
|
||||
"gmake" if your system's standard make complains.
|
||||
"gmake" if your system's standard make complains.
|
||||
|
||||
NOTE: If you build using make line variables and re-build LAMMPS twice
|
||||
with different KOKKOS options and the *same* target, e.g. g++ in the
|
||||
@ -394,7 +394,7 @@ additional parallelism (beyond MPI) will be invoked on the host
|
||||
CPU(s).
|
||||
|
||||
You can compare the performance running in different modes:
|
||||
|
||||
|
||||
run with 1 MPI task/node and N threads/task
|
||||
run with N MPI tasks/node and 1 thread/task
|
||||
run with settings in between these extremes :ul
|
||||
@ -427,7 +427,7 @@ e.g. src/MAKE/Makefile.cuda, is correct for your GPU hardware/software
|
||||
details).
|
||||
|
||||
The -np setting of the mpirun command should set the number of MPI
|
||||
tasks/node to be equal to the # of physical GPUs on the node.
|
||||
tasks/node to be equal to the # of physical GPUs on the node.
|
||||
|
||||
Use the "-k" "command-line switch"_Section_commands.html#start_7 to
|
||||
specify the number of GPUs per node, and the number of threads per MPI
|
||||
|
||||
@ -96,7 +96,7 @@ variable.
|
||||
|
||||
Depending on which styles are accelerated, you should look for a
|
||||
reduction in the "Pair time", "Bond time", "KSpace time", and "Loop
|
||||
time" values printed at the end of a run.
|
||||
time" values printed at the end of a run.
|
||||
|
||||
You may see a small performance advantage (5 to 20%) when running a
|
||||
USER-OMP style (in serial or parallel) with a single thread per MPI
|
||||
|
||||
@ -21,11 +21,11 @@ angle_coeff 6 2.1 180.0 :pre
|
||||
[Description:]
|
||||
|
||||
The {dipole} angle style is used to control the orientation of a dipolar
|
||||
atom within a molecule "(Orsi)"_#Orsi. Specifically, the {dipole} angle
|
||||
style restrains the orientation of a point dipole mu_j (embedded in atom
|
||||
'j') with respect to a reference (bond) vector r_ij = r_i - r_j, where 'i'
|
||||
is another atom of the same molecule (typically, 'i' and 'j' are also
|
||||
covalently bonded).
|
||||
atom within a molecule "(Orsi)"_#Orsi. Specifically, the {dipole} angle
|
||||
style restrains the orientation of a point dipole mu_j (embedded in atom
|
||||
'j') with respect to a reference (bond) vector r_ij = r_i - r_j, where 'i'
|
||||
is another atom of the same molecule (typically, 'i' and 'j' are also
|
||||
covalently bonded).
|
||||
|
||||
It is convenient to define an angle gamma between the 'free' vector mu_j
|
||||
and the reference (bond) vector r_ij:
|
||||
@ -37,21 +37,21 @@ The {dipole} angle style uses the potential:
|
||||
:c,image(Eqs/angle_dipole_potential.jpg)
|
||||
|
||||
where K is a rigidity constant and gamma0 is an equilibrium (reference)
|
||||
angle.
|
||||
angle.
|
||||
|
||||
The torque on the dipole can be obtained by differentiating the
|
||||
potential using the 'chain rule' as in appendix C.3 of
|
||||
The torque on the dipole can be obtained by differentiating the
|
||||
potential using the 'chain rule' as in appendix C.3 of
|
||||
"(Allen)"_#Allen:
|
||||
|
||||
:c,image(Eqs/angle_dipole_torque.jpg)
|
||||
|
||||
Example: if gamma0 is set to 0 degrees, the torque generated by
|
||||
the potential will tend to align the dipole along the reference
|
||||
the potential will tend to align the dipole along the reference
|
||||
direction defined by the (bond) vector r_ij (in other words, mu_j is
|
||||
restrained to point towards atom 'i').
|
||||
|
||||
The dipolar torque T_j must be counterbalanced in order to conserve
|
||||
the local angular momentum. This is achieved via an additional force
|
||||
The dipolar torque T_j must be counterbalanced in order to conserve
|
||||
the local angular momentum. This is achieved via an additional force
|
||||
couple generating a torque equivalent to the opposite of T_j:
|
||||
|
||||
:c,image(Eqs/angle_dipole_couple.jpg)
|
||||
@ -118,7 +118,7 @@ This angle style should not be used with SHAKE.
|
||||
:line
|
||||
|
||||
:link(Orsi)
|
||||
[(Orsi)] Orsi & Essex, The ELBA force field for coarse-grain modeling of
|
||||
[(Orsi)] Orsi & Essex, The ELBA force field for coarse-grain modeling of
|
||||
lipid membranes, PloS ONE 6(12): e28637, 2011.
|
||||
|
||||
:link(Allen)
|
||||
|
||||
@ -62,7 +62,7 @@ more instructions on how to use the accelerated styles effectively.
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
|
||||
USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
|
||||
section for more info on packages.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
@ -61,7 +61,7 @@ more instructions on how to use the accelerated styles effectively.
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
|
||||
USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
|
||||
section for more info on packages.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
@ -68,7 +68,7 @@ more instructions on how to use the accelerated styles effectively.
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
|
||||
USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
|
||||
section for more info on packages.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
@ -43,7 +43,7 @@ internally; hence the units of K are in energy/radian^2.
|
||||
The also required {lj/sdk} parameters will be extracted automatically
|
||||
from the pair_style.
|
||||
|
||||
[Restrictions:]
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
USER-CG-CMM package. See the "Making
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS
|
||||
Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
@ -156,12 +156,12 @@ used with a group-ID that is not "all".
|
||||
|
||||
[Default:]
|
||||
|
||||
By default, {id} is yes. By default, atomic systems (no bond topology
|
||||
info) do not use a map. For molecular systems (with bond topology
|
||||
info), a map is used. The default map style is array if no atom ID is
|
||||
larger than 1 million, otherwise the default is hash. By default, a
|
||||
"first" group is not defined. By default, sorting is enabled with a
|
||||
frequency of 1000 and a binsize of 0.0, which means the neighbor
|
||||
By default, {id} is yes. By default, atomic systems (no bond topology
|
||||
info) do not use a map. For molecular systems (with bond topology
|
||||
info), a map is used. The default map style is array if no atom ID is
|
||||
larger than 1 million, otherwise the default is hash. By default, a
|
||||
"first" group is not defined. By default, sorting is enabled with a
|
||||
frequency of 1000 and a binsize of 0.0, which means the neighbor
|
||||
cutoff will be used to set the bin size.
|
||||
|
||||
:line
|
||||
|
||||
@ -193,7 +193,7 @@ For the {body} style, the particles are arbitrary bodies with internal
|
||||
attributes defined by the "style" of the bodies, which is specified by
|
||||
the {bstyle} argument. Body particles can represent complex entities,
|
||||
such as surface meshes of discrete points, collections of
|
||||
sub-particles, deformable objects, etc.
|
||||
sub-particles, deformable objects, etc.
|
||||
|
||||
The "body"_body.html doc page descibes the body styles LAMMPS
|
||||
currently supports, and provides more details as to the kind of body
|
||||
@ -269,7 +269,7 @@ The {line} and {tri} styles are part of the ASPHERE package.
|
||||
|
||||
The {body} style is part of the BODY package.
|
||||
|
||||
The {dipole} style is part of the DIPOLE package.
|
||||
The {dipole} style is part of the DIPOLE package.
|
||||
|
||||
The {peri} style is part of the PERI package for Peridynamics.
|
||||
|
||||
|
||||
@ -490,7 +490,7 @@ per processor. Note that the 4 sub-domains share vertices, so there
|
||||
will be duplicate nodes in the list.
|
||||
|
||||
The "SQUARES" section lists the node IDs of the 4 vertices in a
|
||||
rectangle for each processor (1 to 4).
|
||||
rectangle for each processor (1 to 4).
|
||||
|
||||
For a 3d problem, the syntax is similar with 8 vertices listed for
|
||||
each processor, instead of 4, and "SQUARES" replaced by "CUBES".
|
||||
|
||||
@ -125,7 +125,7 @@ in the {Bodies} section of the data file:
|
||||
|
||||
atom-ID 1 M
|
||||
N
|
||||
ixx iyy izz ixy ixz iyz
|
||||
ixx iyy izz ixy ixz iyz
|
||||
x1 y1 z1
|
||||
...
|
||||
xN yN zN :pre
|
||||
@ -198,11 +198,11 @@ in the {Bodies} section of the data file:
|
||||
|
||||
atom-ID 1 M
|
||||
N
|
||||
ixx iyy izz ixy ixz iyz
|
||||
ixx iyy izz ixy ixz iyz
|
||||
x1 y1 z1
|
||||
...
|
||||
xN yN zN
|
||||
i j j k k ...
|
||||
i j j k k ...
|
||||
radius :pre
|
||||
|
||||
N is the number of vertices in the body particle. M = 6 + 3*N + 2*N +
|
||||
@ -230,11 +230,11 @@ particles whose edge length is sqrt(2):
|
||||
|
||||
3 1 27
|
||||
4
|
||||
1 1 4 0 0 0
|
||||
-0.7071 -0.7071 0
|
||||
-0.7071 0.7071 0
|
||||
0.7071 0.7071 0
|
||||
0.7071 -0.7071 0
|
||||
1 1 4 0 0 0
|
||||
-0.7071 -0.7071 0
|
||||
-0.7071 0.7071 0
|
||||
0.7071 0.7071 0
|
||||
0.7071 -0.7071 0
|
||||
0 1 1 2 2 3 3 0
|
||||
1.0 :pre
|
||||
|
||||
|
||||
@ -173,7 +173,7 @@ change_box all x scale 1.1 y volume z volume :pre
|
||||
|
||||
The {volume} style changes the associated dimension so that the
|
||||
overall box volume is unchanged relative to its value before the
|
||||
preceding keyword was invoked.
|
||||
preceding keyword was invoked.
|
||||
|
||||
If the following command is used, then the z box length will shrink by
|
||||
the same 1.1 factor the x box length was increased by:
|
||||
|
||||
@ -13,7 +13,7 @@ compute cna/atom command :h3
|
||||
compute ID group-ID cna/atom cutoff :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
cna/atom = style name of this compute command
|
||||
cna/atom = style name of this compute command
|
||||
cutoff = cutoff distance for nearest neighbors (distance units) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
@ -63,4 +63,4 @@ LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
"compute damage/atom"_compute_damage_atom.html,
|
||||
"compute plasticity/atom"_compute_plasticity_atom.html
|
||||
|
||||
[Default:] none
|
||||
[Default:] none
|
||||
|
||||
@ -19,7 +19,7 @@ charge-correction = {mass} or {geometry}, use COM or geometric center for charge
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 fluid dipole/chunk molchunk
|
||||
compute 1 fluid dipole/chunk molchunk
|
||||
compute dw water dipole/chunk 1 geometry :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
@ -46,7 +46,7 @@ output options.
|
||||
|
||||
The vector values will be in energy and temperature "units"_units.html.
|
||||
|
||||
[Restrictions:]
|
||||
[Restrictions:]
|
||||
|
||||
This command is part of the USER-DPD package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
@ -64,7 +64,7 @@ command.
|
||||
|
||||
:line
|
||||
|
||||
:link(Larentzos)
|
||||
:link(Larentzos)
|
||||
[(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and
|
||||
W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
|
||||
Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
|
||||
|
||||
@ -22,7 +22,7 @@ compute 1 all dpd/atom
|
||||
[Description:]
|
||||
|
||||
Define a computation that accesses the per-particle internal
|
||||
conductive energy (u_cond), internal mechanical energy (u_mech),
|
||||
conductive energy (u_cond), internal mechanical energy (u_mech),
|
||||
internal chemical energy (u_chem) and
|
||||
internal temperatures (dpdTheta) for each particle in a group. See
|
||||
the "compute dpd"_compute_dpd.html command if you want the total
|
||||
@ -39,10 +39,10 @@ that uses per-particle values from a compute as input. See
|
||||
"Section 6.15"_Section_howto.html#howto_15 for an overview of
|
||||
LAMMPS output options.
|
||||
|
||||
The per-particle array values will be in energy (u_cond, u_mech, u_chem)
|
||||
The per-particle array values will be in energy (u_cond, u_mech, u_chem)
|
||||
and temperature (dpdTheta) "units"_units.html.
|
||||
|
||||
[Restrictions:]
|
||||
[Restrictions:]
|
||||
|
||||
This command is part of the USER-DPD package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
|
||||
@ -26,7 +26,7 @@ Define a computation that flags an "event" if any particle in the
|
||||
group has moved a distance greater than the specified threshold
|
||||
distance when compared to a previously stored reference state
|
||||
(i.e. the previous event). This compute is typically used in
|
||||
conjunction with the "prd"_prd.html and "tad"_tad.html commands,
|
||||
conjunction with the "prd"_prd.html and "tad"_tad.html commands,
|
||||
to detect if a transition
|
||||
to a new minimum energy basin has occurred.
|
||||
|
||||
@ -34,8 +34,8 @@ This value calculated by the compute is equal to 0 if no particle has
|
||||
moved far enough, and equal to 1 if one or more particles have moved
|
||||
further than the threshold distance.
|
||||
|
||||
NOTE: If the system is undergoing significant center-of-mass motion,
|
||||
due to thermal motion, an external force, or an initial net momentum,
|
||||
NOTE: If the system is undergoing significant center-of-mass motion,
|
||||
due to thermal motion, an external force, or an initial net momentum,
|
||||
then this compute will not be able to distinguish that motion from
|
||||
local atom displacements and may generate "false postives."
|
||||
|
||||
|
||||
@ -64,7 +64,7 @@ these atoms:
|
||||
A coupling parameter \(\lambda\) varying from 0 to 1 connects the
|
||||
reference and perturbed systems:
|
||||
|
||||
:c,image(Eqs/compute_fep_lambda.jpg)
|
||||
:c,image(Eqs/compute_fep_lambda.jpg)
|
||||
|
||||
It is possible but not necessary that the coupling parameter (or a
|
||||
function thereof) appears as a multiplication factor of the potential
|
||||
|
||||
@ -28,7 +28,7 @@ compute 2 molecule gyration/chunk molchunk tensor :pre
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates the radius of gyration Rg for
|
||||
multiple chunks of atoms.
|
||||
multiple chunks of atoms.
|
||||
|
||||
In LAMMPS, chunks are collections of atoms defined by a "compute
|
||||
chunk/atom"_compute_chunk_atom.html command, which assigns each atom
|
||||
|
||||
@ -20,7 +20,7 @@ stress-ID = ID of a compute that calculates per-atom stress :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute myFlux all heat/flux myKE myPE myStress :pre
|
||||
compute myFlux all heat/flux myKE myPE myStress :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
@ -38,7 +38,7 @@ subtracted to a group of atoms.
|
||||
The compute takes three arguments which are IDs of other
|
||||
"computes"_compute.html. One calculates per-atom kinetic energy
|
||||
({ke-ID}), one calculates per-atom potential energy ({pe-ID)}, and the
|
||||
third calcualtes per-atom stress ({stress-ID}).
|
||||
third calcualtes per-atom stress ({stress-ID}).
|
||||
|
||||
NOTE: These other computes should provide values for all the atoms in
|
||||
the group this compute specifies. That means the other computes could
|
||||
|
||||
@ -15,7 +15,7 @@ compute ID group-ID hexorder/atom keyword values ... :pre
|
||||
ID, group-ID are documented in "compute"_compute.html command :ulb,l
|
||||
hexorder/atom = style name of this compute command :l
|
||||
one or more keyword/value pairs may be appended :l
|
||||
keyword = {degree} or {nnn} or {cutoff}
|
||||
keyword = {degree} or {nnn} or {cutoff}
|
||||
{cutoff} value = distance cutoff
|
||||
{nnn} value = number of nearest neighbors
|
||||
{degree} value = degree {n} of order parameter :pre
|
||||
@ -24,27 +24,27 @@ keyword = {degree} or {nnn} or {cutoff}
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all hexorder/atom
|
||||
compute 1 all hexorder/atom
|
||||
compute 1 all hexorder/atom degree 4 nnn 4 cutoff 1.2 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates {qn} the bond-orientational
|
||||
order parameter for each atom in a group. The hexatic ({n} = 6) order
|
||||
Define a computation that calculates {qn} the bond-orientational
|
||||
order parameter for each atom in a group. The hexatic ({n} = 6) order
|
||||
parameter was introduced by "Nelson and Halperin"_#Nelson as a way to detect
|
||||
hexagonal symmetry in two-dimensional systems. For each atom, {qn}
|
||||
hexagonal symmetry in two-dimensional systems. For each atom, {qn}
|
||||
is a complex number (stored as two real numbers) defined as follows:
|
||||
|
||||
:c,image(Eqs/hexorder.jpg)
|
||||
|
||||
where the sum is over the {nnn} nearest neighbors
|
||||
where the sum is over the {nnn} nearest neighbors
|
||||
of the central atom. The angle theta
|
||||
is formed by the bond vector rij and the {x} axis. theta is calculated
|
||||
only using the {x} and {y} components, whereas the distance from the
|
||||
central atom is calculated using all three
|
||||
central atom is calculated using all three
|
||||
{x}, {y}, and {z} components of the bond vector.
|
||||
Neighbor atoms not in the group
|
||||
are included in the order parameter of atoms in the group.
|
||||
Neighbor atoms not in the group
|
||||
are included in the order parameter of atoms in the group.
|
||||
|
||||
The optional keyword {cutoff} defines the distance cutoff
|
||||
used when searching for neighbors. The default value, also
|
||||
@ -53,22 +53,22 @@ by the pair style.
|
||||
|
||||
The optional keyword {nnn} defines the number of nearest
|
||||
neighbors used to calculate {qn}. The default value is 6.
|
||||
If the value is NULL, then all neighbors up to the
|
||||
If the value is NULL, then all neighbors up to the
|
||||
distance cutoff are used.
|
||||
|
||||
The optional keyword {degree} sets the degree {n} of the order parameter.
|
||||
The default value is 6. For a perfect hexagonal lattice with
|
||||
The optional keyword {degree} sets the degree {n} of the order parameter.
|
||||
The default value is 6. For a perfect hexagonal lattice with
|
||||
{nnn} = 6,
|
||||
{q}6 = exp(6 i phi) for all atoms, where the constant 0 < phi < pi/3
|
||||
depends only on the orientation of the lattice relative to the {x} axis.
|
||||
In an isotropic liquid, local neighborhoods may still exhibit
|
||||
{q}6 = exp(6 i phi) for all atoms, where the constant 0 < phi < pi/3
|
||||
depends only on the orientation of the lattice relative to the {x} axis.
|
||||
In an isotropic liquid, local neighborhoods may still exhibit
|
||||
weak hexagonal symmetry, but because the orientational correlation
|
||||
decays quickly with distance, the value of phi will be different for
|
||||
different atoms, and so when {q}6 is averaged over all the atoms
|
||||
different atoms, and so when {q}6 is averaged over all the atoms
|
||||
in the system, \|<{q}6>\| << 1.
|
||||
|
||||
The value of {qn} is set to zero for atoms not in the
|
||||
specified compute group, as well as for atoms that have less than
|
||||
specified compute group, as well as for atoms that have less than
|
||||
{nnn} neighbors within the distance cutoff.
|
||||
|
||||
The neighbor list needed to compute this quantity is constructed each
|
||||
@ -92,7 +92,7 @@ the neighbor list.
|
||||
[Output info:]
|
||||
|
||||
This compute calculates a per-atom array with 2 columns, giving the
|
||||
real and imaginary parts {qn}, a complex number restricted to the
|
||||
real and imaginary parts {qn}, a complex number restricted to the
|
||||
unit disk of the complex plane i.e. Re({qn})^2 + Im({qn})^2 <= 1 .
|
||||
|
||||
These values can be accessed by any command that uses
|
||||
@ -106,7 +106,7 @@ options.
|
||||
|
||||
"compute orientorder/atom"_compute_orientorder_atom.html, "compute coord/atom"_compute_coord_atom.html, "compute centro/atom"_compute_centro_atom.html
|
||||
|
||||
[Default:]
|
||||
[Default:]
|
||||
|
||||
The option defaults are {cutoff} = pair style cutoff, {nnn} = 6, {degree} = 6
|
||||
|
||||
|
||||
@ -23,7 +23,7 @@ compute 1 fluid inertia/chunk molchunk :pre
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates the inertia tensor for multiple
|
||||
chunks of atoms.
|
||||
chunks of atoms.
|
||||
|
||||
In LAMMPS, chunks are collections of atoms defined by a "compute
|
||||
chunk/atom"_compute_chunk_atom.html command, which assigns each atom
|
||||
|
||||
@ -48,9 +48,9 @@ thermodynamic output by using the "thermo_modify"_thermo_modify.html
|
||||
command, as shown in the following example:
|
||||
|
||||
compute effTemp all temp/eff
|
||||
thermo_style custom step etotal pe ke temp press
|
||||
thermo_style custom step etotal pe ke temp press
|
||||
thermo_modify temp effTemp :pre
|
||||
|
||||
|
||||
The value of the kinetic energy will be 0.0 for atoms (nuclei or
|
||||
electrons) not in the specified compute group.
|
||||
|
||||
|
||||
@ -52,9 +52,9 @@ printed with thermodynamic output by using the
|
||||
example:
|
||||
|
||||
compute effTemp all temp/eff
|
||||
thermo_style custom step etotal pe ke temp press
|
||||
thermo_style custom step etotal pe ke temp press
|
||||
thermo_modify temp effTemp :pre
|
||||
|
||||
|
||||
See "compute temp/eff"_compute_temp_eff.html.
|
||||
|
||||
[Output info:]
|
||||
|
||||
@ -61,4 +61,4 @@ the temperature is correctly normalized.
|
||||
[Default:]
|
||||
|
||||
The option defaults are extra = 2 or 3 for 2d or 3d systems and
|
||||
dynamic = no.
|
||||
dynamic = no.
|
||||
|
||||
@ -44,7 +44,7 @@ proportional to the diffusion coefficient of the diffusing atoms.
|
||||
|
||||
The displacement of an atom is from its reference position. This is
|
||||
normally the original position at the time
|
||||
the compute command was issued, unless the {average} keyword is set to {yes}.
|
||||
the compute command was issued, unless the {average} keyword is set to {yes}.
|
||||
The value of the displacement will be
|
||||
0.0 for atoms not in the specified compute group.
|
||||
|
||||
|
||||
@ -15,7 +15,7 @@ compute ID group-ID orientorder/atom keyword values ... :pre
|
||||
ID, group-ID are documented in "compute"_compute.html command :ulb,l
|
||||
orientorder/atom = style name of this compute command :l
|
||||
one or more keyword/value pairs may be appended :l
|
||||
keyword = {cutoff} or {nnn} or {ql}
|
||||
keyword = {cutoff} or {nnn} or {ql}
|
||||
{cutoff} value = distance cutoff
|
||||
{nnn} value = number of nearest neighbors
|
||||
{degrees} values = nlvalues, l1, l2,... :pre
|
||||
@ -24,30 +24,30 @@ keyword = {cutoff} or {nnn} or {ql}
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all orientorder/atom
|
||||
compute 1 all orientorder/atom
|
||||
compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates a set of bond-orientational
|
||||
Define a computation that calculates a set of bond-orientational
|
||||
order parameters {Ql} for each atom in a group. These order parameters
|
||||
were introduced by "Steinhardt et al."_#Steinhardt as a way to
|
||||
characterize the local orientational order in atomic structures.
|
||||
characterize the local orientational order in atomic structures.
|
||||
For each atom, {Ql} is a real number defined as follows:
|
||||
|
||||
:c,image(Eqs/orientorder.jpg)
|
||||
|
||||
The first equation defines the spherical harmonic order parameters.
|
||||
These are complex number components of the 3D analog of the 2D order
|
||||
parameter {qn}, which is implemented as LAMMPS compute
|
||||
"hexorder/atom"_compute_hexorder_atom.html.
|
||||
The summation is over the {nnn} nearest
|
||||
neighbors of the central atom.
|
||||
The angles theta and phi are the standard spherical polar angles
|
||||
The first equation defines the spherical harmonic order parameters.
|
||||
These are complex number components of the 3D analog of the 2D order
|
||||
parameter {qn}, which is implemented as LAMMPS compute
|
||||
"hexorder/atom"_compute_hexorder_atom.html.
|
||||
The summation is over the {nnn} nearest
|
||||
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
|
||||
over all the components of degree {l}.
|
||||
rotationally invariant scalar quantity obtained by summing
|
||||
over all the components of degree {l}.
|
||||
|
||||
The optional keyword {cutoff} defines the distance cutoff
|
||||
used when searching for neighbors. The default value, also
|
||||
@ -56,23 +56,23 @@ by the pair style.
|
||||
|
||||
The optional keyword {nnn} defines the number of nearest
|
||||
neighbors used to calculate {Ql}. The default value is 12.
|
||||
If the value is NULL, then all neighbors up to the
|
||||
If the value is NULL, then all neighbors up to the
|
||||
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
|
||||
be computed. The first argument {nlvalues} is the number of order
|
||||
parameters. This is followed by that number of integers giving the
|
||||
degree of each order parameter. Because {Q}2 and all odd-degree
|
||||
order parameters are zero for atoms in cubic crystals
|
||||
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, {Q}6, {Q}8, {Q}10, and {Q}12. For the
|
||||
FCC crystal with {nnn}=12, {Q}4 = 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
|
||||
for a range of commonly encountered high-symmetry structures are given
|
||||
in Table I of "Mickel et al."_#Mickel.
|
||||
|
||||
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
|
||||
specified compute group, as well as for atoms that have less than
|
||||
{nnn} neighbors within the distance cutoff.
|
||||
|
||||
The neighbor list needed to compute this quantity is constructed each
|
||||
@ -109,9 +109,9 @@ options.
|
||||
|
||||
"compute coord/atom"_compute_coord_atom.html, "compute centro/atom"_compute_centro_atom.html, "compute hexorder/atom"_compute_hexorder_atom.html
|
||||
|
||||
[Default:]
|
||||
[Default:]
|
||||
|
||||
The option defaults are {cutoff} = pair style cutoff, {nnn} = 12, {degrees} = 5 4 6 8 9 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.
|
||||
The option defaults are {cutoff} = pair style cutoff, {nnn} = 12, {degrees} = 5 4 6 8 9 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -30,7 +30,7 @@ The plasticity for a Peridynamic particle is the so-called consistency
|
||||
parameter (lambda). For elastic deformation lambda = 0, otherwise
|
||||
lambda > 0 for plastic deformation. For details, see
|
||||
"(Mitchell)"_#Mitchell and the PDF doc included in the LAMMPS
|
||||
distro in "doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf.
|
||||
distro in "doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf.
|
||||
|
||||
This command can be invoked for one of the Peridynamic "pair
|
||||
styles"_pair_peri.html: peri/eps.
|
||||
@ -57,7 +57,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
"compute damage/atom"_compute_damage_atom.html,
|
||||
"compute dilatation/atom"_compute_dilatation_atom.html
|
||||
|
||||
[Default:] none
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -50,7 +50,7 @@ ordered xx, yy, zz, xy, xz, yz. The equation for the I,J components
|
||||
(where I and J = x,y,z) is similar to the above formula, except that
|
||||
the first term uses components of the kinetic energy tensor and the
|
||||
second term uses components of the virial tensor:
|
||||
|
||||
|
||||
:c,image(Eqs/pressure_tensor.jpg)
|
||||
|
||||
If no extra keywords are listed, the entire equations above are
|
||||
|
||||
@ -80,7 +80,7 @@ input = one or more atom attributes :l
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all property/atom xs vx fx mux
|
||||
compute 1 all property/atom xs vx fx mux
|
||||
compute 2 all property/atom type
|
||||
compute 1 all property/atom ix iy iz :pre
|
||||
|
||||
|
||||
@ -16,7 +16,7 @@ ID, group-ID are documented in "compute"_compute.html command :ulb,l
|
||||
property/chunk = style name of this compute command :l
|
||||
input = one or more attributes :l
|
||||
attributes = count, id, coord1, coord2, coord3
|
||||
count = # of atoms in chunk
|
||||
count = # of atoms in chunk
|
||||
id = original chunk IDs before compression by "compute chunk/atom"_compute_chunk_atom.html
|
||||
coord123 = coordinates for spatial bins calculated by "compute chunk/atom"_compute_chunk_atom.html :pre
|
||||
:ule
|
||||
|
||||
@ -18,10 +18,10 @@ rigidID = ID of fix rigid/small command or one of its variants :l
|
||||
input = one or more rigid body attributes :l
|
||||
possible attributes = id, mol, mass,
|
||||
x, y, z, xu, yu, zu, ix, iy, iz
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
omegax, omegay, omegaz,
|
||||
angmomx, angmomy, angmomz,
|
||||
quatw, quati, quatj, quatk,
|
||||
quatw, quati, quatj, quatk,
|
||||
tqx, tqy, tqz,
|
||||
inertiax, inertiay, inertiaz
|
||||
id = atom ID of atom within body which owns body properties
|
||||
@ -29,7 +29,7 @@ input = one or more rigid body attributes :l
|
||||
mass = total mass of body
|
||||
x,y,z = center of mass coords of body
|
||||
xu,yu,zu = unwrapped center of mass coords of body
|
||||
ix,iy,iz = box image that the center of mass is in
|
||||
ix,iy,iz = box image that the center of mass is in
|
||||
vx,vy,vz = center of mass velocities
|
||||
fx,fy,fz = force of center of mass
|
||||
omegax,omegay,omegaz = angular velocity of body
|
||||
@ -71,7 +71,7 @@ it is skipped (only one atom per body is so assigned). If it is the
|
||||
assigned atom, then the info for that body is output. This means that
|
||||
information for N bodies is generated. N may be less than the # of
|
||||
bodies defined by the fix rigid command, if the atoms in some bodies
|
||||
are not in the {group-ID}.
|
||||
are not in the {group-ID}.
|
||||
|
||||
NOTE: Which atom in a body owns the body info is determined internal
|
||||
to LAMMPS; it's the one nearest the geometric center of the body.
|
||||
@ -109,7 +109,7 @@ sigma, etc). Use {xu}, {yu}, {zu} if you want the COM "unwrapped" by
|
||||
the image flags for each atobody. Unwrapped means that if the body
|
||||
COM has passed thru a periodic boundary one or more times, the value
|
||||
is generated what the COM coordinate would be if it had not been
|
||||
wrapped back into the periodic box.
|
||||
wrapped back into the periodic box.
|
||||
|
||||
The image flags for the body can be generated directly using the {ix},
|
||||
{iy}, {iz} attributes. For periodic dimensions, they specify which
|
||||
|
||||
@ -19,18 +19,18 @@ type1 type2 ... typeN = chemical symbol of each atom type (see valid options bel
|
||||
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {Kmax} or {Zone} or {dR_Ewald} or {c} or {manual} or {echo} :l
|
||||
{Kmax} value = Maximum distance explored from reciprocal space origin
|
||||
{Kmax} value = Maximum distance explored from reciprocal space origin
|
||||
(inverse length units)
|
||||
{Zone} values = z1 z2 z3
|
||||
z1,z2,z3 = Zone axis of incident radiation. If z1=z2=z3=0 all
|
||||
z1,z2,z3 = Zone axis of incident radiation. If z1=z2=z3=0 all
|
||||
reciprocal space will be meshed up to {Kmax}
|
||||
{dR_Ewald} value = Thickness of Ewald sphere slice intercepting
|
||||
{dR_Ewald} value = Thickness of Ewald sphere slice intercepting
|
||||
reciprocal space (inverse length units)
|
||||
{c} values = c1 c2 c3
|
||||
c1,c2,c3 = parameters to adjust the spacing of the reciprocal
|
||||
c1,c2,c3 = parameters to adjust the spacing of the reciprocal
|
||||
lattice nodes in the h, k, and l directions respectively
|
||||
{manual} = flag to use manual spacing of reciprocal lattice points
|
||||
based on the values of the {c} parameters
|
||||
{manual} = flag to use manual spacing of reciprocal lattice points
|
||||
based on the values of the {c} parameters
|
||||
{echo} = flag to provide extra output for debugging purposes :pre
|
||||
:ule
|
||||
|
||||
@ -44,22 +44,22 @@ fix saed/vtk 1 1 1 c_2 file Ni_000.saed :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates electron diffraction intensity as
|
||||
described in "(Coleman)"_#saed-Coleman on a mesh of reciprocal lattice nodes
|
||||
defined by the entire simulation domain (or manually) using simulated
|
||||
radiation of wavelength lambda.
|
||||
Define a computation that calculates electron diffraction intensity as
|
||||
described in "(Coleman)"_#saed-Coleman on a mesh of reciprocal lattice nodes
|
||||
defined by the entire simulation domain (or manually) using simulated
|
||||
radiation of wavelength lambda.
|
||||
|
||||
The electron diffraction intensity I at each reciprocal lattice point
|
||||
The electron diffraction intensity I at each reciprocal lattice point
|
||||
is computed from the structure factor F using the equations:
|
||||
|
||||
:c,image(Eqs/compute_saed1.jpg)
|
||||
:c,image(Eqs/compute_saed1.jpg)
|
||||
:c,image(Eqs/compute_saed2.jpg)
|
||||
|
||||
Here, K is the location of the reciprocal lattice node, rj is the
|
||||
Here, K is the location of the reciprocal lattice node, rj is the
|
||||
position of each atom, fj are atomic scattering factors.
|
||||
|
||||
Diffraction intensities are calculated on a three-dimensional mesh of
|
||||
reciprocal lattice nodes. The mesh spacing is defined either (a) by
|
||||
Diffraction intensities are calculated on a three-dimensional mesh of
|
||||
reciprocal lattice nodes. The mesh spacing is defined either (a) by
|
||||
the entire simulation domain or (b) manually using selected values as
|
||||
shown in the 2D diagram below.
|
||||
|
||||
@ -74,12 +74,12 @@ average of the (inversed) box lengths with periodic boundary conditions.
|
||||
Meshes defined by the simulation domain must contain at least one periodic
|
||||
boundary.
|
||||
|
||||
If the {manual} flag is included, the mesh of reciprocal lattice nodes
|
||||
will defined using the {c} values for the spacing along each reciprocal
|
||||
lattice axis. Note that manual mapping of the reciprocal space mesh is
|
||||
good for comparing diffraction results from multiple simulations; however
|
||||
it can reduce the likelihood that Bragg reflections will be satisfied
|
||||
unless small spacing parameters <0.05 Angstrom^(-1) are implemented.
|
||||
If the {manual} flag is included, the mesh of reciprocal lattice nodes
|
||||
will defined using the {c} values for the spacing along each reciprocal
|
||||
lattice axis. Note that manual mapping of the reciprocal space mesh is
|
||||
good for comparing diffraction results from multiple simulations; however
|
||||
it can reduce the likelihood that Bragg reflections will be satisfied
|
||||
unless small spacing parameters <0.05 Angstrom^(-1) are implemented.
|
||||
Meshes with manual spacing do not require a periodic boundary.
|
||||
|
||||
The limits of the reciprocal lattice mesh are determined by the use of
|
||||
@ -98,17 +98,17 @@ in the below image.
|
||||
|
||||
:c,image(JPG/saed_ewald_intersect_small.jpg,JPG/saed_ewald_intersect.jpg)
|
||||
|
||||
The atomic scattering factors, fj, accounts for the reduction in
|
||||
diffraction intensity due to Compton scattering. Compute saed uses
|
||||
analytical approximations of the atomic scattering factors that vary
|
||||
for each atom type (type1 type2 ... typeN) and angle of diffraction.
|
||||
The atomic scattering factors, fj, accounts for the reduction in
|
||||
diffraction intensity due to Compton scattering. Compute saed uses
|
||||
analytical approximations of the atomic scattering factors that vary
|
||||
for each atom type (type1 type2 ... typeN) and angle of diffraction.
|
||||
The analytic approximation is computed using the formula
|
||||
"(Brown)"_#Brown:
|
||||
|
||||
:c,image(Eqs/compute_saed3.jpg)
|
||||
|
||||
Coefficients parameterized by "(Fox)"_#Fox are assigned for each
|
||||
atom type designating the chemical symbol and charge of each atom
|
||||
Coefficients parameterized by "(Fox)"_#Fox are assigned for each
|
||||
atom type designating the chemical symbol and charge of each atom
|
||||
type. Valid chemical symbols for compute saed are:
|
||||
|
||||
H: He: Li: Be: B:
|
||||
@ -133,14 +133,14 @@ type. Valid chemical symbols for compute saed are:
|
||||
Cm: Bk: Cf:tb(c=5,s=:)
|
||||
|
||||
|
||||
If the {echo} keyword is specified, compute saed will provide extra
|
||||
reporting information to the screen.
|
||||
If the {echo} keyword is specified, compute saed will provide extra
|
||||
reporting information to the screen.
|
||||
|
||||
[Output info:]
|
||||
|
||||
This compute calculates a global vector. The length of the vector is
|
||||
the number of reciprocal lattice nodes that are explored by the mesh.
|
||||
The entries of the global vector are the computed diffraction
|
||||
This compute calculates a global vector. The length of the vector is
|
||||
the number of reciprocal lattice nodes that are explored by the mesh.
|
||||
The entries of the global vector are the computed diffraction
|
||||
intensities as described above.
|
||||
|
||||
The vector can be accessed by any command that uses global values
|
||||
@ -148,21 +148,21 @@ from a compute as input. See "this
|
||||
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
All array values calculated by this compute are "intensive".
|
||||
All array values calculated by this compute are "intensive".
|
||||
|
||||
[Restrictions:]
|
||||
[Restrictions:]
|
||||
|
||||
This compute is part of the USER-DIFFRACTION 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.
|
||||
|
||||
The compute_saed command does not work for triclinic cells.
|
||||
The compute_saed command does not work for triclinic cells.
|
||||
|
||||
[Related commands:]
|
||||
[Related commands:]
|
||||
|
||||
"fix saed_vtk"_fix_saed_vtk.html, "compute xrd"_compute_xrd.html
|
||||
|
||||
[Default:]
|
||||
[Default:]
|
||||
|
||||
The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald =
|
||||
0.01.
|
||||
@ -174,7 +174,7 @@ The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald =
|
||||
(2013).
|
||||
|
||||
:link(Brown)
|
||||
[(Brown)] Brown et al. International Tables for Crystallography
|
||||
[(Brown)] Brown et al. International Tables for Crystallography
|
||||
Volume C: Mathematical and Chemical Tables, 554-95 (2004).
|
||||
|
||||
:link(Fox)
|
||||
|
||||
@ -22,7 +22,7 @@ compute 1 all smd/damage :pre
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates the damage status of SPH particles
|
||||
according to the damage model which is defined via the SMD SPH pair styles, e.g., the maximum plastic strain failure criterion.
|
||||
according to the damage model which is defined via the SMD SPH pair styles, e.g., the maximum plastic strain failure criterion.
|
||||
|
||||
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
|
||||
|
||||
|
||||
@ -31,7 +31,7 @@ keyword = {diagonal} or {rmin0} or {switchflag} :l
|
||||
{2} = subset satisfying j1 == j2 == j3
|
||||
{3} = subset satisfying j2 <= j1 <= j
|
||||
{rmin0} value = parameter in distance to angle conversion (distance units)
|
||||
{switchflag} value = {0} or {1}
|
||||
{switchflag} value = {0} or {1}
|
||||
{0} = do not use switching function
|
||||
{1} = use switching function :pre
|
||||
:ule
|
||||
@ -60,12 +60,12 @@ onto the 3-sphere, the surface of the unit ball in a four-dimensional
|
||||
space. The radial distance {r} within {R_ii'} is mapped on to a third
|
||||
polar angle {theta0} defined by,
|
||||
|
||||
:c,image(Eqs/compute_sna_atom1.jpg)
|
||||
:c,image(Eqs/compute_sna_atom1.jpg)
|
||||
|
||||
In this way, all possible neighbor positions are mapped on to a subset
|
||||
of the 3-sphere. Points south of the latitude {theta0max=rfac0*Pi}
|
||||
are excluded.
|
||||
|
||||
|
||||
The natural basis for functions on the 3-sphere is formed by the 4D
|
||||
hyperspherical harmonics {U^j_m,m'(theta, phi, theta0).} These
|
||||
functions are better known as {D^j_m,m',} the elements of the Wigner
|
||||
@ -78,7 +78,7 @@ radial distance. Expanding this density function as a generalized
|
||||
Fourier series in the basis functions, we can write each Fourier
|
||||
coefficient as
|
||||
|
||||
:c,image(Eqs/compute_sna_atom2.jpg)
|
||||
:c,image(Eqs/compute_sna_atom2.jpg)
|
||||
|
||||
The {w_i'} neighbor weights are dimensionless numbers that are chosen
|
||||
to distinguish atoms of different types, while the central atom is
|
||||
@ -86,7 +86,7 @@ arbitrarily assigned a unit weight. The function {fc(r)} ensures that
|
||||
the contribution of each neighbor atom goes smoothly to zero at
|
||||
{R_ii'}:
|
||||
|
||||
:c,image(Eqs/compute_sna_atom4.jpg)
|
||||
:c,image(Eqs/compute_sna_atom4.jpg)
|
||||
|
||||
The expansion coefficients {u^j_m,m'} are complex-valued and they are
|
||||
not directly useful as descriptors, because they are not invariant
|
||||
@ -94,7 +94,7 @@ under rotation of the polar coordinate frame. However, the following
|
||||
scalar triple products of expansion coefficients can be shown to be
|
||||
real-valued and invariant under rotation "(Bartok)"_#Bartok2010.
|
||||
|
||||
:c,image(Eqs/compute_sna_atom3.jpg)
|
||||
:c,image(Eqs/compute_sna_atom3.jpg)
|
||||
|
||||
The constants {H^jmm'_j1m1m1'_j2m2m2'} are coupling coefficients,
|
||||
analogous to Clebsch-Gordan coefficients for rotations on the
|
||||
@ -112,17 +112,17 @@ atom.
|
||||
Compute {snad/atom} calculates the derivative of the bispectrum components
|
||||
summed separately for each atom type:
|
||||
|
||||
:c,image(Eqs/compute_sna_atom5.jpg)
|
||||
:c,image(Eqs/compute_sna_atom5.jpg)
|
||||
|
||||
The sum is over all atoms {i'} of atom type {I}. For each atom {i},
|
||||
this compute evaluates the above expression for each direction, each
|
||||
atom type, and each bispectrum component. See section below on output
|
||||
for a detailed explanation.
|
||||
|
||||
|
||||
Compute {snav/atom} calculates the virial contribution due to the
|
||||
derivatives:
|
||||
|
||||
:c,image(Eqs/compute_sna_atom6.jpg)
|
||||
:c,image(Eqs/compute_sna_atom6.jpg)
|
||||
|
||||
Again, the sum is over all atoms {i'} of atom type {I}. For each atom
|
||||
{i}, this compute evaluates the above expression for each of the six
|
||||
@ -140,7 +140,7 @@ too frequently.
|
||||
|
||||
The argument {rcutfac} is a scale factor that controls the ratio of
|
||||
atomic radius to radial cutoff distance.
|
||||
|
||||
|
||||
The argument {rfac0} and the optional keyword {rmin0} define the
|
||||
linear mapping from radial distance to polar angle {theta0} on the
|
||||
3-sphere.
|
||||
@ -176,18 +176,18 @@ each column depend on the values of {twojmax} and {diagonal}, as
|
||||
described by the following piece of python code:
|
||||
|
||||
for j1 in range(0,twojmax+1):
|
||||
if(diagonal==2):
|
||||
if(diagonal==2):
|
||||
print j1/2.,j1/2.,j1/2.
|
||||
elif(diagonal==1):
|
||||
for j in range(0,min(twojmax,2*j1)+1,2):
|
||||
for j in range(0,min(twojmax,2*j1)+1,2):
|
||||
print j1/2.,j1/2.,j/2.
|
||||
elif(diagonal==0):
|
||||
for j2 in range(0,j1+1):
|
||||
for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
|
||||
for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
|
||||
print j1/2.,j2/2.,j/2.
|
||||
elif(diagonal==3):
|
||||
for j2 in range(0,j1+1):
|
||||
for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
|
||||
for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
|
||||
if (j>=j1): print j1/2.,j2/2.,j/2. :pre
|
||||
|
||||
Compute {snad/atom} evaluates a per-atom array. The columns are
|
||||
@ -227,7 +227,7 @@ The optional keyword defaults are {diagonal} = 0, {rmin0} = 0,
|
||||
:line
|
||||
|
||||
:link(Thompson2014)
|
||||
[(Thompson)] Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint
|
||||
[(Thompson)] Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint
|
||||
available at "arXiv:1409.3880"_http://arxiv.org/abs/1409.3880
|
||||
|
||||
:link(Bartok2010)
|
||||
@ -235,7 +235,7 @@ available at "arXiv:1409.3880"_http://arxiv.org/abs/1409.3880
|
||||
|
||||
:link(Meremianin2006)
|
||||
[(Meremianin)] Meremianin, J. Phys. A, 39, 3099 (2006).
|
||||
|
||||
|
||||
:link(Varshalovich1987)
|
||||
[(Varshalovich)] Varshalovich, Moskalev, Khersonskii, Quantum Theory
|
||||
of Angular Momentum, World Scientific, Singapore (1987).
|
||||
|
||||
@ -88,7 +88,7 @@ potentials only include the pair potential portion of the EAM
|
||||
interaction when used by this compute, not the embedding term. Also
|
||||
bonded or Kspace interactions do not contribute to this compute.
|
||||
|
||||
[Related commands:]
|
||||
[Related commands:]
|
||||
|
||||
{compute group/group}_compute_group_group.html, {compute
|
||||
heat/flux}_compute_heat_flux.html
|
||||
|
||||
@ -16,7 +16,7 @@ ID, group-ID are documented in "compute"_compute.html command
|
||||
temp/cs = style name of this compute command
|
||||
group1 = group-ID of either cores or shells
|
||||
group2 = group-ID of either shells or cores :ul
|
||||
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute oxygen_c-s all temp/cs O_core O_shell
|
||||
@ -64,7 +64,7 @@ calculated by this compute for use in the computation of a pressure
|
||||
tensor. The formula for the components of the tensor is the same as
|
||||
the above formula, except that v^2 is replaced by vx*vy for the xy
|
||||
component, etc. The 6 components of the vector are ordered xx, yy,
|
||||
zz, xy, xz, yz. In contrast to the temperature, the velocity of
|
||||
zz, xy, xz, yz. In contrast to the temperature, the velocity of
|
||||
each core or shell atom is taken individually.
|
||||
|
||||
The change this fix makes to core/shell atom velocities is essentially
|
||||
|
||||
@ -14,7 +14,7 @@ compute ID group-ID temp/drude :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
temp/drude = style name of this compute command :ul
|
||||
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute TDRUDE all temp/drude :pre
|
||||
@ -68,7 +68,7 @@ are "extensive".
|
||||
[Restrictions:]
|
||||
|
||||
The number of degrees of freedom contributing to the temperature is
|
||||
assumed to be constant for the duration of the run unless the
|
||||
assumed to be constant for the duration of the run unless the
|
||||
{fix_modify} command sets the option {dynamic yes}.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
@ -49,9 +49,9 @@ reported by LAMMPS in the thermodynamic quantities reported via the
|
||||
example:
|
||||
|
||||
compute effTemp all temp/eff
|
||||
thermo_style custom step etotal pe ke temp press
|
||||
thermo_style custom step etotal pe ke temp press
|
||||
thermo_modify temp effTemp :pre
|
||||
|
||||
|
||||
A 6-component kinetic energy tensor is also calculated by this compute
|
||||
for use in the computation of a pressure tensor. The formula for the
|
||||
components of the tensor is the same as the above formula, except that
|
||||
@ -80,7 +80,7 @@ is independent of the number of atoms in the simulation. The vector
|
||||
values are "extensive", meaning they scale with the number of atoms in
|
||||
the simulation.
|
||||
|
||||
[Restrictions:]
|
||||
[Restrictions:]
|
||||
|
||||
This compute is part of the USER-EFF package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
|
||||
@ -68,7 +68,7 @@ temp/berendsen"_fix_temp_berendsen.html, and "fix
|
||||
langevin"_fix_langevin.html. This means that when this compute
|
||||
is used to calculate the temperature for any of the thermostatting
|
||||
fixes via the "fix modify temp"_fix_modify.html command, the thermostat
|
||||
will operate only on atoms that are currently in the geometric
|
||||
will operate only on atoms that are currently in the geometric
|
||||
region.
|
||||
|
||||
Unlike other compute styles that calculate temperature, this compute
|
||||
|
||||
@ -122,7 +122,7 @@ vector values will be in energy "units"_units.html.
|
||||
|
||||
This fix requires that atoms store torque and angular velocity (omega)
|
||||
and a radius as defined by the "atom_style sphere"_atom_style.html
|
||||
command.
|
||||
command.
|
||||
|
||||
All particles in the group must be finite-size spheres, or point
|
||||
particles with radius = 0.0.
|
||||
|
||||
@ -6,7 +6,7 @@
|
||||
|
||||
:line
|
||||
|
||||
compute ti command :h3
|
||||
compute ti command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
@ -35,7 +35,7 @@ keyword = pair style (lj/cut, gauss, born, etc) or {tail} or {kspace} :l
|
||||
compute 1 all ti lj/cut 1 v_lj v_dlj coul/long 2 v_c v_dc kspace 1 v_ks v_dks
|
||||
compute 1 all ti lj/cut 1*3 v_lj v_dlj coul/long * v_c v_dc kspace * v_ks v_dks :pre
|
||||
|
||||
[Description:]
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates the derivative of the interaction
|
||||
potential with respect to {lambda}, the coupling parameter used in a
|
||||
@ -107,7 +107,7 @@ du/dl can be found in the paper by "Eike"_#Eike.
|
||||
|
||||
:line
|
||||
|
||||
[Output info:]
|
||||
[Output info:]
|
||||
|
||||
This compute calculates a global scalar, namely dUs/dlambda. This
|
||||
value can be used by any command that uses a global scalar value from
|
||||
|
||||
@ -15,7 +15,7 @@ compute ID group-ID voronoi/atom keyword arg ... :pre
|
||||
ID, group-ID are documented in "compute"_compute.html command :ulb,l
|
||||
voronoi/atom = style name of this compute command :l
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {only_group} or {surface} or {radius} or {edge_histo} or {edge_threshold}
|
||||
keyword = {only_group} or {surface} or {radius} or {edge_histo} or {edge_threshold}
|
||||
or {face_threshold} or {neighbors} or {peratom} :l
|
||||
{only_group} = no arg
|
||||
{occupation} = no arg
|
||||
@ -25,7 +25,7 @@ or {face_threshold} or {neighbors} or {peratom} :l
|
||||
{radius} arg = v_r
|
||||
v_r = radius atom style variable for a poly-disperse Voronoi tessellation
|
||||
{edge_histo} arg = maxedge
|
||||
maxedge = maximum number of Voronoi cell edges to be accounted in the histogram
|
||||
maxedge = maximum number of Voronoi cell edges to be accounted in the histogram
|
||||
{edge_threshold} arg = minlength
|
||||
minlength = minimum length for an edge to be counted
|
||||
{face_threshold} arg = minarea
|
||||
@ -38,7 +38,7 @@ or {face_threshold} or {neighbors} or {peratom} :l
|
||||
|
||||
compute 1 all voronoi/atom
|
||||
compute 2 precipitate voronoi/atom surface matrix
|
||||
compute 3b precipitate voronoi/atom radius v_r
|
||||
compute 3b precipitate voronoi/atom radius v_r
|
||||
compute 4 solute voronoi/atom only_group
|
||||
compute 5 defects voronoi/atom occupation
|
||||
compute 6 all voronoi/atom neighbors yes :pre
|
||||
@ -53,11 +53,11 @@ in the group.
|
||||
By default two per-atom quantities are calculated by this compute.
|
||||
The first is the volume of the Voronoi cell around each atom. Any
|
||||
point in an atom's Voronoi cell is closer to that atom than any other.
|
||||
The second is the number of faces of the Voronoi cell. This is
|
||||
The second is the number of faces of the Voronoi cell. This is
|
||||
equal to the number of nearest neighbors of the central atom,
|
||||
plus any exterior faces (see note below). If the {peratom} keyword
|
||||
is set to "no", the per-atom quantities are still calculated,
|
||||
but they are not accessible.
|
||||
plus any exterior faces (see note below). If the {peratom} keyword
|
||||
is set to "no", the per-atom quantities are still calculated,
|
||||
but they are not accessible.
|
||||
|
||||
:line
|
||||
|
||||
@ -122,23 +122,23 @@ to locate vacancies (the coordinates are given by the atom coordinates
|
||||
at the time step when the compute was first invoked), while column two
|
||||
data can be used to identify interstitial atoms.
|
||||
|
||||
If the {neighbors} value is set to yes, then
|
||||
If the {neighbors} value is set to yes, then
|
||||
this compute creates a local array with 3 columns. There
|
||||
is one row for each face of each Voronoi cell. The
|
||||
3 columns are the atom ID of the atom that owns the cell,
|
||||
the atom ID of the atom in the neighboring cell
|
||||
(or zero if the face is external), and the area of the face.
|
||||
is one row for each face of each Voronoi cell. The
|
||||
3 columns are the atom ID of the atom that owns the cell,
|
||||
the atom ID of the atom in the neighboring cell
|
||||
(or zero if the face is external), and the area of the face.
|
||||
The array can be accessed by any command that
|
||||
uses local values from a compute as input. See "this
|
||||
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
|
||||
options. More specifically, the array can be accessed by a
|
||||
options. More specifically, the array can be accessed by a
|
||||
"dump local"_dump.html command to write a file containing
|
||||
all the Voronoi neighbors in a system:
|
||||
|
||||
compute 6 all voronoi/atom neighbors yes
|
||||
dump d2 all local 1 dump.neighbors index c_6\[1\] c_6\[2\] c_6\[3\] :pre
|
||||
|
||||
If the {face_threshold} keyword is used, then only faces
|
||||
If the {face_threshold} keyword is used, then only faces
|
||||
with areas greater than the threshold are stored.
|
||||
|
||||
:line
|
||||
@ -190,7 +190,7 @@ per-atom values from a compute as input. See "Section
|
||||
6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
|
||||
options. If the {peratom} keyword is set to "no", the per-atom array
|
||||
is still created, but it is not accessible.
|
||||
|
||||
|
||||
If the {edge_histo} keyword is used, then this compute generates a
|
||||
global vector of length {maxedge}+1, containing a histogram of the
|
||||
number of edges per face.
|
||||
|
||||
@ -20,21 +20,21 @@ type1 type2 ... typeN = chemical symbol of each atom type (see valid options bel
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {2Theta} or {c} or {LP} or {manual} or {echo} :l
|
||||
{2Theta} values = Min2Theta Max2Theta
|
||||
Min2Theta,Max2Theta = minimum and maximum 2 theta range to explore
|
||||
Min2Theta,Max2Theta = minimum and maximum 2 theta range to explore
|
||||
(radians or degrees)
|
||||
{c} values = c1 c2 c3
|
||||
c1,c2,c3 = parameters to adjust the spacing of the reciprocal
|
||||
c1,c2,c3 = parameters to adjust the spacing of the reciprocal
|
||||
lattice nodes in the h, k, and l directions respectively
|
||||
{LP} value = switch to apply Lorentz-polarization factor
|
||||
0/1 = off/on
|
||||
{manual} = flag to use manual spacing of reciprocal lattice points
|
||||
based on the values of the {c} parameters
|
||||
{manual} = flag to use manual spacing of reciprocal lattice points
|
||||
based on the values of the {c} parameters
|
||||
{echo} = flag to provide extra output for debugging purposes :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all xrd 1.541838 Al O 2Theta 0.087 0.87 c 1 1 1 LP 1 echo
|
||||
compute 1 all xrd 1.541838 Al O 2Theta 0.087 0.87 c 1 1 1 LP 1 echo
|
||||
compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual :pre
|
||||
|
||||
fix 1 all ave/histo/weight 1 1 1 0.087 0.87 250 c_1\[1\] c_1\[2\] mode vector file Rad2Theta.xrd
|
||||
@ -43,11 +43,11 @@ fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2\[1\] c_2\[2\] mode vector file D
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates x-ray diffraction intensity as described
|
||||
in "(Coleman)"_#xrd-Coleman on a mesh of reciprocal lattice nodes defined
|
||||
in "(Coleman)"_#xrd-Coleman on a mesh of reciprocal lattice nodes defined
|
||||
by the entire simulation domain (or manually) using a simulated radiation
|
||||
of wavelength lambda.
|
||||
of wavelength lambda.
|
||||
|
||||
The x-ray diffraction intensity, I, at each reciprocal lattice point, k,
|
||||
The x-ray diffraction intensity, I, at each reciprocal lattice point, k,
|
||||
is computed from the structure factor, F, using the equations:
|
||||
|
||||
:c,image(Eqs/compute_xrd1.jpg)
|
||||
@ -55,14 +55,14 @@ is computed from the structure factor, F, using the equations:
|
||||
:c,image(Eqs/compute_xrd3.jpg)
|
||||
:c,image(Eqs/compute_xrd4.jpg)
|
||||
|
||||
Here, K is the location of the reciprocal lattice node, rj is the
|
||||
position of each atom, fj are atomic scattering factors, LP is the
|
||||
Lorentz-polarization factor, and theta is the scattering angle of
|
||||
diffraction. The Lorentz-polarization factor can be turned off using
|
||||
Here, K is the location of the reciprocal lattice node, rj is the
|
||||
position of each atom, fj are atomic scattering factors, LP is the
|
||||
Lorentz-polarization factor, and theta is the scattering angle of
|
||||
diffraction. The Lorentz-polarization factor can be turned off using
|
||||
the optional {LP} keyword.
|
||||
|
||||
Diffraction intensities are calculated on a three-dimensional mesh of
|
||||
reciprocal lattice nodes. The mesh spacing is defined either (a)
|
||||
Diffraction intensities are calculated on a three-dimensional mesh of
|
||||
reciprocal lattice nodes. The mesh spacing is defined either (a)
|
||||
by the entire simulation domain or (b) manually using selected values as
|
||||
shown in the 2D diagram below.
|
||||
|
||||
@ -101,8 +101,8 @@ The analytic approximation is computed using the formula
|
||||
|
||||
:c,image(Eqs/compute_xrd5.jpg)
|
||||
|
||||
Coefficients parameterized by "(Peng)"_#Peng are assigned for each
|
||||
atom type designating the chemical symbol and charge of each atom
|
||||
Coefficients parameterized by "(Peng)"_#Peng are assigned for each
|
||||
atom type designating the chemical symbol and charge of each atom
|
||||
type. Valid chemical symbols for compute xrd are:
|
||||
|
||||
H| He1-| He| Li| Li1+|
|
||||
@ -148,39 +148,39 @@ type. Valid chemical symbols for compute xrd are:
|
||||
Np4+| Np6+| Pu| Pu3+| Pu4+|
|
||||
Pu6+| Am| Cm| Bk| Cf :tb(c=5,s=|)
|
||||
|
||||
If the {echo} keyword is specified, compute xrd will provide extra
|
||||
reporting information to the screen.
|
||||
If the {echo} keyword is specified, compute xrd will provide extra
|
||||
reporting information to the screen.
|
||||
|
||||
[Output info:]
|
||||
|
||||
This compute calculates a global array. The number of rows in the
|
||||
array is the number of reciprocal lattice nodes that are explored
|
||||
which by the mesh. The global array has 2 columns.
|
||||
This compute calculates a global array. The number of rows in the
|
||||
array is the number of reciprocal lattice nodes that are explored
|
||||
which by the mesh. The global array has 2 columns.
|
||||
|
||||
The first column contains the diffraction angle in the units (radians
|
||||
or degrees) provided with the {2Theta} values. The second column contains
|
||||
or degrees) provided with the {2Theta} values. The second column contains
|
||||
the computed diffraction intensities as described above.
|
||||
|
||||
The array can be accessed by any command that uses global values from
|
||||
a compute as input. See "this section"_Section_howto.html#howto_15
|
||||
for an overview of LAMMPS output options.
|
||||
|
||||
All array values calculated by this compute are "intensive".
|
||||
All array values calculated by this compute are "intensive".
|
||||
|
||||
[Restrictions:]
|
||||
[Restrictions:]
|
||||
|
||||
This compute is part of the USER-DIFFRACTION 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.
|
||||
|
||||
The compute_xrd command does not work for triclinic cells.
|
||||
The compute_xrd command does not work for triclinic cells.
|
||||
|
||||
[Related commands:]
|
||||
[Related commands:]
|
||||
|
||||
"fix ave/histo"_fix_ave_histo.html,
|
||||
"compute saed"_compute_saed.html
|
||||
|
||||
[Default:]
|
||||
[Default:]
|
||||
|
||||
The option defaults are 2Theta = 1 179 (degrees), c = 1 1 1, LP = 1,
|
||||
no manual flag, no echo flag.
|
||||
@ -192,7 +192,7 @@ no manual flag, no echo flag.
|
||||
(2013).
|
||||
|
||||
:link(Colliex)
|
||||
[(Colliex)] Colliex et al. International Tables for Crystallography
|
||||
[(Colliex)] Colliex et al. International Tables for Crystallography
|
||||
Volume C: Mathematical and Chemical Tables, 249-429 (2004).
|
||||
|
||||
:link(Peng)
|
||||
|
||||
@ -48,7 +48,7 @@ keyword = {mol} or {basis} or {remap} or {var} or {set} or {units} :l
|
||||
|
||||
create_atoms 1 box
|
||||
create_atoms 3 region regsphere basis 2 3
|
||||
create_atoms 3 single 0 0 5
|
||||
create_atoms 3 single 0 0 5
|
||||
create_atoms 1 box var v set x xpos set y ypos :pre
|
||||
|
||||
[Description:]
|
||||
@ -245,7 +245,7 @@ style. A {box} value selects standard distance units as defined by
|
||||
the "units"_units.html command, e.g. Angstroms for units = real or
|
||||
metal. A {lattice} value means the distance units are in lattice
|
||||
spacings.
|
||||
|
||||
|
||||
:line
|
||||
|
||||
Atom IDs are assigned to created atoms in the following way. The
|
||||
|
||||
@ -121,7 +121,7 @@ The {special} keyword is invoked at the end of the delete_bonds
|
||||
operation, after (optional) removal. It re-computes the pairwise 1-2,
|
||||
1-3, 1-4 weighting list. The weighting list computation treats
|
||||
turned-off bonds the same as turned-on. Thus, turned-off bonds must
|
||||
be removed if you wish to change the weighting list.
|
||||
be removed if you wish to change the weighting list.
|
||||
|
||||
Note that the choice of {remove} and {special} options affects how
|
||||
1-2, 1-3, 1-4 pairwise interactions will be computed across bonds that
|
||||
|
||||
@ -6,7 +6,7 @@
|
||||
|
||||
:line
|
||||
|
||||
dielectric command :h3
|
||||
dielectric command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
|
||||
@ -17,10 +17,10 @@ dihedral_style class2 :pre
|
||||
|
||||
dihedral_style class2
|
||||
dihedral_coeff 1 100 75 100 70 80 60
|
||||
dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228
|
||||
dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228
|
||||
dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010
|
||||
dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270
|
||||
dihedral_coeff * aat -13.5271 110.2453 105.1270
|
||||
dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270
|
||||
dihedral_coeff * aat -13.5271 110.2453 105.1270
|
||||
dihedral_coeff * bb13 0.0 1.0119 1.1010 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
@ -66,7 +66,7 @@ more instructions on how to use the accelerated styles effectively.
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
|
||||
USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
|
||||
section for more info on packages.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
@ -63,7 +63,7 @@ more instructions on how to use the accelerated styles effectively.
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
|
||||
USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
|
||||
section for more info on packages.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
@ -33,7 +33,7 @@ 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/radian^2)
|
||||
K (energy/radian^2)
|
||||
phi0 (degrees) :ul
|
||||
|
||||
:line
|
||||
@ -64,7 +64,7 @@ more instructions on how to use the accelerated styles effectively.
|
||||
[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
|
||||
USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
|
||||
section for more info on packages.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
@ -14,7 +14,7 @@ dihedral_style spherical :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0
|
||||
dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0
|
||||
dihedral_coeff 1 3 286.1 1 114 1 1 90 0 1 90.0 0 &
|
||||
17.3 0 0.0 0 1 158 1 0 0.0 0 &
|
||||
15.1 0 0.0 0 0 0.0 0 1 167.3 1 :pre
|
||||
@ -76,7 +76,7 @@ wn (typically 0.0 or 1.0) :ul
|
||||
[Restrictions:]
|
||||
|
||||
This dihedral style can only be used if LAMMPS was built with the
|
||||
USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
|
||||
USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
|
||||
section for more info on packages.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
@ -5,7 +5,7 @@
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
dump command :h3
|
||||
"dump custom/vtk"_dump_custom_vtk.html command :h3
|
||||
"dump h5md"_dump_h5md.html command :h3
|
||||
@ -55,7 +55,7 @@ args = list of arguments for a particular style :l
|
||||
|
||||
{custom} or {custom/gz} or {custom/mpiio} args = list of atom attributes
|
||||
possible attributes = id, mol, proc, procp1, type, element, mass,
|
||||
x, y, z, xs, ys, zs, xu, yu, zu,
|
||||
x, y, z, xs, ys, zs, xu, yu, zu,
|
||||
xsu, ysu, zsu, ix, iy, iz,
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
q, mux, muy, muz, mu,
|
||||
@ -211,7 +211,7 @@ bounding box which encloses the triclinic simulation box is output,
|
||||
along with the 3 tilt factors (xy, xz, yz) of the triclinic box,
|
||||
formatted as follows:
|
||||
|
||||
ITEM: BOX BOUNDS xy xz yz xx yy zz
|
||||
ITEM: BOX BOUNDS xy xz yz xx yy zz
|
||||
xlo_bound xhi_bound xy
|
||||
ylo_bound yhi_bound xz
|
||||
zlo_bound zhi_bound yz :pre
|
||||
@ -305,8 +305,8 @@ by the GROMACS molecular dynamics package, and described
|
||||
The precision used in XTC files can be adjusted via the
|
||||
"dump_modify"_dump_modify.html command. The default value of 1000
|
||||
means that coordinates are stored to 1/1000 nanometer accuracy. XTC
|
||||
files are portable binary files written in the NFS XDR data format,
|
||||
so that any machine which supports XDR should be able to read them.
|
||||
files are portable binary files written in the NFS XDR data format,
|
||||
so that any machine which supports XDR should be able to read them.
|
||||
The number of atoms per snapshot cannot change with the {xtc} style.
|
||||
The {unwrap} option of the "dump_modify"_dump_modify.html command allows
|
||||
XTC coordinates to be written "unwrapped" by the image flags for each
|
||||
@ -499,7 +499,7 @@ values.
|
||||
Here is an example of how to dump bond info for a system, including
|
||||
the distance and energy of each bond:
|
||||
|
||||
compute 1 all property/local batom1 batom2 btype
|
||||
compute 1 all property/local batom1 batom2 btype
|
||||
compute 2 all bond/local dist eng
|
||||
dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_2\[1\] c_2\[2\] :pre
|
||||
|
||||
|
||||
@ -5,7 +5,7 @@
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
dump custom/vtk command :h3
|
||||
|
||||
[Syntax:]
|
||||
@ -20,7 +20,7 @@ file = name of file to write dump info to :l
|
||||
args = list of arguments for a particular style :l
|
||||
{custom/vtk} args = list of atom attributes
|
||||
possible attributes = id, mol, proc, procp1, type, element, mass,
|
||||
x, y, z, xs, ys, zs, xu, yu, zu,
|
||||
x, y, z, xs, ys, zs, xu, yu, zu,
|
||||
xsu, ysu, zsu, ix, iy, iz,
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
q, mux, muy, muz, mu,
|
||||
|
||||
@ -587,7 +587,7 @@ b) Use the freely available mplayer or ffplay tool to view a
|
||||
movie. Both are available for multiple OSes and support a large
|
||||
variety of file formats and decoders. :l
|
||||
|
||||
% mplayer foo.mpg
|
||||
% mplayer foo.mpg
|
||||
% ffplay bar.avi :pre
|
||||
|
||||
c) Use the "Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html
|
||||
@ -631,9 +631,9 @@ Note that since FFmpeg is run as an external program via a pipe,
|
||||
LAMMPS has limited control over its execution and no knowledge about
|
||||
errors and warnings printed by it. Those warnings and error messages
|
||||
will be printed to the screen only. Due to the way image data is
|
||||
communicated to FFmpeg, it will often print the message
|
||||
communicated to FFmpeg, it will often print the message
|
||||
|
||||
pipe:: Input/output error :pre
|
||||
pipe:: Input/output error :pre
|
||||
|
||||
which can be safely ignored. Other warnings
|
||||
and errors have to be addressed according to the FFmpeg documentation.
|
||||
|
||||
@ -54,7 +54,7 @@ keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} o
|
||||
these 3 args can be replaced by the word "none" to turn off thresholding
|
||||
{unwrap} arg = {yes} or {no} :pre
|
||||
these keywords apply only to the {image} and {movie} "styles"_dump_image.html :l
|
||||
keyword = {acolor} or {adiam} or {amap} or {backcolor} or {bcolor} or {bdiam} or {boxcolor} or {color} or {bitrate} or {framerate} :l
|
||||
keyword = {acolor} or {adiam} or {amap} or {backcolor} or {bcolor} or {bdiam} or {boxcolor} or {color} or {bitrate} or {framerate} :l
|
||||
{acolor} args = type color
|
||||
type = atom type or range of types (see below)
|
||||
color = name of color or color1/color2/...
|
||||
@ -491,7 +491,7 @@ simulation box since the last dump. (Note that atoms that crossed
|
||||
once and then crossed back between the two dump timesteps would not be
|
||||
included.)
|
||||
|
||||
region foo sphere 10 20 10 15
|
||||
region foo sphere 10 20 10 15
|
||||
variable inregion atom rmask(foo)
|
||||
dump_modify ... thresh v_inregion |^ LAST
|
||||
|
||||
|
||||
@ -17,17 +17,17 @@ group = name of group fix is to be applied :l
|
||||
type = {thermal} or {two_temperature} or {hardy} or {field} :l
|
||||
{thermal} = thermal coupling with fields: temperature
|
||||
{two_temperature} = electron-phonon coupling with field: temperature and electron_temperature
|
||||
{hardy} = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields)
|
||||
{field} = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) :pre
|
||||
{hardy} = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields)
|
||||
{field} = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) :pre
|
||||
parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file :l
|
||||
:ule
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix AtC internal atc thermal Ar_thermal.dat
|
||||
fix AtC internal atc thermal Ar_thermal.dat
|
||||
fix AtC internal atc two_temperature Ar_ttm.mat
|
||||
fix AtC internal atc hardy
|
||||
fix AtC internal atc field :pre
|
||||
fix AtC internal atc field :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
@ -38,67 +38,67 @@ This fix is the beginning to creating a coupled FE/MD simulation and/or an on-th
|
||||
The following coupling example is typical, but non-exhaustive:
|
||||
# ... commands to create and initialize the MD system :pre
|
||||
|
||||
# initial fix to designate coupling type and group to apply it to
|
||||
# tag group physics material_file
|
||||
# initial fix to designate coupling type and group to apply it to
|
||||
# tag group physics material_file
|
||||
fix AtC internal atc thermal Ar_thermal.mat :pre
|
||||
|
||||
# create a uniform 12 x 2 x 2 mesh that covers region contain the group
|
||||
# nx ny nz region periodicity
|
||||
|
||||
# create a uniform 12 x 2 x 2 mesh that covers region contain the group
|
||||
# nx ny nz region periodicity
|
||||
fix_modify AtC mesh create 12 2 2 mdRegion f p p :pre
|
||||
|
||||
# specify the control method for the type of coupling
|
||||
# physics control_type
|
||||
|
||||
# specify the control method for the type of coupling
|
||||
# physics control_type
|
||||
fix_modify AtC thermal control flux :pre
|
||||
|
||||
# specify the initial values for the empirical field "temperature"
|
||||
# field node_group value
|
||||
|
||||
# specify the initial values for the empirical field "temperature"
|
||||
# field node_group value
|
||||
fix_modify AtC initial temperature all 30 :pre
|
||||
|
||||
# create an output stream for nodal fields
|
||||
# filename output_frequency
|
||||
|
||||
# create an output stream for nodal fields
|
||||
# filename output_frequency
|
||||
fix_modify AtC output atc_fe_output 100 :pre
|
||||
|
||||
run 1000 :pre
|
||||
|
||||
likewise for this post-processing example:
|
||||
|
||||
run 1000 :pre
|
||||
|
||||
likewise for this post-processing example:
|
||||
|
||||
# ... commands to create and initialize the MD system :pre
|
||||
|
||||
# initial fix to designate post-processing and the group to apply it to
|
||||
# no material file is allowed nor required
|
||||
# initial fix to designate post-processing and the group to apply it to
|
||||
# no material file is allowed nor required
|
||||
fix AtC internal atc hardy :pre
|
||||
|
||||
# for hardy fix, specific kernel function (function type and range) to # be used as a localization function
|
||||
fix AtC kernel quartic_sphere 10.0 :pre
|
||||
|
||||
# create a uniform 1 x 1 x 1 mesh that covers region contain the group
|
||||
# with periodicity this effectively creats a system average
|
||||
fix_modify AtC mesh create 1 1 1 box p p p :pre
|
||||
|
||||
# change from default lagrangian map to eulerian
|
||||
# refreshed every 100 steps
|
||||
# for hardy fix, specific kernel function (function type and range) to # be used as a localization function
|
||||
fix AtC kernel quartic_sphere 10.0 :pre
|
||||
|
||||
# create a uniform 1 x 1 x 1 mesh that covers region contain the group
|
||||
# with periodicity this effectively creats a system average
|
||||
fix_modify AtC mesh create 1 1 1 box p p p :pre
|
||||
|
||||
# change from default lagrangian map to eulerian
|
||||
# refreshed every 100 steps
|
||||
fix_modify AtC atom_element_map eulerian 100 :pre
|
||||
|
||||
# start with no field defined
|
||||
# add mass density, potential energy density, stress and temperature
|
||||
|
||||
# start with no field defined
|
||||
# add mass density, potential energy density, stress and temperature
|
||||
fix_modify AtC fields add density energy stress temperature :pre
|
||||
|
||||
# create an output stream for nodal fields
|
||||
# filename output_frequency
|
||||
# create an output stream for nodal fields
|
||||
# filename output_frequency
|
||||
fix_modify AtC output nvtFE 100 text :pre
|
||||
|
||||
run 1000 :pre
|
||||
|
||||
the mesh's linear interpolation functions can be used as the localization function
|
||||
by using the field option:
|
||||
|
||||
fix AtC internal atc field
|
||||
|
||||
fix_modify AtC mesh create 1 1 1 box p p p
|
||||
the mesh's linear interpolation functions can be used as the localization function
|
||||
by using the field option:
|
||||
|
||||
...
|
||||
fix AtC internal atc field
|
||||
|
||||
Note coupling and post-processing can be combined in the same simulations using separate fixes.
|
||||
fix_modify AtC mesh create 1 1 1 box p p p
|
||||
|
||||
...
|
||||
|
||||
Note coupling and post-processing can be combined in the same simulations using separate fixes.
|
||||
|
||||
:line
|
||||
|
||||
@ -108,17 +108,17 @@ No information about this fix is written to "binary restart files"_restart.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc.
|
||||
Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc.
|
||||
|
||||
Currently,
|
||||
- the coupling is restricted to thermal physics
|
||||
Currently,
|
||||
- the coupling is restricted to thermal physics
|
||||
- the FE computations are done in serial on each processor. :ul
|
||||
|
||||
[Related commands:]
|
||||
|
||||
After specifying this fix in your input script, several other "fix_modify"_fix_modify.html commands are used to setup the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.
|
||||
|
||||
fix_modify commands for setup:
|
||||
fix_modify commands for setup:
|
||||
|
||||
"fix_modify AtC mesh create"_USER/atc/man_mesh_create.html
|
||||
"fix_modify AtC mesh quadrature"_USER/atc/man_mesh_quadrature.html
|
||||
@ -149,7 +149,7 @@ fix_modify commands for boundary and initial conditions:
|
||||
"fix_modify AtC source"_USER/atc/man_source.html
|
||||
"fix_modify AtC remove_source"_USER/atc/man_remove_source.html :ul
|
||||
|
||||
fix_modify commands for control and filtering:
|
||||
fix_modify commands for control and filtering:
|
||||
|
||||
"fix_modify AtC control"_USER/atc/man_control.html
|
||||
"fix_modify AtC control thermal"_USER/atc/man_control_thermal.html
|
||||
@ -165,7 +165,7 @@ fix_modify commands for control and filtering:
|
||||
"fix_modify AtC extrinsic exchange"_USER/atc/man_extrinsic_exchange.html
|
||||
"fix_modify AtC poisson_solver"_USER/atc/man_poisson_solver.html :ul
|
||||
|
||||
fix_modify commands for output:
|
||||
fix_modify commands for output:
|
||||
|
||||
"fix_modify AtC output"_USER/atc/man_output.html
|
||||
"fix_modify AtC output nodeset"_USER/atc/man_output_nodeset.html
|
||||
@ -176,7 +176,7 @@ fix_modify commands for output:
|
||||
"fix_modify AtC write_restart"_USER/atc/man_write_restart.html
|
||||
"fix_modify AtC read_restart"_USER/atc/man_read_restart.html :ul
|
||||
|
||||
fix_modify commands for post-processing:
|
||||
fix_modify commands for post-processing:
|
||||
|
||||
"fix_modify AtC kernel"_USER/atc/man_hardy_kernel.html
|
||||
"fix_modify AtC fields"_USER/atc/man_hardy_fields.html
|
||||
@ -188,7 +188,7 @@ fix_modify commands for post-processing:
|
||||
"fix_modify AtC sample_frequency"_USER/atc/man_sample_frequency.html
|
||||
"fix_modify AtC set"_USER/atc/man_set.html :ul
|
||||
|
||||
miscellaneous fix_modify commands:
|
||||
miscellaneous fix_modify commands:
|
||||
|
||||
"fix_modify AtC atom_element_map"_USER/atc/man_atom_element_map.html
|
||||
"fix_modify AtC atom_weight"_USER/atc/man_atom_weight.html
|
||||
@ -210,35 +210,35 @@ miscellaneous fix_modify commands:
|
||||
"fix_modify AtC remove_species"_USER/atc/man_remove_species.html
|
||||
"fix_modify AtC remove_molecule"_USER/atc/man_remove_molecule.html :ul
|
||||
|
||||
Note: a set of example input files with the attendant material files are included with this package
|
||||
Note: a set of example input files with the attendant material files are included with this package
|
||||
|
||||
[Default:]
|
||||
None
|
||||
None
|
||||
|
||||
:line
|
||||
|
||||
For detailed exposition of the theory and algorithms please see:
|
||||
|
||||
:link(Wagner)
|
||||
[(Wagner)] Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, "An atomistic-to-continuum coupling method for heat transfer in solids." Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351.
|
||||
[(Wagner)] Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, "An atomistic-to-continuum coupling method for heat transfer in solids." Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351.
|
||||
|
||||
:link(Zimmeman2004)
|
||||
[(Zimmerman2004)] Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319.
|
||||
[(Zimmerman2004)] Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319.
|
||||
|
||||
:link(Zimmerman2010)
|
||||
[(Zimmerman2010)] Zimmerman, JA; Jones, RE; Templeton, JA, "A material frame approach for evaluating continuum variables in atomistic simulations." Journal of Computational Physics (2010), 229:2364.
|
||||
[(Zimmerman2010)] Zimmerman, JA; Jones, RE; Templeton, JA, "A material frame approach for evaluating continuum variables in atomistic simulations." Journal of Computational Physics (2010), 229:2364.
|
||||
|
||||
:link(Templeton2010)
|
||||
[(Templeton2010)] Templeton, JA; Jones, RE; Wagner, GJ, "Application of a field-based method to spatially varying thermal transport problems in molecular dynamics." Modelling and Simulation in Materials Science and Engineering (2010), 18:085007.
|
||||
[(Templeton2010)] Templeton, JA; Jones, RE; Wagner, GJ, "Application of a field-based method to spatially varying thermal transport problems in molecular dynamics." Modelling and Simulation in Materials Science and Engineering (2010), 18:085007.
|
||||
|
||||
:link(Jones)
|
||||
[(Jones)] Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, "Electron transport enhanced molecular dynamics for metals and semi-metals." International Journal for Numerical Methods in Engineering (2010), 83:940.
|
||||
[(Jones)] Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, "Electron transport enhanced molecular dynamics for metals and semi-metals." International Journal for Numerical Methods in Engineering (2010), 83:940.
|
||||
|
||||
:link(Templeton2011)
|
||||
[(Templeton2011)] Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, "A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling." Journal of Chemical Theory and Computation (2011), 7:1736.
|
||||
[(Templeton2011)] Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, "A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling." Journal of Chemical Theory and Computation (2011), 7:1736.
|
||||
|
||||
:link(Mandadapu)
|
||||
[(Mandadapu)] Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization as a field variable from molecular dynamics simulations." Journal of Chemical Physics (2013), 139:054115.
|
||||
[(Mandadapu)] Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization as a field variable from molecular dynamics simulations." Journal of Chemical Physics (2013), 139:054115.
|
||||
|
||||
Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes " The finite element method ", Dover 2003, for the basics of FE simulation.
|
||||
|
||||
|
||||
@ -35,7 +35,7 @@ keyword = {types} or {mu} or {ke} or {semi-grand} or {region} :l
|
||||
[Examples:]
|
||||
|
||||
fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
|
||||
fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
|
||||
fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
|
||||
fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 0.0 4.3 -5.0 :pre
|
||||
|
||||
[Description:]
|
||||
@ -78,15 +78,15 @@ atoms remains constant. Whereas in the semi-grand canonical ensemble,
|
||||
the composition of the system can change. Note that when using
|
||||
{semi-grand}, atoms in the fix group whose type is not listed
|
||||
in the {types} keyword are ineligible for attempted
|
||||
conversion. An attempt is made to switch
|
||||
the selected atom (if eligible) to one of the other listed types
|
||||
conversion. An attempt is made to switch
|
||||
the selected atom (if eligible) to one of the other listed types
|
||||
with equal probability. Acceptance of each attempt depends upon the Metropolis criterion.
|
||||
|
||||
The {mu} keyword allows users to specify chemical
|
||||
potentials. This is required and allowed only when using {semi-grand}.
|
||||
All chemical potentials are absolute, so there is one for
|
||||
each swap type listed following the {types} keyword.
|
||||
In semi-grand canonical ensemble simulations the chemical composition
|
||||
potentials. This is required and allowed only when using {semi-grand}.
|
||||
All chemical potentials are absolute, so there is one for
|
||||
each swap type listed following the {types} keyword.
|
||||
In semi-grand canonical ensemble simulations the chemical composition
|
||||
of the system is controlled by the difference in these values. So
|
||||
shifting all values by a constant amount will have no effect
|
||||
on the simulation.
|
||||
@ -103,17 +103,17 @@ LAMMPS will warn you if any of the atoms eligible for swapping have a
|
||||
non-zero molecule ID, but does not check for this at the time of
|
||||
swapping.
|
||||
|
||||
If not using {semi-grand} this fix checks to ensure all atoms of the
|
||||
given types have the same atomic charge. LAMMPS doesn't enforce this
|
||||
in general, but it is needed for this fix to simplify the
|
||||
swapping procedure. Successful swaps will swap the atom type and charge
|
||||
If not using {semi-grand} this fix checks to ensure all atoms of the
|
||||
given types have the same atomic charge. LAMMPS doesn't enforce this
|
||||
in general, but it is needed for this fix to simplify the
|
||||
swapping procedure. Successful swaps will swap the atom type and charge
|
||||
of the swapped atoms. Conversely, when using {semi-grand}, it is assumed that all the atom
|
||||
types involved in switches have the same charge. Otherwise, charge
|
||||
would not be conserved. As a consequence, no checks on atomic charges are
|
||||
performed, and successful switches update the atom type but not the
|
||||
atom charge. While it is possible to use {semi-grand} with groups of
|
||||
atom charge. While it is possible to use {semi-grand} with groups of
|
||||
atoms that have different charges, these charges will not be changed when the
|
||||
atom types change.
|
||||
atom types change.
|
||||
|
||||
Since this fix computes total potential energies before and after
|
||||
proposed swaps, so even complicated potential energy calculations are
|
||||
@ -123,15 +123,15 @@ OK, including the following:
|
||||
many body pair styles
|
||||
hybrid pair styles
|
||||
eam pair styles
|
||||
triclinic systems
|
||||
triclinic systems
|
||||
need to include potential energy contributions from other fixes :ul
|
||||
|
||||
Some fixes have an associated potential energy. Examples of such fixes
|
||||
include: "efield"_fix_efield.html, "gravity"_fix_gravity.html,
|
||||
"addforce"_fix_addforce.html, "langevin"_fix_langevin.html,
|
||||
"restrain"_fix_restrain.html, "temp/berendsen"_fix_temp_berendsen.html,
|
||||
"temp/rescale"_fix_temp_rescale.html, and "wall fixes"_fix_wall.html.
|
||||
For that energy to be included in the total potential energy of the
|
||||
include: "efield"_fix_efield.html, "gravity"_fix_gravity.html,
|
||||
"addforce"_fix_addforce.html, "langevin"_fix_langevin.html,
|
||||
"restrain"_fix_restrain.html, "temp/berendsen"_fix_temp_berendsen.html,
|
||||
"temp/rescale"_fix_temp_rescale.html, and "wall fixes"_fix_wall.html.
|
||||
For that energy to be included in the total potential energy of the
|
||||
system (the quantity used when performing GCMC moves),
|
||||
you MUST enable the "fix_modify"_fix_modify.html {energy} option for
|
||||
that fix. The doc pages for individual "fix"_fix.html commands
|
||||
@ -170,18 +170,18 @@ LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix nvt"_fix_nh.html, "neighbor"_neighbor.html,
|
||||
"fix nvt"_fix_nh.html, "neighbor"_neighbor.html,
|
||||
"fix deposit"_fix_deposit.html, "fix evaporate"_fix_evaporate.html,
|
||||
"delete_atoms"_delete_atoms.html, "fix gcmc"_fix_gcmc.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The option defaults are ke = yes, semi-grand = no, mu = 0.0 for
|
||||
The option defaults are ke = yes, semi-grand = no, mu = 0.0 for
|
||||
all atom types.
|
||||
|
||||
:line
|
||||
|
||||
:link(Sadigh)
|
||||
[(Sadigh)] B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and
|
||||
[(Sadigh)] B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and
|
||||
L Zepeda-Ruiz, Phys. Rev. B, 85, 184203 (2012).
|
||||
|
||||
|
||||
@ -79,7 +79,7 @@ equivalent, since the "compute stress/atom"_compute_stress_atom.html
|
||||
command creates a per-atom array with 6 columns:
|
||||
|
||||
compute my_stress all stress/atom NULL
|
||||
fix 1 all ave/atom 10 20 1000 c_my_stress\[*\]
|
||||
fix 1 all ave/atom 10 20 1000 c_my_stress\[*\]
|
||||
fix 1 all ave/atom 10 20 1000 c_my_stress\[1\] c_my_stress\[1\] &
|
||||
c_my_stress\[3\] c_my_stress\[4\] &
|
||||
c_my_stress\[5\] c_my_stress\[6\] :pre
|
||||
@ -93,8 +93,8 @@ that are a multiple of {Nfreq}. The average is over {Nrepeat}
|
||||
quantities, computed in the preceding portion of the simulation every
|
||||
{Nevery} timesteps. {Nfreq} must be a multiple of {Nevery} and
|
||||
{Nevery} must be non-zero even if {Nrepeat} is 1. Also, the timesteps
|
||||
contributing to the average value cannot overlap,
|
||||
i.e. Nrepeat*Nevery can not exceed Nfreq.
|
||||
contributing to the average value cannot overlap,
|
||||
i.e. Nrepeat*Nevery can not exceed Nfreq.
|
||||
|
||||
For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
|
||||
timesteps 90,92,94,96,98,100 will be used to compute the final average
|
||||
|
||||
@ -77,7 +77,7 @@ fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile
|
||||
|
||||
could be replaced by:
|
||||
|
||||
compute cc1 flow chunk/atom bin/1d y 0.0 1.0
|
||||
compute cc1 flow chunk/atom bin/1d y 0.0 1.0
|
||||
fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
@ -176,7 +176,7 @@ output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html
|
||||
or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for
|
||||
these commands which give the IDs of these computes. Users can also
|
||||
write code for their own compute styles and "add them to
|
||||
LAMMPS"_Section_modify.html.
|
||||
LAMMPS"_Section_modify.html.
|
||||
|
||||
If a value begins with "f_", a fix ID must follow which has been
|
||||
previously defined in the input script. If no bracketed term is
|
||||
@ -184,7 +184,7 @@ appended, the global scalar calculated by the fix is used. If a
|
||||
bracketed term is appended, the Ith element of the global vector
|
||||
calculated by the fix is used. See the discussion above for how I can
|
||||
be specified with a wildcard asterisk to effectively specify multiple
|
||||
values.
|
||||
values.
|
||||
|
||||
Note that some fixes only produce their values on certain timesteps,
|
||||
which must be compatible with {Nevery}, else an error will result.
|
||||
|
||||
@ -61,7 +61,7 @@ keyword = {mode} or {file} or {ave} or {start} or {beyond} or {overwrite} or {ti
|
||||
fix 1 all ave/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running
|
||||
fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press\[2\] c_thermo_press\[3\] title1 "My output values"
|
||||
fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press\[*\]
|
||||
fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra
|
||||
fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra
|
||||
fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD\[1\] c_XRD\[2\] :pre
|
||||
|
||||
[Description:]
|
||||
@ -149,8 +149,8 @@ multiple of {Nfreq}. It is averaged over {Nrepeat} histograms,
|
||||
computed in the preceding portion of the simulation every {Nevery}
|
||||
timesteps. {Nfreq} must be a multiple of {Nevery} and {Nevery} must
|
||||
be non-zero even if {Nrepeat} is 1. Also, the timesteps
|
||||
contributing to the histogram value cannot overlap,
|
||||
i.e. Nrepeat*Nevery can not exceed Nfreq.
|
||||
contributing to the histogram value cannot overlap,
|
||||
i.e. Nrepeat*Nevery can not exceed Nfreq.
|
||||
|
||||
For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then input values
|
||||
on timesteps 90,92,94,96,98,100 will be used to compute the final
|
||||
|
||||
@ -137,8 +137,8 @@ that are a mlutiple of {Nfreq}. The average is over {Nrepeat}
|
||||
quantities, computed in the preceding portion of the simulation every
|
||||
{Nevery} timesteps. {Nfreq} must be a multiple of {Nevery} and
|
||||
{Nevery} must be non-zero even if {Nrepeat} is 1. Also, the timesteps
|
||||
contributing to the average value cannot overlap,
|
||||
i.e. Nrepeat*Nevery can not exceed Nfreq.
|
||||
contributing to the average value cannot overlap,
|
||||
i.e. Nrepeat*Nevery can not exceed Nfreq.
|
||||
|
||||
For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
|
||||
timesteps 90,92,94,96,98,100 will be used to compute the final average
|
||||
|
||||
@ -330,7 +330,7 @@ per processor. Note that the 4 sub-domains share vertices, so there
|
||||
will be duplicate nodes in the list.
|
||||
|
||||
The "SQUARES" section lists the node IDs of the 4 vertices in a
|
||||
rectangle for each processor (1 to 4).
|
||||
rectangle for each processor (1 to 4).
|
||||
|
||||
For a 3d problem, the syntax is similar with 8 vertices listed for
|
||||
each processor, instead of 4, and "SQUARES" replaced by "CUBES".
|
||||
|
||||
@ -56,7 +56,7 @@ possible bonds to break. Every atom checks its list of possible bonds
|
||||
to break and labels the longest such bond as its "sole" bond to break.
|
||||
After this is done, if atom I is bonded to atom J in its sole bond,
|
||||
and atom J is bonded to atom I in its sole bond, then the I,J bond is
|
||||
"eligible" to be broken.
|
||||
"eligible" to be broken.
|
||||
|
||||
Note that these rules mean an atom will only be part of at most one
|
||||
broken bond on a given timestep. It also means that if atom I chooses
|
||||
@ -112,7 +112,7 @@ resulting from broken bonds (and angles, dihedrals, impropers).
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
||||
are relevant to this fix.
|
||||
are relevant to this fix.
|
||||
|
||||
This fix computes two statistics which it stores in a global vector of
|
||||
length 2, which can be accessed by various "output
|
||||
|
||||
@ -208,7 +208,7 @@ created bonds (and angles, dihedrals, impropers).
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
||||
are relevant to this fix.
|
||||
are relevant to this fix.
|
||||
|
||||
This fix computes two statistics which it stores in a global vector of
|
||||
length 2, which can be accessed by various "output
|
||||
|
||||
@ -15,13 +15,13 @@ fix ID group-ID box/relax keyword value ... :pre
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
box/relax = style name of this fix command :l
|
||||
one or more keyword value pairs may be appended
|
||||
keyword = {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {nreset} or {vmax} or {dilate} or {scaleyz} or {scalexz} or {scalexy} or {fixedpoint}
|
||||
keyword = {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {nreset} or {vmax} or {dilate} or {scaleyz} or {scalexz} or {scalexy} or {fixedpoint}
|
||||
{iso} or {aniso} or {tri} value = Ptarget = desired pressure (pressure units)
|
||||
{x} or {y} or {z} or {xy} or {yz} or {xz} value = Ptarget = desired pressure (pressure units)
|
||||
{couple} = {none} or {xyz} or {xy} or {yz} or {xz}
|
||||
{nreset} value = reset reference cell every this many minimizer iterations
|
||||
{vmax} value = fraction = max allowed volume change in one iteration
|
||||
{dilate} value = {all} or {partial}
|
||||
{dilate} value = {all} or {partial}
|
||||
{scaleyz} value = {yes} or {no} = scale yz with lz
|
||||
{scalexz} value = {yes} or {no} = scale xz with lz
|
||||
{scalexy} value = {yes} or {no} = scale xy with ly
|
||||
@ -99,8 +99,8 @@ chosen will not move during the simulation. For example, if the lower
|
||||
periodic boundaries pass through (0,0,0), and this point is provided
|
||||
to {fixedpoint}, then the lower periodic boundaries will remain at
|
||||
(0,0,0), while the upper periodic boundaries will move twice as
|
||||
far. In all cases, the particle positions at each iteration are
|
||||
unaffected by the chosen value, except that all particles are
|
||||
far. In all cases, the particle positions at each iteration are
|
||||
unaffected by the chosen value, except that all particles are
|
||||
displaced by the same amount, different on each iteration.
|
||||
|
||||
NOTE: Appling an external pressure to tilt dimensions {xy}, {xz}, {yz}
|
||||
@ -178,9 +178,9 @@ these 7 keywords:
|
||||
x Ptarget
|
||||
y Ptarget
|
||||
z Ptarget
|
||||
xy 0.0
|
||||
yz 0.0
|
||||
xz 0.0
|
||||
xy 0.0
|
||||
yz 0.0
|
||||
xz 0.0
|
||||
couple none :pre
|
||||
|
||||
:line
|
||||
@ -201,7 +201,7 @@ With this fix, the potential energy used by the minimizer is augmented
|
||||
by an additional energy provided by the fix. The overall objective
|
||||
function then is:
|
||||
|
||||
:c,image(Eqs/fix_box_relax1.jpg)
|
||||
:c,image(Eqs/fix_box_relax1.jpg)
|
||||
|
||||
where {U} is the system potential energy, {P}_t is the desired
|
||||
hydrostatic pressure, {V} and {V}_0 are the system and reference
|
||||
@ -211,14 +211,14 @@ Taking derivatives of {E} w.r.t. the box dimensions, and setting these
|
||||
to zero, we find that at the minimum of the objective function, the
|
||||
global system stress tensor [P] will satisfy the relation:
|
||||
|
||||
:c,image(Eqs/fix_box_relax2.jpg)
|
||||
:c,image(Eqs/fix_box_relax2.jpg)
|
||||
|
||||
where [I] is the identity matrix, [h]_0 is the box dimension tensor of
|
||||
the reference cell, and [h]_0{d} is the diagonal part of
|
||||
[h]_0. [S]_{t} is a symmetric stress tensor that is chosen by LAMMPS
|
||||
so that the upper-triangular components of [P] equal the stress tensor
|
||||
specified by the user.
|
||||
|
||||
|
||||
This equation only applies when the box dimensions are equal to those
|
||||
of the reference dimensions. If this is not the case, then the
|
||||
converged stress tensor will not equal that specified by the user. We
|
||||
|
||||
@ -33,7 +33,7 @@ cvar = name of control variable :l
|
||||
|
||||
|
||||
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 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
|
||||
|
||||
[Description:]
|
||||
|
||||
@ -57,9 +57,9 @@ minimization"_minimize.html.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
[Related commands:]
|
||||
|
||||
"fix spring"_fix_spring.html, "fix spring/self"_fix_spring_self.html,
|
||||
"fix spring"_fix_spring.html, "fix spring/self"_fix_spring_self.html,
|
||||
"fix spring/rg"_fix_spring_rg.html, "fix smd"_fix_smd.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
@ -61,12 +61,12 @@ Velocities: \begin\{equation\} V' = \frac \{M\, V + m\, v\} \{M'\}
|
||||
Forces: \begin\{equation\} F' = F + f \end\{equation\}
|
||||
\begin\{equation\} f' = \frac \{ M\, f - m\, F\} \{M'\}
|
||||
\end\{equation\}
|
||||
|
||||
|
||||
This transform conserves the total kinetic energy
|
||||
\begin\{equation\} \frac 1 2 \, (M\, V^2\ + m\, v^2)
|
||||
\begin\{equation\} \frac 1 2 \, (M\, V^2\ + m\, v^2)
|
||||
= \frac 1 2 \, (M'\, V'^2\ + m'\, v'^2) \end\{equation\}
|
||||
and the virial defined with absolute positions
|
||||
\begin\{equation\} X\, F + x\, f = X'\, F' + x'\, f' \end\{equation\}
|
||||
\begin\{equation\} X\, F + x\, f = X'\, F' + x'\, f' \end\{equation\}
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -63,7 +63,7 @@ If the {region} keyword is used, the atom must also be in the
|
||||
specified geometric "region"_region.html in order to have force added
|
||||
to it.
|
||||
|
||||
:line
|
||||
:line
|
||||
|
||||
Adding a force or torque to atoms implies a change in their potential
|
||||
energy as they move or rotate due to the applied E-field.
|
||||
@ -108,12 +108,12 @@ due to the electric field were a spring-like F = kx, then the energy
|
||||
formula should be E = -0.5kx^2. If you don't do this correctly, the
|
||||
minimization will not converge properly.
|
||||
|
||||
:line
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html.
|
||||
files"_restart.html.
|
||||
|
||||
The "fix_modify"_fix_modify.html {energy} option is supported by this
|
||||
fix to add the potential "energy" inferred by the added force due to
|
||||
|
||||
@ -34,15 +34,15 @@ keyword = {region} or {constrain} or {com} or {hex} :l
|
||||
fix fnve all nve
|
||||
# specify regions rhot and rcold
|
||||
...
|
||||
fix fhot all ehex 1 0.15 region rhot
|
||||
fix fhot all ehex 1 0.15 region rhot
|
||||
fix fcold all ehex 1 -0.15 region rcold :pre
|
||||
|
||||
# SPC/E water, from examples/in.ehex.spce
|
||||
fix fnve all nve
|
||||
fix fnve all nve
|
||||
# specify regions rhot and rcold
|
||||
...
|
||||
fix fhot all ehex 1 0.075 region rhot constrain com
|
||||
fix fcold all ehex 1 -0.075 region rcold constrain com
|
||||
fix fcold all ehex 1 -0.075 region rcold constrain com
|
||||
fix frattle all rattle 1e-10 400 0 b 1 a 1 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
@ -36,7 +36,7 @@ possible.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
[Restrictions:]
|
||||
|
||||
This command is part of the USER-DPD package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
|
||||
@ -87,7 +87,7 @@ On each line, the 1st value is the index from 1 to N, the 2nd value is
|
||||
the internal temperature (in temperature units), the 3rd value is the
|
||||
internal energy (in energy units).
|
||||
|
||||
Note that the internal temperature and internal energy values must
|
||||
Note that the internal temperature and internal energy values must
|
||||
increase from one line to the next.
|
||||
|
||||
Note that one file can contain many sections, each with a tabulated
|
||||
@ -96,7 +96,7 @@ one that matches the specified keyword.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
[Restrictions:]
|
||||
|
||||
This command is part of the USER-DPD package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
|
||||
@ -26,37 +26,37 @@ fix 1 all eos/table/rx linear eos.table 10000 KEYWORD thermo.table :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Fix {eos/table/rx} applies a tabulated mesoparticle equation
|
||||
of state to relate the concentration-dependent particle internal
|
||||
energy (u_i) to the particle internal temperature (dpdTheta_i).
|
||||
Fix {eos/table/rx} applies a tabulated mesoparticle equation
|
||||
of state to relate the concentration-dependent particle internal
|
||||
energy (u_i) to the particle internal temperature (dpdTheta_i).
|
||||
|
||||
The concentration-dependent particle internal energy (u_i) is
|
||||
The concentration-dependent particle internal energy (u_i) is
|
||||
computed according to the following relation:
|
||||
|
||||
:c,image(Eqs/fix_eos_table_rx.jpg)
|
||||
|
||||
where {m} is the number of species, {c_i,j} is the concentration of
|
||||
where {m} is the number of species, {c_i,j} is the concentration of
|
||||
species {j} in particle {i}, {u_j} is the internal energy of species j,
|
||||
{DeltaH_f,j} is the heat of formation of species {j}, N is the number of
|
||||
molecules represented by the coarse-grained particle, kb is the
|
||||
{DeltaH_f,j} is the heat of formation of species {j}, N is the number of
|
||||
molecules represented by the coarse-grained particle, kb is the
|
||||
Boltzmann constant, and T is the temperature of the system.
|
||||
|
||||
Fix {eos/table/rx} creates interpolation tables of length {N} from {m}
|
||||
internal energy values of each species {u_j} listed in a file as a
|
||||
function of internal temperature. During a simulation, these tables
|
||||
are used to interpolate internal energy or temperature values as needed.
|
||||
The interpolation is done with the {linear} style. For the {linear} style,
|
||||
the internal temperature is used to find 2 surrounding table values from
|
||||
internal energy values of each species {u_j} listed in a file as a
|
||||
function of internal temperature. During a simulation, these tables
|
||||
are used to interpolate internal energy or temperature values as needed.
|
||||
The interpolation is done with the {linear} style. For the {linear} style,
|
||||
the internal temperature is used to find 2 surrounding table values from
|
||||
which an internal energy is computed by linear interpolation. A secant
|
||||
solver is used to determine the internal temperature from the internal energy.
|
||||
|
||||
The first filename specifies a file containing tabulated internal
|
||||
temperature and {m} internal energy values for each species {u_j}.
|
||||
The keyword specifies a section of the file. The format of this
|
||||
The first filename specifies a file containing tabulated internal
|
||||
temperature and {m} internal energy values for each species {u_j}.
|
||||
The keyword specifies a section of the file. The format of this
|
||||
file is described below.
|
||||
|
||||
The second filename specifies a file containing heat of formation
|
||||
{DeltaH_f,j} for each species.
|
||||
{DeltaH_f,j} for each species.
|
||||
|
||||
:line
|
||||
|
||||
@ -77,22 +77,22 @@ A section begins with a non-blank line whose 1st character is not a
|
||||
"#"; blank lines or lines starting with "#" can be used as comments
|
||||
between sections. The first line begins with a keyword which
|
||||
identifies the section. The line can contain additional text, but the
|
||||
initial text must match the argument specified in the fix command.
|
||||
initial text must match the argument specified in the fix command.
|
||||
|
||||
The next line lists the number of table entries and the species names
|
||||
that correspond with all the species listed in the reaction equations
|
||||
through the {fix rx} command.
|
||||
that correspond with all the species listed in the reaction equations
|
||||
through the {fix rx} command.
|
||||
The parameter "N" is required and its value is the number of table
|
||||
entries that follow. Let Nfile = "N" in the tabulated file.
|
||||
What LAMMPS does is a preliminary interpolation by creating splines
|
||||
using the Nfile tabulated values as nodal points.
|
||||
entries that follow. Let Nfile = "N" in the tabulated file.
|
||||
What LAMMPS does is a preliminary interpolation by creating splines
|
||||
using the Nfile tabulated values as nodal points.
|
||||
|
||||
Following a blank line, the next N lines list the tabulated values.
|
||||
On each line, the 1st value is the index from 1 to N, the 2nd value is
|
||||
the internal temperature (in temperature units), the 3rd value until
|
||||
the {m+3} value are the internal energies of the m species (in energy units).
|
||||
|
||||
Note that all internal temperature and internal energy values must
|
||||
Note that all internal temperature and internal energy values must
|
||||
increase from one line to the next.
|
||||
|
||||
Note that one file can contain many sections, each with a tabulated
|
||||
@ -107,18 +107,18 @@ parenthesized comments):
|
||||
# HEAT OF FORMATION TABLE (one or more comment or blank lines) :pre
|
||||
(blank)
|
||||
h2 0.00 (species name, heat of formation)
|
||||
no2 0.34
|
||||
n2 0.00
|
||||
no2 0.34
|
||||
n2 0.00
|
||||
...
|
||||
no 0.93 :pre
|
||||
|
||||
Note that the species can be listed in any order. The tag that is
|
||||
Note that the species can be listed in any order. The tag that is
|
||||
used as the species name must correspond with the tags used to define
|
||||
the reactions with the "fix rx"_fix_rx.html command.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
[Restrictions:]
|
||||
|
||||
This command is part of the USER-DPD package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
|
||||
@ -120,7 +120,7 @@ insure this energy setting is used appropriately in a minimization.
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html.
|
||||
files"_restart.html.
|
||||
|
||||
The "fix_modify"_fix_modify.html {energy} option is supported by this
|
||||
fix to add the potential "energy" set by the external driver to the
|
||||
@ -140,7 +140,7 @@ No parameter of this fix can be used with the {start/stop} keywords of
|
||||
the "run"_run.html command.
|
||||
|
||||
The forces due to this fix are imposed during an energy minimization,
|
||||
invoked by the "minimize"_minimize.html command.
|
||||
invoked by the "minimize"_minimize.html command.
|
||||
|
||||
NOTE: If you want the fictitious potential energy associated with the
|
||||
added forces to be included in the total potential energy of the
|
||||
|
||||
@ -26,7 +26,7 @@ keyword = {energy} :l
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix GD fluid flow/gauss 1 0 0
|
||||
fix GD fluid flow/gauss 1 0 0
|
||||
fix GD fluid flow/gauss 1 1 1 energy yes :pre
|
||||
|
||||
[Description:]
|
||||
@ -111,8 +111,8 @@ output"_thermo_style.html.
|
||||
|
||||
This fix computes a global scalar and a global 3-vector of forces,
|
||||
which can be accessed by various "output
|
||||
commands"_Section_howto.html#howto_15. The scalar is the negative of the
|
||||
work done on the system, see above discussion. The vector is the total force
|
||||
commands"_Section_howto.html#howto_15. The scalar is the negative of the
|
||||
work done on the system, see above discussion. The vector is the total force
|
||||
that this fix applied to the group of atoms on the current timestep.
|
||||
The scalar and vector values calculated by this fix are "extensive".
|
||||
|
||||
|
||||
@ -29,15 +29,15 @@ keyword = {mol}, {region}, {maxangle}, {pressure}, {fugacity_coeff}, {full_energ
|
||||
{shake} value = fix-ID
|
||||
fix-ID = ID of "fix shake"_fix_shake.html command
|
||||
{region} value = region-ID
|
||||
region-ID = ID of region where MC moves are allowed
|
||||
{maxangle} value = maximum molecular rotation angle (degrees)
|
||||
region-ID = ID of region where MC moves are allowed
|
||||
{maxangle} value = maximum molecular rotation angle (degrees)
|
||||
{pressure} value = pressure of the gas reservoir (pressure units)
|
||||
{fugacity_coeff} value = fugacity coefficient of the gas reservoir (unitless)
|
||||
{fugacity_coeff} value = fugacity coefficient of the gas reservoir (unitless)
|
||||
{full_energy} = compute the entire system energy when performing MC moves
|
||||
{charge} value = charge of inserted atoms (charge units)
|
||||
{group} value = group-ID
|
||||
group-ID = group-ID for inserted atoms (string)
|
||||
{grouptype} values = type group-ID
|
||||
{grouptype} values = type group-ID
|
||||
type = atom type (int)
|
||||
group-ID = group-ID for inserted atoms (string)
|
||||
{intra_energy} value = intramolecular energy (energy units)
|
||||
@ -66,11 +66,11 @@ or deletions) of gas atoms or molecules of
|
||||
the given type between the simulation cell and the imaginary
|
||||
reservoir. It also attempts a number of Monte Carlo
|
||||
moves (translations and molecule rotations) of gas of the given type
|
||||
within the simulation cell or region. The average number of
|
||||
within the simulation cell or region. The average number of
|
||||
attempted GCMC exchanges is X. The average number of attempted MC moves is M.
|
||||
M should typically be chosen to be
|
||||
approximately equal to the expected number of gas atoms or molecules
|
||||
of the given type within the simulation cell or region,
|
||||
of the given type within the simulation cell or region,
|
||||
which will result in roughly one
|
||||
MC translation per atom or molecule per MC cycle.
|
||||
|
||||
@ -85,9 +85,9 @@ All inserted particles are always assigned to two groups: the default group
|
||||
be "all"). In addition, particles are also added to any groups specified
|
||||
by the {group} and {grouptype} keywords.
|
||||
If inserted particles are individual atoms, they are
|
||||
assigned the atom type given by the type argument. If they are molecules,
|
||||
the type argument has no effect and must be set to zero. Instead,
|
||||
the type of each atom in the inserted molecule is specified
|
||||
assigned the atom type given by the type argument. If they are molecules,
|
||||
the type argument has no effect and must be set to zero. Instead,
|
||||
the type of each atom in the inserted molecule is specified
|
||||
in the file read by the "molecule"_molecule.html command.
|
||||
|
||||
This fix cannot be used to perform MC insertions of gas atoms or
|
||||
@ -100,20 +100,20 @@ smaller-than-usual timestep size may be needed when running such a
|
||||
hybrid simulation, especially if the inserted molecules are not well
|
||||
equilibrated.
|
||||
|
||||
This command may optionally use the {region} keyword to define an
|
||||
exchange and move volume. The specified region must have been
|
||||
previously defined with a "region"_region.html command. It must be
|
||||
defined with side = {in}. Insertion attempts occur only within the
|
||||
specified region. For non-rectangular regions, random trial
|
||||
This command may optionally use the {region} keyword to define an
|
||||
exchange and move volume. The specified region must have been
|
||||
previously defined with a "region"_region.html command. It must be
|
||||
defined with side = {in}. Insertion attempts occur only within the
|
||||
specified region. For non-rectangular regions, random trial
|
||||
points are generated within the rectangular bounding box until a point is found
|
||||
that lies inside the region. If no valid point is generated after 1000 trials,
|
||||
no insertion is performed, but it is counted as an attempted insertion.
|
||||
Move and deletion attempt candidates are selected
|
||||
Move and deletion attempt candidates are selected
|
||||
from gas atoms or molecules within the region. If there are no candidates,
|
||||
no move or deletion is performed, but it is counted as an attempt move
|
||||
or deletion. If an attempted move places the atom or molecule center-of-mass outside
|
||||
the specified region, a new attempted move is generated. This process is repeated
|
||||
until the atom or molecule center-of-mass is inside the specified region.
|
||||
or deletion. If an attempted move places the atom or molecule center-of-mass outside
|
||||
the specified region, a new attempted move is generated. This process is repeated
|
||||
until the atom or molecule center-of-mass is inside the specified region.
|
||||
|
||||
If used with "fix nvt"_fix_nh.html, the temperature of the imaginary
|
||||
reservoir, T, should be set to be equivalent to the target temperature
|
||||
@ -122,7 +122,7 @@ will not be in thermal equilibrium with the simulation cell. Also,
|
||||
it is important that the temperature used by fix nvt be dynamic,
|
||||
which can be achieved as follows:
|
||||
|
||||
compute mdtemp mdatoms temp
|
||||
compute mdtemp mdatoms temp
|
||||
compute_modify mdtemp dynamic yes
|
||||
fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
|
||||
fix_modify mdnvt temp mdtemp :pre
|
||||
@ -134,7 +134,7 @@ interactions. Specifically, avoid performing so many MC translations
|
||||
per timestep that atoms can move beyond the neighbor list skin
|
||||
distance. See the "neighbor"_neighbor.html command for details.
|
||||
|
||||
When an atom or molecule is to be inserted, its
|
||||
When an atom or molecule is to be inserted, its
|
||||
coordinates are chosen at a random position within the current
|
||||
simulation cell or region, and new atom velocities are randomly chosen from
|
||||
the specified temperature distribution given by T. The effective
|
||||
@ -165,40 +165,40 @@ their bonds or angles constrained via SHAKE, use the {shake} keyword,
|
||||
specifying as its value the ID of a separate "fix
|
||||
shake"_fix_shake.html command which also appears in your input script.
|
||||
|
||||
Optionally, users may specify the maximum rotation angle for
|
||||
Optionally, users may specify the maximum rotation angle for
|
||||
molecular rotations using the {maxangle} keyword and specifying
|
||||
the angle in degrees. Rotations are performed by generating a random
|
||||
point on the unit sphere and a random rotation angle on the
|
||||
range \[0,maxangle). The molecule is then rotated by that angle about an
|
||||
axis passing through the molecule center of mass. The axis is parallel
|
||||
to the unit vector defined by the point on the unit sphere.
|
||||
axis passing through the molecule center of mass. The axis is parallel
|
||||
to the unit vector defined by the point on the unit sphere.
|
||||
The same procedure is used for randomly rotating molecules when they
|
||||
are inserted, except that the maximum angle is 360 degrees.
|
||||
|
||||
Note that fix GCMC does not use configurational bias
|
||||
MC or any other kind of sampling of intramolecular degrees of freedom.
|
||||
Inserted molecules can have different orientations, but they will all
|
||||
have the same intramolecular configuration,
|
||||
which was specified in the molecule command input.
|
||||
Note that fix GCMC does not use configurational bias
|
||||
MC or any other kind of sampling of intramolecular degrees of freedom.
|
||||
Inserted molecules can have different orientations, but they will all
|
||||
have the same intramolecular configuration,
|
||||
which was specified in the molecule command input.
|
||||
|
||||
For atomic gasses, inserted atoms have the specified atom type, but
|
||||
deleted atoms are any atoms that have been inserted or that belong
|
||||
to the user-specified fix group. For molecular gasses, exchanged
|
||||
molecules use the same atom types as in the template molecule
|
||||
deleted atoms are any atoms that have been inserted or that belong
|
||||
to the user-specified fix group. For molecular gasses, exchanged
|
||||
molecules use the same atom types as in the template molecule
|
||||
supplied by the user. In both cases, exchanged
|
||||
atoms/molecules are assigned to two groups: the default group "all"
|
||||
and the group specified in the fix gcmc command (which can also be
|
||||
"all").
|
||||
and the group specified in the fix gcmc command (which can also be
|
||||
"all").
|
||||
|
||||
The gas reservoir pressure can be specified using the {pressure}
|
||||
keyword, in which case the user-specified chemical potential is
|
||||
ignored. For non-ideal gas reservoirs, the user may also specify the
|
||||
The gas reservoir pressure can be specified using the {pressure}
|
||||
keyword, in which case the user-specified chemical potential is
|
||||
ignored. For non-ideal gas reservoirs, the user may also specify the
|
||||
fugacity coefficient using the {fugacity_coeff} keyword.
|
||||
|
||||
The {full_energy} option means that fix GCMC will compute the total
|
||||
potential energy of the entire simulated system. The total system
|
||||
energy before and after the proposed GCMC move is then used in the
|
||||
Metropolis criterion to determine whether or not to accept the
|
||||
Metropolis criterion to determine whether or not to accept the
|
||||
proposed GCMC move. By default, this option is off, in which case
|
||||
only partial energies are computed to determine the difference in
|
||||
energy that would be caused by the proposed GCMC move.
|
||||
@ -216,8 +216,8 @@ potential energy calculations, including the following:
|
||||
In these cases, LAMMPS will automatically apply the {full_energy}
|
||||
keyword and issue a warning message.
|
||||
|
||||
When the {mol} keyword is used, the {full_energy} option also includes
|
||||
the intramolecular energy of inserted and deleted molecules. If this
|
||||
When the {mol} keyword is used, the {full_energy} option also includes
|
||||
the intramolecular energy of inserted and deleted molecules. If this
|
||||
is not desired, the {intra_energy} keyword can be used to define an
|
||||
amount of energy that is subtracted from the final energy when a molecule
|
||||
is inserted, and added to the initial energy when a molecule is
|
||||
@ -230,30 +230,30 @@ specified temperature T. Because the relative velocity of
|
||||
all atoms in the molecule is zero, this may result in inserted molecules
|
||||
that are systematically too cold. In addition, the intramolecular potential
|
||||
energy of the inserted molecule may cause the kinetic energy
|
||||
of the molecule to quickly increase or decrease after insertion.
|
||||
of the molecule to quickly increase or decrease after insertion.
|
||||
The {tfac_insert} keyword allows the user to counteract these effects
|
||||
by changing the temperature used to assign velocities to
|
||||
by changing the temperature used to assign velocities to
|
||||
inserted atoms and molecules by a constant factor. For a
|
||||
particular application, some experimentation may be required
|
||||
to find a value of {tfac_insert} that results in inserted molecules that
|
||||
equilibrate quickly to the correct temperature.
|
||||
|
||||
Some fixes have an associated potential energy. Examples of such fixes
|
||||
include: "efield"_fix_efield.html, "gravity"_fix_gravity.html,
|
||||
"addforce"_fix_addforce.html, "langevin"_fix_langevin.html,
|
||||
"restrain"_fix_restrain.html, "temp/berendsen"_fix_temp_berendsen.html,
|
||||
"temp/rescale"_fix_temp_rescale.html, and "wall fixes"_fix_wall.html.
|
||||
For that energy to be included in the total potential energy of the
|
||||
include: "efield"_fix_efield.html, "gravity"_fix_gravity.html,
|
||||
"addforce"_fix_addforce.html, "langevin"_fix_langevin.html,
|
||||
"restrain"_fix_restrain.html, "temp/berendsen"_fix_temp_berendsen.html,
|
||||
"temp/rescale"_fix_temp_rescale.html, and "wall fixes"_fix_wall.html.
|
||||
For that energy to be included in the total potential energy of the
|
||||
system (the quantity used when performing GCMC moves),
|
||||
you MUST enable the "fix_modify"_fix_modify.html {energy} option for
|
||||
that fix. The doc pages for individual "fix"_fix.html commands
|
||||
specify if this should be done.
|
||||
|
||||
Use the {charge} option to insert atoms with a user-specified point
|
||||
charge. Note that doing so will cause the system to become non-neutral.
|
||||
LAMMPS issues a warning when using long-range electrostatics (kspace)
|
||||
with non-neutral systems. See the
|
||||
"compute group/group"_compute_group_group.html documentation for more
|
||||
Use the {charge} option to insert atoms with a user-specified point
|
||||
charge. Note that doing so will cause the system to become non-neutral.
|
||||
LAMMPS issues a warning when using long-range electrostatics (kspace)
|
||||
with non-neutral systems. See the
|
||||
"compute group/group"_compute_group_group.html documentation for more
|
||||
details about simulating non-neutral systems with kspace on.
|
||||
|
||||
Use of this fix typically will cause the number of atoms to fluctuate,
|
||||
@ -270,9 +270,9 @@ derived from LJ parameters for argon, where h* = h/sqrt(sigma^2 *
|
||||
epsilon * mass), sigma = 3.429 angstroms, epsilon/k = 121.85 K, and
|
||||
mass = 39.948 amu.
|
||||
|
||||
The {group} keyword assigns all inserted atoms to the "group"_group.html
|
||||
of the group-ID value. The {grouptype} keyword assigns all
|
||||
inserted atoms of the specified type to the "group"_group.html
|
||||
The {group} keyword assigns all inserted atoms to the "group"_group.html
|
||||
of the group-ID value. The {grouptype} keyword assigns all
|
||||
inserted atoms of the specified type to the "group"_group.html
|
||||
of the group-ID value.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
@ -294,7 +294,7 @@ values are the following global cumulative quantities:
|
||||
1 = translation attempts
|
||||
2 = translation successes
|
||||
3 = insertion attempts
|
||||
4 = insertion successes
|
||||
4 = insertion successes
|
||||
5 = deletion attempts
|
||||
6 = deletion successes
|
||||
7 = rotation attempts
|
||||
@ -315,30 +315,30 @@ LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
Do not set "neigh_modify once yes" or else this fix will never be
|
||||
called. Reneighboring is required.
|
||||
|
||||
Can be run in parallel, but aspects of the GCMC part will not scale
|
||||
Can be run in parallel, but aspects of the GCMC part will not scale
|
||||
well in parallel. Only usable for 3D simulations.
|
||||
|
||||
Note that very lengthy simulations involving insertions/deletions of
|
||||
billions of gas molecules may run out of atom or molecule IDs and
|
||||
trigger an error, so it is better to run multiple shorter-duration
|
||||
trigger an error, so it is better to run multiple shorter-duration
|
||||
simulations. Likewise, very large molecules have not been tested
|
||||
and may turn out to be problematic.
|
||||
|
||||
Use of multiple fix gcmc commands in the same input script can be
|
||||
problematic if using a template molecule. The issue is that the
|
||||
Use of multiple fix gcmc commands in the same input script can be
|
||||
problematic if using a template molecule. The issue is that the
|
||||
user-referenced template molecule in the second fix gcmc command
|
||||
may no longer exist since it might have been deleted by the first
|
||||
fix gcmc command. An existing template molecule will need to be
|
||||
referenced by the user for each subsequent fix gcmc command.
|
||||
|
||||
Because molecule insertion does not work in combination with
|
||||
fix rigid, simulataneous use of fix rigid or fix rigid/small
|
||||
fix rigid, simulataneous use of fix rigid or fix rigid/small
|
||||
with this fix is not allowed.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix atom/swap"_fix_atom_swap.html,
|
||||
"fix nvt"_fix_nh.html, "neighbor"_neighbor.html,
|
||||
"fix nvt"_fix_nh.html, "neighbor"_neighbor.html,
|
||||
"fix deposit"_fix_deposit.html, "fix evaporate"_fix_evaporate.html,
|
||||
"delete_atoms"_delete_atoms.html
|
||||
|
||||
@ -351,5 +351,5 @@ listed above.
|
||||
:line
|
||||
|
||||
:link(Frenkel)
|
||||
[(Frenkel)] Frenkel and Smit, Understanding Molecular Simulation,
|
||||
[(Frenkel)] Frenkel and Smit, Understanding Molecular Simulation,
|
||||
Academic Press, London, 2002.
|
||||
|
||||
@ -126,7 +126,7 @@ sense, a restarted simulation should produce the same behavior.
|
||||
|
||||
None of the "fix_modify"_fix_modify.html options are relevant to this
|
||||
fix. No global or per-atom quantities are stored by this fix for
|
||||
access by various "output commands"_Section_howto.html#howto_15.
|
||||
access by various "output commands"_Section_howto.html#howto_15.
|
||||
|
||||
This fix can ramp its target temperature over multiple runs, using the
|
||||
{start} and {stop} keywords of the "run"_run.html command. See the
|
||||
|
||||
@ -20,7 +20,7 @@ Amatrix = file to read the drift matrix A from :l
|
||||
seed = random number seed to use for generating noise (positive integer) :l
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {noneq} or {every}
|
||||
{noneq} Cmatrix = file to read the non-equilibrium covariance matrix from
|
||||
{noneq} Cmatrix = file to read the non-equilibrium covariance matrix from
|
||||
{every} stride = apply the GLE once every time steps. Reduces the accuracy
|
||||
of the integration of the GLE, but has *no effect* on the accuracy of equilibrium
|
||||
sampling. It might change sampling properties when used together with {noneq}. :pre
|
||||
@ -35,13 +35,13 @@ fix 1 all gle 6 300 300 31415 qt-300k.A noneq qt-300k.C :pre
|
||||
|
||||
Apply a Generalized Langevin Equation (GLE) thermostat as described
|
||||
in "(Ceriotti)"_#Ceriotti. The formalism allows one to obtain a number
|
||||
of different effects ranging from efficient sampling of all
|
||||
vibrational modes in the system to inexpensive (approximate)
|
||||
modelling of nuclear quantum effects. Contrary to
|
||||
"fix langevin"_fix_langevin.html, this fix performs both
|
||||
thermostatting and evolution of the Hamiltonian equations of motion, so it
|
||||
should not be used together with "fix nve"_fix_nve.html -- at least not
|
||||
on the same atom groups.
|
||||
of different effects ranging from efficient sampling of all
|
||||
vibrational modes in the system to inexpensive (approximate)
|
||||
modelling of nuclear quantum effects. Contrary to
|
||||
"fix langevin"_fix_langevin.html, this fix performs both
|
||||
thermostatting and evolution of the Hamiltonian equations of motion, so it
|
||||
should not be used together with "fix nve"_fix_nve.html -- at least not
|
||||
on the same atom groups.
|
||||
|
||||
Each degree of freedom in the thermostatted group is supplemented
|
||||
with Ns additional degrees of freedom s, and the equations of motion
|
||||
@ -50,30 +50,30 @@ become
|
||||
dq/dt=p/m
|
||||
d(p,s)/dt=(F,0) - A(p,s) + B dW/dt :pre
|
||||
|
||||
where F is the physical force, A is the drift matrix (that generalizes
|
||||
the friction in Langevin dynamics), B is the diffusion term and dW/dt
|
||||
where F is the physical force, A is the drift matrix (that generalizes
|
||||
the friction in Langevin dynamics), B is the diffusion term and dW/dt
|
||||
un-correlated Gaussian random forces. The A matrix couples the physical
|
||||
(q,p) dynamics with that of the additional degrees of freedom,
|
||||
and makes it possible to obtain effectively a history-dependent
|
||||
noise and friction kernel.
|
||||
(q,p) dynamics with that of the additional degrees of freedom,
|
||||
and makes it possible to obtain effectively a history-dependent
|
||||
noise and friction kernel.
|
||||
|
||||
The drift matrix should be given as an external file {Afile},
|
||||
as a (Ns+1 x Ns+1) matrix in inverse time units. Matrices that are
|
||||
optimal for a given application and the system of choice can be
|
||||
optimal for a given application and the system of choice can be
|
||||
obtained from "(GLE4MD)"_#GLE4MD.
|
||||
|
||||
Equilibrium sampling a temperature T is obtained by specifiying the
|
||||
target value as the {Tstart} and {Tstop} arguments, so that the diffusion
|
||||
Equilibrium sampling a temperature T is obtained by specifiying the
|
||||
target value as the {Tstart} and {Tstop} arguments, so that the diffusion
|
||||
matrix that gives canonical sampling for a given A is computed automatically.
|
||||
However, the GLE framework also allow for non-equilibrium sampling, that
|
||||
can be used for instance to model inexpensively zero-point energy
|
||||
effects "(Ceriotti2)"_#Ceriotti2. This is achieved specifying the
|
||||
effects "(Ceriotti2)"_#Ceriotti2. This is achieved specifying the
|
||||
{noneq} keyword followed by the name of the file that contains the
|
||||
static covariance matrix for the non-equilibrium dynamics.
|
||||
|
||||
Since integrating GLE dynamics can be costly when used together with
|
||||
simple potentials, one can use the {every} optional keyword to
|
||||
apply the Langevin terms only once every several MD steps, in a
|
||||
Since integrating GLE dynamics can be costly when used together with
|
||||
simple potentials, one can use the {every} optional keyword to
|
||||
apply the Langevin terms only once every several MD steps, in a
|
||||
multiple time-step fashion. This should be used with care when doing
|
||||
non-equilibrium sampling, but should have no effect on equilibrium
|
||||
averages when using canonical sampling.
|
||||
@ -82,15 +82,15 @@ The random number {seed} must be a positive integer. A Marsaglia random
|
||||
number generator is used. Each processor uses the input seed to
|
||||
generate its own unique seed and its own stream of random numbers.
|
||||
Thus the dynamics of the system will not be identical on two runs on
|
||||
different numbers of processors.
|
||||
different numbers of processors.
|
||||
|
||||
Note also that the Generalized Langevin Dynamics scheme that is
|
||||
Note also that the Generalized Langevin Dynamics scheme that is
|
||||
implemented by the "fix gld"_fix_gld.html scheme is closely related
|
||||
to the present one. In fact, it should be always possible to cast the
|
||||
Prony series form of the memory kernel used by GLD into an appropriate
|
||||
input matrix for "fix gle"_fix_gle.html. While the GLE scheme is more
|
||||
general, the form used by "fix gld"_fix_gld.html can be more directly
|
||||
related to the representation of an implicit solvent environment.
|
||||
related to the representation of an implicit solvent environment.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
@ -101,9 +101,9 @@ do "exact" restarts with this fix, where the simulation continues on
|
||||
the same as if no restart had taken place. However, in a statistical
|
||||
sense, a restarted simulation should produce the same behavior.
|
||||
Note however that you should use a different seed each time you
|
||||
restart, otherwise the same sequence of random numbers will be used
|
||||
each time, which might lead to stochastic synchronization and
|
||||
subtle artefacts in the sampling.
|
||||
restart, otherwise the same sequence of random numbers will be used
|
||||
each time, which might lead to stochastic synchronization and
|
||||
subtle artefacts in the sampling.
|
||||
|
||||
This fix can ramp its target temperature over multiple runs, using the
|
||||
{start} and {stop} keywords of the "run"_run.html command. See the
|
||||
@ -112,24 +112,24 @@ This fix can ramp its target temperature over multiple runs, using the
|
||||
The "fix_modify"_fix_modify.html {energy} option is supported by this
|
||||
fix to add the energy change induced by Langevin thermostatting to the
|
||||
system's potential energy as part of "thermodynamic
|
||||
output"_thermo_style.html.
|
||||
output"_thermo_style.html.
|
||||
|
||||
This fix computes a global scalar which can be accessed by various
|
||||
"output commands"_Section_howto.html#howto_15. The scalar is the
|
||||
cummulative energy change due to this fix. The scalar value
|
||||
calculated by this fix is "extensive".
|
||||
calculated by this fix is "extensive".
|
||||
|
||||
[Restrictions:]
|
||||
[Restrictions:]
|
||||
|
||||
The GLE thermostat in its current implementation should not be used
|
||||
with rigid bodies, SHAKE or RATTLE. It is expected that all the
|
||||
thermostatted degrees of freedom are fully flexible, and the sampled
|
||||
ensemble will not be correct otherwise.
|
||||
|
||||
In order to perform constant-pressure simulations please use
|
||||
"fix press/berendsen"_fix_press_berendsen.html, rather than
|
||||
In order to perform constant-pressure simulations please use
|
||||
"fix press/berendsen"_fix_press_berendsen.html, rather than
|
||||
"fix npt"_fix_nh.html, to avoid duplicate integration of the
|
||||
equations of motion.
|
||||
equations of motion.
|
||||
|
||||
This fix is part of the USER-MISC package. It is only enabled if LAMMPS
|
||||
was built with that package. See the "Making
|
||||
@ -144,12 +144,12 @@ dpd/tstat"_pair_dpd.html, "fix gld"_fix_gld.html
|
||||
:line
|
||||
|
||||
:link(Ceriotti)
|
||||
[(Ceriotti)] Ceriotti, Bussi and Parrinello, J Chem Theory Comput 6,
|
||||
[(Ceriotti)] Ceriotti, Bussi and Parrinello, J Chem Theory Comput 6,
|
||||
1170-80 (2010)
|
||||
|
||||
:link(GLE4MD)
|
||||
[(GLE4MD)] "http://epfl-cosmo.github.io/gle4md/"_http://epfl-cosmo.github.io/gle4md/
|
||||
|
||||
:link(Ceriotti2)
|
||||
[(Ceriotti2)] Ceriotti, Bussi and Parrinello, Phys Rev Lett 103,
|
||||
[(Ceriotti2)] Ceriotti, Bussi and Parrinello, Phys Rev Lett 103,
|
||||
030603 (2009)
|
||||
|
||||
@ -113,7 +113,7 @@ more instructions on how to use the accelerated styles effectively.
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html.
|
||||
files"_restart.html.
|
||||
|
||||
The "fix_modify"_fix_modify.html {energy} option is supported by this
|
||||
fix to add the gravitational potential energy of the system to the
|
||||
|
||||
@ -110,9 +110,9 @@ are relevant to this fix.
|
||||
This fix computes a global scalar which can be accessed by various
|
||||
"output commands"_Section_howto.html#howto_15. This scalar is the
|
||||
most recent value by which velocites were scaled. The scalar value
|
||||
calculated by this fix is "intensive". If {eflux} is specified as
|
||||
calculated by this fix is "intensive". If {eflux} is specified as
|
||||
an atom-style variable, this fix computes the average value by which
|
||||
the velocities were scaled for all of the atoms that had their
|
||||
the velocities were scaled for all of the atoms that had their
|
||||
velocities scaled.
|
||||
|
||||
No parameter of this fix can be used with the {start/stop} keywords of
|
||||
|
||||
@ -29,7 +29,7 @@ keyword = {unwrap} or {fscale} or {trate} :l
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix vmd all imd 5678
|
||||
fix vmd all imd 5678
|
||||
fix comm all imd 8888 trate 5 unwrap on fscale 10.0 :pre
|
||||
|
||||
[Description:]
|
||||
@ -103,7 +103,7 @@ prompts appears, one types the command line:
|
||||
|
||||
imd connect localhost 5678 :pre
|
||||
|
||||
This assumes that {fix imd} was started with 5678 as a port
|
||||
This assumes that {fix imd} was started with 5678 as a port
|
||||
number for the IMD protocol.
|
||||
|
||||
The steps to do interactive manipulation of a running simulation in
|
||||
@ -116,10 +116,10 @@ apply forces to your simulation. Click on an atom, residue, or
|
||||
fragment and drag to apply a force. Click quickly without moving the
|
||||
mouse to turn the force off. You can also use a variety of 3D position
|
||||
trackers to apply forces to your simulation. Game controllers or haptic
|
||||
devices with force-feedback such as the Novint Falcon or Sensable
|
||||
devices with force-feedback such as the Novint Falcon or Sensable
|
||||
PHANTOM allow you to feel the resistance due to inertia or interactions
|
||||
with neighbors that the atoms experience you are trying to move, as if
|
||||
they were real objects. See the "VMD IMD Homepage"_imdvmd and the
|
||||
with neighbors that the atoms experience you are trying to move, as if
|
||||
they were real objects. See the "VMD IMD Homepage"_imdvmd and the
|
||||
"VRPN-ICMS Homepage"_vrpnicms for more details.
|
||||
|
||||
If IMD control messages are received, a line of text describing the
|
||||
@ -127,8 +127,8 @@ message and its effect will be printed to the LAMMPS output screen, if
|
||||
screen output is active.
|
||||
|
||||
:link(VMD,http://www.ks.uiuc.edu/Research/vmd)
|
||||
:link(imdvmd,http://www.ks.uiuc.edu/Research/vmd/imd/)
|
||||
:link(vrpnicms,http://sites.google.com/site/akohlmey/software/vrpn-icms)
|
||||
:link(imdvmd,http://www.ks.uiuc.edu/Research/vmd/imd/)
|
||||
:link(vrpnicms,http://sites.google.com/site/akohlmey/software/vrpn-icms)
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
|
||||
@ -62,7 +62,7 @@ coordinates received from i-PI before forces are ever evaluated.
|
||||
There is no restart information associated with this fix, since all
|
||||
the dynamical parameters are dealt with by i-PI.
|
||||
|
||||
[Restrictions:]
|
||||
[Restrictions:]
|
||||
|
||||
Using this fix on anything other than all atoms requires particular
|
||||
care, since i-PI will know nothing on atoms that are not those whose
|
||||
|
||||
@ -239,7 +239,7 @@ limit of the integrator), while still producing the correct Boltzmann
|
||||
distribution of atom positions. It is implemented within LAMMPS, by
|
||||
changing how the the random force is applied so that it is composed of
|
||||
the average of two random forces representing half-contributions from
|
||||
the previous and current time intervals.
|
||||
the previous and current time intervals.
|
||||
|
||||
In common with all methods based on Verlet integration, the
|
||||
discretized velocities generated by this method in conjunction with
|
||||
@ -340,5 +340,5 @@ types, tally = no, zero = no, gjf = no.
|
||||
|
||||
:link(Gronbech-Jensen)
|
||||
[(Gronbech-Jensen)] Gronbech-Jensen and Farago, Mol Phys, 111, 983
|
||||
(2013); Gronbech-Jensen, Hayre, and Farago, Comp Phys Comm,
|
||||
(2013); Gronbech-Jensen, Hayre, and Farago, Comp Phys Comm,
|
||||
185, 524 (2014)
|
||||
|
||||
@ -64,15 +64,15 @@ Masses:
|
||||
The Langevin forces are computed as
|
||||
\begin\{equation\} F' = - \frac \{M'\} \{\mathtt\{damp\_com\}\}\, V' + F_r' \end\{equation\}
|
||||
\begin\{equation\} f' = - \frac \{m'\} \{\mathtt\{damp\_drude\}\}\, v' + f_r' \end\{equation\}
|
||||
\(F_r'\) is a random force proportional to
|
||||
\(\sqrt \{ \frac \{2\, k_B \mathtt\{Tcom\}\, m'\}
|
||||
\{\mathrm dt\, \mathtt\{damp\_com\} \}
|
||||
\(F_r'\) is a random force proportional to
|
||||
\(\sqrt \{ \frac \{2\, k_B \mathtt\{Tcom\}\, m'\}
|
||||
\{\mathrm dt\, \mathtt\{damp\_com\} \}
|
||||
\} \). :b
|
||||
\(f_r'\) is a random force proportional to
|
||||
\(\sqrt \{ \frac \{2\, k_B \mathtt\{Tdrude\}\, m'\}
|
||||
\{\mathrm dt\, \mathtt\{damp\_drude\} \}
|
||||
\(f_r'\) is a random force proportional to
|
||||
\(\sqrt \{ \frac \{2\, k_B \mathtt\{Tdrude\}\, m'\}
|
||||
\{\mathrm dt\, \mathtt\{damp\_drude\} \}
|
||||
\} \). :b
|
||||
Then the real forces acting on the particles are computed from the inverse
|
||||
Then the real forces acting on the particles are computed from the inverse
|
||||
transform:
|
||||
\begin\{equation\} F = \frac M \{M'\}\, F' - f' \end\{equation\}
|
||||
\begin\{equation\} f = \frac m \{M'\}\, F' + f' \end\{equation\}
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user