forked from lijiext/lammps
minor formatting edits
This commit is contained in:
Steve Plimpton
parent
95a3abc74e
commit
ea24ec8d6a
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@ -65,32 +65,30 @@ highly overlapped atoms from being moved long distances (e.g. through
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another atom) due to large forces.
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The choice of line search algorithm for the *cg* and *sd* minimization
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styles can be selected via the *line* keyword.
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The default *quadratic* line search algorithm starts out using
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the robust backtracking method described below. However, once
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the system gets close to a local
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minimum and the linesearch steps get small, so that the energy
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is approximately quadratic in the step length, it uses the
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estimated location of zero gradient as the linesearch step,
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provided the energy change is downhill.
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This becomes more efficient than backtracking
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for highly-converged relaxations. The *forcezero*
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line search algorithm is similar to *quadratic*\ .
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It may be more efficient than *quadratic* on some systems.
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styles can be selected via the *line* keyword. The default
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*quadratic* line search algorithm starts out using the robust
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backtracking method described below. However, once the system gets
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close to a local minimum and the linesearch steps get small, so that
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the energy is approximately quadratic in the step length, it uses the
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estimated location of zero gradient as the linesearch step, provided
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the energy change is downhill. This becomes more efficient than
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backtracking for highly-converged relaxations. The *forcezero* line
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search algorithm is similar to *quadratic*\ . It may be more
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efficient than *quadratic* on some systems.
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The backtracking search is robust and should always find a local energy
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minimum. However, it will "converge" when it can no longer reduce the
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energy of the system. Individual atom forces may still be larger than
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desired at this point, because the energy change is measured as the
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difference of two large values (energy before and energy after) and
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that difference may be smaller than machine epsilon even if atoms
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could move in the gradient direction to reduce forces further.
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The backtracking search is robust and should always find a local
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energy minimum. However, it will "converge" when it can no longer
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reduce the energy of the system. Individual atom forces may still be
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larger than desired at this point, because the energy change is
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measured as the difference of two large values (energy before and
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energy after) and that difference may be smaller than machine epsilon
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even if atoms could move in the gradient direction to reduce forces
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further.
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The choice of a norm can be modified for the min styles *cg*\ , *sd*\ ,
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*quickmin*\ , *fire*\ , *spin*\ , *spin/cg* and *spin/lbfgs* using
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the *norm* keyword.
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The default *two* norm computes the 2-norm (Euclidean length) of the
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global force vector:
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The choice of a norm can be modified for the min styles *cg*\ , *sd*\
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, *quickmin*\ , *fire*\ , *spin*\ , *spin/cg* and *spin/lbfgs* using
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the *norm* keyword. The default *two* norm computes the 2-norm
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(Euclidean length) of the global force vector:
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.. image:: Eqs/norm_two.jpg
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:align: center
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@ -111,57 +109,57 @@ all atoms in the system:
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For the min styles *spin*\ , *spin/cg* and *spin/lbfgs*\ , the force
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norm is replaced by the spin-torque norm.
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Keywords *alpha\_damp* and *discrete\_factor* only make sense when
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a :doc:`min\_spin <min_spin>` command is declared.
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Keyword *alpha\_damp* defines an analog of a magnetic Gilbert
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damping. It defines a relaxation rate toward an equilibrium for
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a given magnetic system.
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Keyword *discrete\_factor* defines a discretization factor for the
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adaptive timestep used in the *spin* minimization.
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See :doc:`min\_spin <min_spin>` for more information about those
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Keywords *alpha\_damp* and *discrete\_factor* should only be used when
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a :doc:`min\_spin <min_spin>` command is declared. Keyword
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*alpha\_damp* defines an analog of a magnetic Gilbert damping. It
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defines a relaxation rate toward an equilibrium for a given magnetic
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system. Keyword *discrete\_factor* defines a discretization factor
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for the adaptive timestep used in the *spin* minimization. See
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:doc:`min\_spin <min_spin>` for more information about those
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quantities.
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The choice of a line search algorithm for the *spin/cg* and
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*spin/lbfgs* styles can be specified via the *line* keyword.
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The *spin\_cubic* and *spin\_none* only make sense when one of those
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two minimization styles is declared.
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The *spin\_cubic* performs the line search based on a cubic interpolation
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of the energy along the search direction. The *spin\_none* keyword
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deactivates the line search procedure.
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The *spin\_none* is a default value for *line* keyword for both *spin/lbfgs*
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and *spin/cg*\ . Convergence of *spin/lbfgs* can be more robust if
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*spin\_cubic* line search is used.
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*spin/lbfgs* styles can be specified via the *line* keyword. The
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*spin\_cubic* and *spin\_none* only make sense when one of those two
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minimization styles is declared. The *spin\_cubic* performs the line
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search based on a cubic interpolation of the energy along the search
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direction. The *spin\_none* keyword deactivates the line search
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procedure. The *spin\_none* is a default value for *line* keyword for
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both *spin/lbfgs* and *spin/cg*\ . Convergence of *spin/lbfgs* can be
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more robust if *spin\_cubic* line search is used.
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The Newton *integrator* used for *fire2* minimization can be selected to be
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either the symplectic Euler (\ *eulerimplicit*\ ) or velocity Verlet (\ *verlet*\ ).
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*tmax* define the maximum value for the adaptive timestep
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during a *fire2* minimization. It is multiplication factor applied
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to the current :doc:`timestep <timestep>` (not in time unit). For example,
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*tmax* = 4.0 in metal :doc:`units <units>` means that the maximum value
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the timestep can reach during a minimization is 4fs (with the default
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:doc:`timestep <timestep>` value). Note that parameters defaults has been
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chosen to be reliable in most cases, but one should consider adjusting
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:doc:`timestep <timestep>` and *tmax* to optimize the minimization for large
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or complex systems.
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Others parameters of the *fire2* minimization can be tuned (\ *tmin*\ , *delaystep*\ ,
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*dtgrow*\ , *dtshrink*\ , *alpha0*\ , and *alphashrink*\ ). Please refer to the article
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describing the *fire2* :doc:`min\_style <min_style>`.
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The Newton *integrator* used for *fire2* minimization can be selected
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to be either the symplectic Euler (\ *eulerimplicit*\ ) or velocity
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Verlet (\ *verlet*\ ). *tmax* define the maximum value for the
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adaptive timestep during a *fire2* minimization. It is multiplication
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factor applied to the current :doc:`timestep <timestep>` (not in time
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unit). For example, *tmax* = 4.0 in metal :doc:`units <units>` means
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that the maximum value the timestep can reach during a minimization is
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4fs (with the default :doc:`timestep <timestep>` value). Note that
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parameter defaults has been chosen to be reliable in most cases, but
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one should consider adjusting :doc:`timestep <timestep>` and *tmax* to
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optimize the minimization for large or complex systems. Other
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parameters of the *fire2* minimization can be tuned (\ *tmin*\ ,
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*delaystep*\ , *dtgrow*\ , *dtshrink*\ , *alpha0*\ , and
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*alphashrink*\ ). Please refer to the article describing the *fire2*
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:doc:`min\_style <min_style>`.
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An additional stopping criteria *vdfmax* is added in order to avoid unnecessary looping
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when it is reasonable to think the system will not be relaxed further.
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Note that in this case the system will NOT be relaxed. This could
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happen when the system comes to be stuck in a local basin of the phase space.
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*vdfmax* is the maximum number of consecutive iterations with P(t) < 0.
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For debugging purposes, it is possible to switch off the inertia correction
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(\ *halfstepback* = *no*\ ) and the initial delay (\ *initialdelay* = *no*\ ).
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An additional stopping criteria *vdfmax* is added in order to avoid
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unnecessary looping when it is reasonable to think the system will not
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be relaxed further. Note that in this case the system will NOT be
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relaxed. This could happen when the system comes to be stuck in a
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local basin of the phase space. *vdfmax* is the maximum number of
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consecutive iterations with P(t) < 0. For debugging purposes, it is
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possible to switch off the inertia correction (\ *halfstepback* =
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*no*\ ) and the initial delay (\ *initialdelay* = *no*\ ).
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Restrictions
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""""""""""""
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For magnetic GNEB calculations, only *spin\_none* value for *line* keyword can be used
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when styles *spin/cg* and *spin/lbfgs* are employed.
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See :doc:`neb/spin <neb_spin>` for more explanation.
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For magnetic GNEB calculations, only *spin\_none* value for *line*
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keyword can be used when styles *spin/cg* and *spin/lbfgs* are
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employed. See :doc:`neb/spin <neb_spin>` for more explanation.
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Related commands
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""""""""""""""""
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@ -173,11 +171,11 @@ Default
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The option defaults are dmax = 0.1, line = quadratic and norm = two.
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For the *spin*\ , *spin/cg* and *spin/lbfgs* styles, the
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option defaults are alpha\_damp = 1.0, discrete\_factor = 10.0,
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line = spin\_none, and norm = euclidean.
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For the *spin*\ , *spin/cg* and *spin/lbfgs* styles, the option
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defaults are alpha\_damp = 1.0, discrete\_factor = 10.0, line =
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spin\_none, and norm = euclidean.
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For the *fire2* style, the option defaults are
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integrator = eulerimplicit, tmax = 10.0, tmin = 0.02,
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delaystep = 20, dtgrow = 1.1, dtshrink = 0.5, alpha0 = 0.25, alphashrink = 0.99,
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vdfmax = 2000, halfstepback = yes and initialdelay = yes.
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For the *fire2* style, the option defaults are integrator =
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eulerimplicit, tmax = 10.0, tmin = 0.02, delaystep = 20, dtgrow = 1.1,
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dtshrink = 0.5, alpha0 = 0.25, alphashrink = 0.99, vdfmax = 2000,
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halfstepback = yes and initialdelay = yes.
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@ -26,8 +26,8 @@ Examples
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Description
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"""""""""""
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Choose a minimization algorithm to use when a :doc:`minimize <minimize>`
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command is performed.
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Choose a minimization algorithm to use when a :doc:`minimize
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<minimize>` command is performed.
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Style *cg* is the Polak-Ribiere version of the conjugate gradient (CG)
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algorithm. At each iteration the force gradient is combined with the
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@ -55,55 +55,55 @@ descent will not converge as quickly as CG, but may be more robust in
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some situations.
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Style *quickmin* is a damped dynamics method described in
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:ref:`(Sheppard) <Sheppard>`, where the damping parameter is related to the
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projection of the velocity vector along the current force vector for
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each atom. The velocity of each atom is initialized to 0.0 by this
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style, at the beginning of a minimization.
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:ref:`(Sheppard) <Sheppard>`, where the damping parameter is related
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to the projection of the velocity vector along the current force
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vector for each atom. The velocity of each atom is initialized to 0.0
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by this style, at the beginning of a minimization.
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Style *fire* is a damped dynamics method described in
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:ref:`(Bitzek) <Bitzek>`, which is similar to *quickmin* but adds a variable
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timestep and alters the projection operation to maintain components of
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the velocity non-parallel to the current force vector. The velocity
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of each atom is initialized to 0.0 by this style, at the beginning of
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a minimization.
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Style *fire* is a damped dynamics method described in :ref:`(Bitzek)
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<Bitzek>`, which is similar to *quickmin* but adds a variable timestep
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and alters the projection operation to maintain components of the
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velocity non-parallel to the current force vector. The velocity of
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each atom is initialized to 0.0 by this style, at the beginning of a
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minimization.
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Style *fire2* is an optimization of the style *fire*\ , including different
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time integration schemes, described in :ref:`(Guenole) <Guenole>`.
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Style *fire2* is an optimization of the style *fire*\ , including
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different time integration schemes, described in :ref:`(Guenole)
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<Guenole>`.
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Style *spin* is a damped spin dynamics with an adaptive
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timestep.
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Style *spin* is a damped spin dynamics with an adaptive timestep.
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Style *spin/cg* uses an orthogonal spin optimization (OSO)
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combined to a conjugate gradient (CG) approach to minimize spin
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configurations.
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Style *spin/cg* uses an orthogonal spin optimization (OSO) combined to
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a conjugate gradient (CG) approach to minimize spin configurations.
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Style *spin/lbfgs* uses an orthogonal spin optimization (OSO)
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combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno
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(LBFGS) approach to minimize spin configurations.
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Style *spin/lbfgs* uses an orthogonal spin optimization (OSO) combined
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to a limited-memory Broyden-Fletcher-Goldfarb-Shanno (LBFGS) approach
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to minimize spin configurations.
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See the :doc:`min/spin <min_spin>` doc page for more information
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about the *spin*\ , *spin/cg* and *spin/lbfgs* styles.
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See the :doc:`min/spin <min_spin>` doc page for more information about
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the *spin*\ , *spin/cg* and *spin/lbfgs* styles.
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Either the *quickmin*\ , *fire* and *fire2* styles are useful in the context of
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nudged elastic band (NEB) calculations via the :doc:`neb <neb>` command.
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Either the *quickmin*\ , *fire* and *fire2* styles are useful in the
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context of nudged elastic band (NEB) calculations via the :doc:`neb
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<neb>` command.
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Either the *spin*\ , *spin/cg* and *spin/lbfgs* styles are useful
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in the context of magnetic geodesic nudged elastic band (GNEB) calculations
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via the :doc:`neb/spin <neb_spin>` command.
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Either the *spin*\ , *spin/cg* and *spin/lbfgs* styles are useful in
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the context of magnetic geodesic nudged elastic band (GNEB)
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calculations via the :doc:`neb/spin <neb_spin>` command.
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.. note::
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The damped dynamic minimizers use whatever timestep you have
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defined via the :doc:`timestep <timestep>` command. Often they will
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converge more quickly if you use a timestep about 10x larger than you
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would normally use for dynamics simulations.
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defined via the :doc:`timestep <timestep>` command. Often they
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will converge more quickly if you use a timestep about 10x larger
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than you would normally use for dynamics simulations.
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.. note::
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The *quickmin*\ , *fire*\ , *hftn*\ , and *cg/kk* styles do not yet
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support the use of the :doc:`fix box/relax <fix_box_relax>` command or
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minimizations involving the electron radius in :doc:`eFF <pair_eff>`
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models.
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support the use of the :doc:`fix box/relax <fix_box_relax>` command
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or minimizations involving the electron radius in :doc:`eFF
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<pair_eff>` models.
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----------
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@ -112,17 +112,19 @@ via the :doc:`neb/spin <neb_spin>` command.
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Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
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page. The accelerated styles take the same arguments and should
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hardware, as discussed on the :doc:`Speed packages <Speed_packages>`
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doc page. The accelerated styles take the same arguments and should
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produce the same results, except for round-off and precision issues.
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These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
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USER-OMP and OPT packages, respectively. They are only enabled if
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LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
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LAMMPS was built with those packages. See the :doc:`Build package
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<Build_package>` doc page for more info.
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You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
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:doc:`suffix <suffix>` command in your input script.
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by including their suffix, or you can use the :doc:`-suffix
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command-line switch <Run_options>` when you invoke LAMMPS, or you can
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use the :doc:`suffix <suffix>` command in your input script.
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See the :doc:`Speed packages <Speed_packages>` doc page for more
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instructions on how to use the accelerated styles effectively.
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@ -38,24 +38,25 @@ be in local potential energy minimum. More precisely, the
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configuration should approximate a critical point for the objective
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function (see below), which may or may not be a local minimum.
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The minimization algorithm used is set by the
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:doc:`min\_style <min_style>` command. Other options are set by the
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:doc:`min\_modify <min_modify>` command. Minimize commands can be
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interspersed with :doc:`run <run>` commands to alternate between
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relaxation and dynamics. The minimizers bound the distance atoms move
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in one iteration, so that you can relax systems with highly overlapped
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atoms (large energies and forces) by pushing the atoms off of each
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other.
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The minimization algorithm used is set by the :doc:`min\_style
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<min_style>` command. Other options are set by the :doc:`min\_modify
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<min_modify>` command. Minimize commands can be interspersed with
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:doc:`run <run>` commands to alternate between relaxation and
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dynamics. The minimizers bound the distance atoms move in one
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iteration, so that you can relax systems with highly overlapped atoms
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(large energies and forces) by pushing the atoms off of each other.
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Alternate means of relaxing a system are to run dynamics with a small
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or :doc:`limited timestep <fix_nve_limit>`. Or dynamics can be run
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using :doc:`fix viscous <fix_viscous>` to impose a damping force that
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slowly drains all kinetic energy from the system. The :doc:`pair\_style soft <pair_soft>` potential can be used to un-overlap atoms while
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running dynamics.
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slowly drains all kinetic energy from the system. The
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:doc:`pair\_style soft <pair_soft>` potential can be used to
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un-overlap atoms while running dynamics.
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Note that you can minimize some atoms in the system while holding the
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coordinates of other atoms fixed by applying :doc:`fix setforce <fix_setforce>` to the other atoms. See a fuller
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discussion of using fixes while minimizing below.
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coordinates of other atoms fixed by applying :doc:`fix setforce
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<fix_setforce>` to the other atoms. See a fuller discussion of using
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fixes while minimizing below.
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The :doc:`minimization styles <min_style>` *cg*\ , *sd*\ , and *hftn*
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involves an outer iteration loop which sets the search direction along
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@ -69,15 +70,15 @@ backtracking method is described in Nocedal and Wright's Numerical
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Optimization (Procedure 3.1 on p 41).
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The :doc:`minimization styles <min_style>` *quickmin*\ , *fire* and
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*fire2* perform damped dynamics using an Euler integration step.
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Thus they require a :doc:`timestep <timestep>` be defined.
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*fire2* perform damped dynamics using an Euler integration step. Thus
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they require a :doc:`timestep <timestep>` be defined.
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.. note::
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The damped dynamic minimizers use whatever timestep you have
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defined via the :doc:`timestep <timestep>` command. Often they will
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converge more quickly if you use a timestep about 10x larger than you
|
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would normally use for dynamics simulations.
|
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defined via the :doc:`timestep <timestep>` command. Often they
|
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will converge more quickly if you use a timestep about 10x larger
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than you would normally use for dynamics simulations.
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----------
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@ -90,13 +91,15 @@ coordinates:
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.. image:: Eqs/min_energy.jpg
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:align: center
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where the first term is the sum of all non-bonded :doc:`pairwise interactions <pair_style>` including :doc:`long-range Coulombic interactions <kspace_style>`, the 2nd through 5th terms are
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:doc:`bond <bond_style>`, :doc:`angle <angle_style>`,
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:doc:`dihedral <dihedral_style>`, and :doc:`improper <improper_style>`
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interactions respectively, and the last term is energy due to
|
||||
:doc:`fixes <fix>` which can act as constraints or apply force to atoms,
|
||||
such as through interaction with a wall. See the discussion below about
|
||||
how fix commands affect minimization.
|
||||
where the first term is the sum of all non-bonded :doc:`pairwise
|
||||
interactions <pair_style>` including :doc:`long-range Coulombic
|
||||
interactions <kspace_style>`, the 2nd through 5th terms are :doc:`bond
|
||||
<bond_style>`, :doc:`angle <angle_style>`, :doc:`dihedral
|
||||
<dihedral_style>`, and :doc:`improper <improper_style>` interactions
|
||||
respectively, and the last term is energy due to :doc:`fixes <fix>`
|
||||
which can act as constraints or apply force to atoms, such as through
|
||||
interaction with a wall. See the discussion below about how fix
|
||||
commands affect minimization.
|
||||
|
||||
The starting point for the minimization is the current configuration
|
||||
of the atoms.
|
||||
|
|
@ -126,9 +129,9 @@ The minimization procedure stops if any of several criteria are met:
|
|||
.. note::
|
||||
|
||||
You can also use the :doc:`fix halt <fix_halt>` command to specify
|
||||
a general criterion for exiting a minimization, that is a calculation
|
||||
performed on the state of the current system, as defined by an
|
||||
:doc:`equal-style variable <variable>`.
|
||||
a general criterion for exiting a minimization, that is a
|
||||
calculation performed on the state of the current system, as
|
||||
defined by an :doc:`equal-style variable <variable>`.
|
||||
|
||||
For the first criterion, the specified energy tolerance *etol* is
|
||||
unitless; it is met when the energy change between successive
|
||||
|
|
@ -163,8 +166,8 @@ freedom, such as from the :doc:`fix box/relax <fix_box_relax>` command.
|
|||
|
||||
Following minimization, a statistical summary is printed that lists
|
||||
which convergence criterion caused the minimizer to stop, as well as
|
||||
information about the energy, force, final line search, and
|
||||
iteration counts. An example is as follows:
|
||||
information about the energy, force, final line search, and iteration
|
||||
counts. An example is as follows:
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
|
|
|
|||
|
|
@ -11,6 +11,11 @@
|
|||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing authors: Julien Guénolé, RWTH Aachen University and
|
||||
Erik Bitzek, FAU Erlangen-Nuernberg
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <cmath>
|
||||
#include "min_fire2.h"
|
||||
#include "universe.h"
|
||||
|
|
@ -55,7 +60,6 @@ void MinFire2::init()
|
|||
alpha = alpha0;
|
||||
last_negative = ntimestep_start = update->ntimestep;
|
||||
vdotf_negatif = 0;
|
||||
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
|
@ -260,6 +264,7 @@ int MinFire2::iterate(int maxiter)
|
|||
x[i][2] -= 0.5 * dtv * v[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
v[i][0] = v[i][1] = v[i][2] = 0.0;
|
||||
}
|
||||
|
|
@ -273,6 +278,7 @@ int MinFire2::iterate(int maxiter)
|
|||
vmax = MAX(vmax,fabs(v[i][2]));
|
||||
if (dtvone*vmax > dmax) dtvone = dmax/vmax;
|
||||
}
|
||||
|
||||
MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,world);
|
||||
|
||||
// min dtv over replicas, if necessary
|
||||
|
|
@ -333,7 +339,7 @@ int MinFire2::iterate(int maxiter)
|
|||
|
||||
// Velocity Verlet integration
|
||||
|
||||
}else if (integrator == 1) {
|
||||
} else if (integrator == 1) {
|
||||
|
||||
dtf = 0.5 * dtv * force->ftm2v;
|
||||
|
||||
|
|
@ -391,7 +397,7 @@ int MinFire2::iterate(int maxiter)
|
|||
|
||||
// Standard Euler integration
|
||||
|
||||
}else if (integrator == 3) {
|
||||
} else if (integrator == 3) {
|
||||
|
||||
dtf = dtv * force->ftm2v;
|
||||
|
||||
|
|
@ -430,7 +436,6 @@ int MinFire2::iterate(int maxiter)
|
|||
eprevious = ecurrent;
|
||||
ecurrent = energy_force(0);
|
||||
neval++;
|
||||
|
||||
}
|
||||
|
||||
// energy tolerance criterion
|
||||
|
|
|
|||
Loading…
Reference in New Issue