forked from lijiext/lammps
Merge branch 'master' into doc-remove-redundant-links
# Conflicts: # doc/src/min_modify.rst # doc/src/min_style.rst # doc/src/minimize.rst
This commit is contained in:
Axel Kohlmeyer
commit
97addd2bee
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@ -26,6 +26,7 @@ vgcore.*
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.vagrant
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\#*#
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.#*
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.vscode
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.DS_Store
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.DS_Store?
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|
|
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@ -15,7 +15,7 @@ Syntax
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.. parsed-literal::
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keyword = *dmax* or *line* or *norm* or *alpha_damp* or *discrete_factor*
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keyword = *dmax* or *line* or *norm* or *alpha_damp* or *discrete_factor* or *integrator* or *tmax*
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*dmax* value = max
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max = maximum distance for line search to move (distance units)
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*line* value = *backtrack* or *quadratic* or *forcezero* or *spin_cubic* or *spin_none*
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@ -28,6 +28,10 @@ Syntax
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damping = fictitious Gilbert damping for spin minimization (adim)
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*discrete_factor* value = factor
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factor = discretization factor for adaptive spin timestep (adim)
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*integrator* value = *eulerimplicit* or *verlet*
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time integration scheme for fire minimization
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*tmax* value = factor
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factor = maximum adaptive timestep for fire minimization (adim)
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@ -38,6 +42,7 @@ Examples
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.. parsed-literal::
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min_modify dmax 0.2
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min_modify integrator verlet tmax 4
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Description
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"""""""""""
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@ -60,32 +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*\ , *fire/old*\ , *spin*\ , *spin/cg* and
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*spin/lbfgs* using the *norm* keyword. The default *two* norm computes
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the 2-norm (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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@ -106,31 +109,64 @@ 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 a
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:doc:`min_spin <min_spin>` command is declared. Keyword *alpha\_damp*
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defines an analog of a magnetic Gilbert damping. It defines a relaxation
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rate toward an equilibrium for a given magnetic system. Keyword
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*discrete\_factor* defines a discretization factor for the adaptive
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timestep used in the *spin* minimization. See :doc:`min_spin
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<min_spin>` for more information about those quantities.
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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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quantities.
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The choice of a line search algorithm for the *spin/cg* and *spin/lbfgs*
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styles can be specified via the *line* keyword. The *spin\_cubic* and
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*spin\_none* options only make sense when one of those two minimization
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styles is declared. The *spin\_cubic* option performs the line search
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based on a cubic interpolation of the energy along the search
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direction. The *spin\_none* option deactivates the line search
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procedure. The *spin\_none* option is a default value for *line*
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keyword for both *spin/lbfgs* and *spin/cg*\ . Convergence of
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*spin/lbfgs* can be more robust if *spin\_cubic* line search is used.
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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. The
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*spin\_cubic* and *spin\_none* keywords 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 *fire* minimization can be selected
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to be either the symplectic Euler (\ *eulerimplicit*\ ) or velocity
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Verlet (\ *verlet*\ ). *tmax* defines the maximum value for the
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adaptive timestep during a *fire* minimization. It is a 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 with a :doc:`timestep <timestep>` of
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2fs, means that the maximum value the timestep can reach during a *fire*
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minimization is 4fs.
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Note that parameter defaults has been chosen to be reliable in most cases,
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but 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 *fire* minimization can be tuned (\ *tmin*\ ,
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*delaystep*\ , *dtgrow*\ , *dtshrink*\ , *alpha0*\ , and
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*alphashrink*\ ). Please refer to the references describing the
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:doc:`min_style <min_style>` *fire*.
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An additional stopping criteria *vdfmax* is used by *fire* 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 have
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reached your minimization criteria. This could happen when the system
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comes to be stuck in a local basin of the phase space. *vdfmax* is
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the maximum number of consecutive iterations with P(t) < 0.
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The :doc:`min_style <min_style>` *fire* is an optimized implementation of
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:doc:`min_style <min_style>` *fire/old*. It can however behave similarly
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to the *fire/old* style by using the following set of parameters:
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.. parsed-literal::
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min_modify integrator eulerexplicit tmax 10.0 tmin 0.0 delaystep 5 &
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dtgrow 1.1 dtshrink 0.5 alpha0 0.1 alphashrink 0.99 &
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vdfmax 100000 halfstepback no initialdelay no
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Restrictions
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""""""""""""
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For magnetic GNEB calculations, only the *spin\_none* value for *line* keyword can be used
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when minimization styles *spin/cg* and *spin/lbfgs* are employed.
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See :doc:`neb/spin <neb_spin>` for more explanations.
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For magnetic GNEB calculations, only *spin\_none* value for *line*
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keyword can be used when minimization 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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@ -142,6 +178,11 @@ 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 *fire* 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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@ -11,7 +11,7 @@ Syntax
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min_style style
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* style = *cg* or *hftn* or *sd* or *quickmin* or *fire* or *spin* or *spin/cg* or *spin/lbfgs*
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* style = *cg* or *hftn* or *sd* or *quickmin* or *fire* or *fire/old* or *spin* or *spin/cg* or *spin/lbfgs*
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Examples
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""""""""
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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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@ -55,52 +55,68 @@ 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. This style correspond to an optimized version described
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in :ref:`(Guenole) <Guenole>` that include different time integration
|
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schemes and defaults parameters. The default parameters can be
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modified with the command :doc:`min_modify <min_modify>`.
|
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|
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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/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 *fire/old* is the original implementation of *fire* in Lammps,
|
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conserved for backward compatibility. The main differences regarding
|
||||
the current version *fire* are: time integration by Explicit Euler
|
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only, different sequence in maintaining velocity components non-parallel
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to the current force vector and hard-coded minimization parameters.
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A complete description of the differences between *fire/old* and *fire*
|
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can be found in :ref:`(Guenole) <Guenole>` (where the current *fire*
|
||||
in lammps is named *fire2.0*). By using an appropriate set of
|
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parameters, *fire* can behave similarly than *fire/old*, as described
|
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in the :doc:`min_modify <min_modify>` command.
|
||||
|
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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* is a damped spin dynamics with an adaptive timestep.
|
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|
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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.
|
||||
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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|
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Either the *quickmin* and *fire* styles are useful in the context of
|
||||
nudged elastic band (NEB) calculations via the :doc:`neb <neb>` command.
|
||||
Style *spin/lbfgs* uses an orthogonal spin optimization (OSO) combined
|
||||
to a limited-memory Broyden-Fletcher-Goldfarb-Shanno (LBFGS) approach
|
||||
to minimize spin configurations.
|
||||
|
||||
Either the *spin*\ , *spin/cg* and *spin/lbfgs* styles are useful
|
||||
in the context of magnetic geodesic nudged elastic band (GNEB) calculations
|
||||
via the :doc:`neb/spin <neb_spin>` command.
|
||||
See the :doc:`min/spin <min_spin>` doc page for more information about
|
||||
the *spin*\ , *spin/cg* and *spin/lbfgs* styles.
|
||||
|
||||
Either the *quickmin*\ , *fire* and *fire/old* styles are useful in the
|
||||
context of nudged elastic band (NEB) calculations via the :doc:`neb
|
||||
<neb>` command.
|
||||
|
||||
Either the *spin*\ , *spin/cg* and *spin/lbfgs* styles are useful in
|
||||
the context of magnetic geodesic nudged elastic band (GNEB)
|
||||
calculations via the :doc:`neb/spin <neb_spin>` command.
|
||||
|
||||
.. note::
|
||||
|
||||
The damped dynamic minimizers use whatever timestep you have
|
||||
defined via the :doc:`timestep <timestep>` command. Often they will
|
||||
converge more quickly if you use a timestep about 10x larger than you
|
||||
would normally use for dynamics simulations.
|
||||
defined via the :doc:`timestep <timestep>` command. Often they
|
||||
will converge more quickly if you use a timestep about 10x larger
|
||||
than you would normally use for dynamics simulations.
|
||||
For *fire*, the default timestep is recommended to be equal to
|
||||
the one you would normally use for dynamics simulations.
|
||||
|
||||
.. note::
|
||||
|
||||
The *quickmin*\ , *fire*\ , *hftn*\ , and *cg/kk* styles do not yet
|
||||
support the use of the :doc:`fix box/relax <fix_box_relax>` command or
|
||||
minimizations involving the electron radius in :doc:`eFF <pair_eff>`
|
||||
models.
|
||||
The *quickmin*\ , *fire*\ , *fire/old*\ , *hftn*\ , and *cg/kk* styles do not yet
|
||||
support the use of the :doc:`fix box/relax <fix_box_relax>` command
|
||||
or minimizations involving the electron radius in :doc:`eFF
|
||||
<pair_eff>` models.
|
||||
|
||||
|
||||
----------
|
||||
|
|
@ -109,17 +125,19 @@ via the :doc:`neb/spin <neb_spin>` command.
|
|||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>`
|
||||
doc page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
LAMMPS was built with those packages. See the :doc:`Build package
|
||||
<Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
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 :doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
|
@ -151,15 +169,16 @@ Default
|
|||
|
||||
.. _Sheppard:
|
||||
|
||||
|
||||
|
||||
**(Sheppard)** Sheppard, Terrell, Henkelman, J Chem Phys, 128, 134106
|
||||
(2008). See ref 1 in this paper for original reference to Qmin in
|
||||
Jonsson, Mills, Jacobsen.
|
||||
|
||||
.. _Bitzek:
|
||||
|
||||
|
||||
|
||||
**(Bitzek)** Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett,
|
||||
97, 170201 (2006).
|
||||
|
||||
.. _Guenole:
|
||||
|
||||
**(Guenole)** Guenole, Noehring, Vaid, Houlle, Xie, Prakash, Bitzek,
|
||||
Comput Mater Sci, (2020), in press (arXiv:190802038).
|
||||
|
|
|
|||
|
|
@ -52,10 +52,12 @@ or :doc:`limited timestep <fix_nve_limit>`. Or dynamics can be run
|
|||
using :doc:`fix viscous <fix_viscous>` to impose a damping force that
|
||||
slowly drains all kinetic energy from the system. The :doc:`pair_style soft <pair_soft>` potential can be used to un-overlap atoms while
|
||||
running dynamics.
|
||||
un-overlap atoms while running dynamics.
|
||||
|
||||
Note that you can minimize some atoms in the system while holding the
|
||||
coordinates of other atoms fixed by applying :doc:`fix setforce <fix_setforce>` to the other atoms. See a fuller
|
||||
discussion of using fixes while minimizing below.
|
||||
coordinates of other atoms fixed by applying :doc:`fix setforce
|
||||
<fix_setforce>` to the other atoms. See a fuller discussion of using
|
||||
fixes while minimizing below.
|
||||
|
||||
The :doc:`minimization styles <min_style>` *cg*\ , *sd*\ , and *hftn*
|
||||
involves an outer iteration loop which sets the search direction along
|
||||
|
|
@ -68,16 +70,16 @@ be more robust than previous line searches we've tried. The
|
|||
backtracking method is described in Nocedal and Wright's Numerical
|
||||
Optimization (Procedure 3.1 on p 41).
|
||||
|
||||
The :doc:`minimization styles <min_style>` *quickmin* and *fire* perform
|
||||
damped dynamics using an Euler integration step. Thus they require a
|
||||
:doc:`timestep <timestep>` be defined.
|
||||
The :doc:`minimization styles <min_style>` *quickmin*\ , *fire* and
|
||||
*fire/old* perform damped dynamics using an Euler integration step. Thus
|
||||
they require a :doc:`timestep <timestep>` be defined.
|
||||
|
||||
.. note::
|
||||
|
||||
The damped dynamic minimizers use whatever timestep you have
|
||||
defined via the :doc:`timestep <timestep>` command. Often they will
|
||||
converge more quickly if you use a timestep about 10x larger than you
|
||||
would normally use for dynamics simulations.
|
||||
defined via the :doc:`timestep <timestep>` command. Often they
|
||||
will converge more quickly if you use a timestep about 10x larger
|
||||
than you would normally use for dynamics simulations.
|
||||
|
||||
|
||||
----------
|
||||
|
|
@ -90,13 +92,15 @@ coordinates:
|
|||
.. image:: Eqs/min_energy.jpg
|
||||
:align: center
|
||||
|
||||
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.
|
||||
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 +130,9 @@ 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 +167,8 @@ 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::
|
||||
|
|
|
|||
|
|
@ -72,6 +72,7 @@ allocaters
|
|||
allosws
|
||||
AlO
|
||||
Alonso
|
||||
alphashrink
|
||||
amap
|
||||
Amatrix
|
||||
AMD
|
||||
|
|
@ -273,8 +274,8 @@ Bouguet
|
|||
Bourne
|
||||
boxcolor
|
||||
bp
|
||||
bpls
|
||||
bpclermont
|
||||
bpls
|
||||
br
|
||||
Branduardi
|
||||
Branicio
|
||||
|
|
@ -557,6 +558,7 @@ defgrad
|
|||
defn
|
||||
deformable
|
||||
del
|
||||
delaystep
|
||||
deleteIDs
|
||||
Dellago
|
||||
delocalization
|
||||
|
|
@ -660,7 +662,9 @@ DRUDE
|
|||
dsf
|
||||
dsmc
|
||||
dt
|
||||
dtgrow
|
||||
dtheta
|
||||
dtshrink
|
||||
du
|
||||
dU
|
||||
Dudarev
|
||||
|
|
@ -816,6 +820,7 @@ ethernet
|
|||
etol
|
||||
etot
|
||||
etotal
|
||||
eulerimplicit
|
||||
Europhys
|
||||
ev
|
||||
eV
|
||||
|
|
@ -958,10 +963,10 @@ Gahler
|
|||
gainsboro
|
||||
Galindo
|
||||
gamA
|
||||
gamR
|
||||
gammaA
|
||||
gammaFactor
|
||||
gammaR
|
||||
gamR
|
||||
Gan
|
||||
GaN
|
||||
ganzenmueller
|
||||
|
|
@ -1053,6 +1058,7 @@ gstyle
|
|||
GTL
|
||||
Gubbins
|
||||
Guericke
|
||||
Guenole
|
||||
gui
|
||||
Gumbsch
|
||||
Gunsteren
|
||||
|
|
@ -1064,6 +1070,7 @@ gz
|
|||
gzipped
|
||||
Haak
|
||||
Hafskjold
|
||||
halfstepback
|
||||
Halperin
|
||||
Halver
|
||||
Hamaker
|
||||
|
|
@ -1124,6 +1131,7 @@ Homebrew
|
|||
hooke
|
||||
Hookean
|
||||
hotpink
|
||||
Houlle
|
||||
howto
|
||||
Howto
|
||||
Hoyt
|
||||
|
|
@ -1197,8 +1205,9 @@ infty
|
|||
inhomogeneities
|
||||
inhomogeneous
|
||||
init
|
||||
initio
|
||||
initialdelay
|
||||
initializations
|
||||
initio
|
||||
InP
|
||||
inregion
|
||||
Institut
|
||||
|
|
@ -1348,7 +1357,6 @@ kcl
|
|||
Kd
|
||||
KDevelop
|
||||
ke
|
||||
kepler
|
||||
KE
|
||||
Keblinski
|
||||
keflag
|
||||
|
|
@ -1356,6 +1364,7 @@ Keir
|
|||
Kelchner
|
||||
Kelkar
|
||||
Kemper
|
||||
kepler
|
||||
keV
|
||||
Keyes
|
||||
Khersonskii
|
||||
|
|
@ -1451,8 +1460,8 @@ lcbop
|
|||
ld
|
||||
ldfftw
|
||||
ldg
|
||||
Lebedeva
|
||||
lebedeva
|
||||
Lebedeva
|
||||
Lebold
|
||||
Lechman
|
||||
Lehoucq
|
||||
|
|
@ -1715,8 +1724,8 @@ Mie
|
|||
Mikami
|
||||
Militzer
|
||||
Minary
|
||||
Mindlin
|
||||
mincap
|
||||
Mindlin
|
||||
mingw
|
||||
minima
|
||||
minimizations
|
||||
|
|
@ -1957,6 +1966,7 @@ Nocedal
|
|||
nocite
|
||||
nocoeff
|
||||
nodeless
|
||||
Noehring
|
||||
noforce
|
||||
Noid
|
||||
nolib
|
||||
|
|
@ -2076,8 +2086,8 @@ ons
|
|||
OO
|
||||
opencl
|
||||
openKIM
|
||||
OpenMP
|
||||
openmp
|
||||
OpenMP
|
||||
openmpi
|
||||
opls
|
||||
Oppelstrup
|
||||
|
|
@ -2250,6 +2260,7 @@ powderblue
|
|||
ppn
|
||||
pppm
|
||||
prd
|
||||
Prakash
|
||||
pre
|
||||
Pre
|
||||
prec
|
||||
|
|
@ -2283,6 +2294,7 @@ pthread
|
|||
pthreads
|
||||
ptm
|
||||
PTM
|
||||
ptol
|
||||
ptr
|
||||
pu
|
||||
purdue
|
||||
|
|
@ -2388,6 +2400,7 @@ reflectionstyle
|
|||
regoin
|
||||
Reinders
|
||||
reinit
|
||||
relaxbox
|
||||
relink
|
||||
relTol
|
||||
remappings
|
||||
|
|
@ -2687,9 +2700,9 @@ Startstep
|
|||
statcoul
|
||||
statcoulombs
|
||||
statvolt
|
||||
stdlib
|
||||
stdin
|
||||
stdio
|
||||
stdlib
|
||||
steelblue
|
||||
Stegailov
|
||||
Steinbach
|
||||
|
|
@ -2853,6 +2866,7 @@ tlsph
|
|||
tmax
|
||||
Tmax
|
||||
tmd
|
||||
tmin
|
||||
Tmin
|
||||
tmp
|
||||
tN
|
||||
|
|
@ -2992,6 +3006,7 @@ uvm
|
|||
uwo
|
||||
Uzdin
|
||||
vacf
|
||||
Vaid
|
||||
valent
|
||||
Valeriu
|
||||
valgrind
|
||||
|
|
@ -3009,6 +3024,7 @@ Vashishta
|
|||
vasp
|
||||
vcm
|
||||
Vcm
|
||||
vdfmax
|
||||
vdim
|
||||
vdisplace
|
||||
vdW
|
||||
|
|
@ -3138,6 +3154,7 @@ xhi
|
|||
xHost
|
||||
Xiaohu
|
||||
Xiaowang
|
||||
Xie
|
||||
xk
|
||||
xlat
|
||||
xlo
|
||||
|
|
@ -3163,8 +3180,8 @@ xy
|
|||
xyz
|
||||
xz
|
||||
xzhou
|
||||
YAFF
|
||||
yaff
|
||||
YAFF
|
||||
Yamada
|
||||
Yazdani
|
||||
Ybar
|
||||
|
|
|
|||
|
|
@ -0,0 +1,23 @@
|
|||
These examples are similar to those in the "min" and "neb" folders.
|
||||
Each example can be run with the following minimization style:
|
||||
- quickmin: qm
|
||||
- fire: fire
|
||||
- fire with optimized options: fire_mod
|
||||
- fire with min_modify options to
|
||||
reproduce fire/old: fire_mod_old
|
||||
- fire/old (previous implementation): fire_old
|
||||
|
||||
Run the NEB examples as:
|
||||
|
||||
mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.sivac.qm
|
||||
mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.sivac.fire
|
||||
mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.sivac.fire_mod
|
||||
mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.sivac.fire_mod_old
|
||||
mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.sivac.fire_old
|
||||
|
||||
mpirun -np 8 lmp_g++ -partition 8x1 -in in.neb.sivac.qm
|
||||
mpirun -np 8 lmp_g++ -partition 8x1 -in in.neb.sivac.fire
|
||||
mpirun -np 8 lmp_g++ -partition 8x1 -in in.neb.sivac.fire_mod
|
||||
mpirun -np 8 lmp_g++ -partition 8x1 -in in.neb.sivac.fire_mod_old
|
||||
mpirun -np 8 lmp_g++ -partition 8x1 -in in.neb.sivac.fire_old
|
||||
|
||||
|
|
@ -0,0 +1,18 @@
|
|||
# DATE: 2007-06-11 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Stillinger and Weber, Phys Rev B, 31, 5262, (1985)
|
||||
# Stillinger-Weber parameters for various elements and mixtures
|
||||
# multiple entries can be added to this file, LAMMPS reads the ones it needs
|
||||
# these entries are in LAMMPS "metal" units:
|
||||
# epsilon = eV; sigma = Angstroms
|
||||
# other quantities are unitless
|
||||
|
||||
# format of a single entry (one or more lines):
|
||||
# element 1, element 2, element 3,
|
||||
# epsilon, sigma, a, lambda, gamma, costheta0, A, B, p, q, tol
|
||||
|
||||
# Here are the original parameters in metal units, for Silicon from:
|
||||
#
|
||||
# Stillinger and Weber, Phys. Rev. B, v. 31, p. 5262, (1985)
|
||||
#
|
||||
|
||||
Si Si Si 2.1683 2.0951 1.80 21.0 1.20 -0.333333333333
|
||||
7.049556277 0.6022245584 4.0 0.0 0.0
|
||||
|
|
@ -0,0 +1,8 @@
|
|||
7
|
||||
174 6.86775 9.49992 9.62069
|
||||
175 9.46441 6.90709 9.62317
|
||||
301 6.87004 6.90631 12.2171
|
||||
304 8.44266 8.48312 11.1965
|
||||
306 10.5121 8.48457 13.2624
|
||||
331 8.44223 10.5435 13.2633
|
||||
337 10.5124 10.5437 11.1959
|
||||
|
|
@ -0,0 +1,45 @@
|
|||
# 2d Lennard-Jones melt and subsequent energy minimization
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
|
||||
lattice sq2 0.8442
|
||||
region box block 0 20 0 20 -0.1 0.1
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 5.0 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 100 dump.min
|
||||
|
||||
#dump 2 all image 50 image.*.jpg type type &
|
||||
# zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 50 movie.mpg type type &
|
||||
# zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
#dump_modify 1 every 25
|
||||
|
||||
thermo 50
|
||||
min_style cg
|
||||
minimize 0.0 1.0e-6 10000 10000
|
||||
|
|
@ -0,0 +1,45 @@
|
|||
# 2d Lennard-Jones melt and subsequent energy minimization
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
|
||||
lattice sq2 0.8442
|
||||
region box block 0 20 0 20 -0.1 0.1
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 5.0 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 100 dump.min
|
||||
|
||||
#dump 2 all image 50 image.*.jpg type type &
|
||||
# zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 50 movie.mpg type type &
|
||||
# zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
#dump_modify 1 every 25
|
||||
|
||||
thermo 50
|
||||
min_style fire
|
||||
minimize 0.0 1.0e-6 10000 10000
|
||||
|
|
@ -0,0 +1,46 @@
|
|||
# 2d Lennard-Jones melt and subsequent energy minimization
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
|
||||
lattice sq2 0.8442
|
||||
region box block 0 20 0 20 -0.1 0.1
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 5.0 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 100 dump.min
|
||||
|
||||
#dump 2 all image 50 image.*.jpg type type &
|
||||
# zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 50 movie.mpg type type &
|
||||
# zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
#dump_modify 1 every 25
|
||||
|
||||
thermo 50
|
||||
min_style fire
|
||||
min_modify alpha0 0.10 integrator verlet
|
||||
minimize 0.0 1.0e-6 10000 10000
|
||||
|
|
@ -0,0 +1,48 @@
|
|||
# 2d Lennard-Jones melt and subsequent energy minimization
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
|
||||
lattice sq2 0.8442
|
||||
region box block 0 20 0 20 -0.1 0.1
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 5.0 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 100 dump.min
|
||||
|
||||
#dump 2 all image 50 image.*.jpg type type &
|
||||
# zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 50 movie.mpg type type &
|
||||
# zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
#dump_modify 1 every 25
|
||||
|
||||
thermo 50
|
||||
min_style fire
|
||||
min_modify integrator eulerexplicit tmax 10.0 tmin 0.0 delaystep 5 &
|
||||
dtgrow 1.1 dtshrink 0.5 alpha0 0.1 alphashrink 0.99 &
|
||||
vdfmax 100000 halfstepback no initialdelay no
|
||||
minimize 0.0 1.0e-6 10000 10000
|
||||
|
|
@ -0,0 +1,45 @@
|
|||
# 2d Lennard-Jones melt and subsequent energy minimization
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
|
||||
lattice sq2 0.8442
|
||||
region box block 0 20 0 20 -0.1 0.1
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 5.0 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 100 dump.min
|
||||
|
||||
#dump 2 all image 50 image.*.jpg type type &
|
||||
# zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 50 movie.mpg type type &
|
||||
# zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
#dump_modify 1 every 25
|
||||
|
||||
thermo 50
|
||||
min_style fire/old
|
||||
minimize 0.0 1.0e-6 10000 10000
|
||||
|
|
@ -0,0 +1,78 @@
|
|||
# NEB simulation of vacancy hopping in silicon crystal
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# coordination number cutoff
|
||||
|
||||
variable r equal 2.835
|
||||
|
||||
# diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a &
|
||||
a1 1.0 0.0 0.0 &
|
||||
a2 0.0 1.0 0.0 &
|
||||
a3 0.0 0.0 1.0 &
|
||||
basis 0.0 0.0 0.0 &
|
||||
basis 0.0 0.5 0.5 &
|
||||
basis 0.5 0.0 0.5 &
|
||||
basis 0.5 0.5 0.0 &
|
||||
basis 0.25 0.25 0.25 &
|
||||
basis 0.25 0.75 0.75 &
|
||||
basis 0.75 0.25 0.75 &
|
||||
basis 0.75 0.75 0.25
|
||||
|
||||
region myreg block 0 4 &
|
||||
0 4 &
|
||||
0 4
|
||||
|
||||
#create_box 1 myreg
|
||||
#create_atoms 1 region myreg
|
||||
#mass 1 28.06
|
||||
#write_data initial.sivac
|
||||
|
||||
read_data initial.sivac
|
||||
|
||||
# make a vacancy
|
||||
|
||||
group Si type 1
|
||||
|
||||
group del id 300
|
||||
delete_atoms group del compress no
|
||||
group vacneigh id 174 175 301 304 306 331 337
|
||||
|
||||
# choose potential
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si
|
||||
|
||||
# set up neb run
|
||||
|
||||
variable u uloop 20
|
||||
|
||||
# only output atoms near vacancy
|
||||
|
||||
#dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z
|
||||
|
||||
# initial minimization to relax vacancy
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 123456
|
||||
minimize 1.0e-6 1.0e-4 1000 10000
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
fix 1 all neb 1.0
|
||||
|
||||
thermo 100
|
||||
|
||||
# run NEB for 2000 steps or to force tolerance
|
||||
|
||||
timestep 0.01
|
||||
min_style fire
|
||||
|
||||
neb 0.0 0.01 100 100 10 final final.sivac
|
||||
|
|
@ -0,0 +1,78 @@
|
|||
# NEB simulation of vacancy hopping in silicon crystal
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# coordination number cutoff
|
||||
|
||||
variable r equal 2.835
|
||||
|
||||
# diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a &
|
||||
a1 1.0 0.0 0.0 &
|
||||
a2 0.0 1.0 0.0 &
|
||||
a3 0.0 0.0 1.0 &
|
||||
basis 0.0 0.0 0.0 &
|
||||
basis 0.0 0.5 0.5 &
|
||||
basis 0.5 0.0 0.5 &
|
||||
basis 0.5 0.5 0.0 &
|
||||
basis 0.25 0.25 0.25 &
|
||||
basis 0.25 0.75 0.75 &
|
||||
basis 0.75 0.25 0.75 &
|
||||
basis 0.75 0.75 0.25
|
||||
|
||||
region myreg block 0 4 &
|
||||
0 4 &
|
||||
0 4
|
||||
|
||||
#create_box 1 myreg
|
||||
#create_atoms 1 region myreg
|
||||
#mass 1 28.06
|
||||
#write_data initial.sivac
|
||||
|
||||
read_data initial.sivac
|
||||
|
||||
# make a vacancy
|
||||
|
||||
group Si type 1
|
||||
|
||||
group del id 300
|
||||
delete_atoms group del compress no
|
||||
group vacneigh id 174 175 301 304 306 331 337
|
||||
|
||||
# choose potential
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si
|
||||
|
||||
# set up neb run
|
||||
|
||||
variable u uloop 20
|
||||
|
||||
# only output atoms near vacancy
|
||||
|
||||
#dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z
|
||||
|
||||
# initial minimization to relax vacancy
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 123456
|
||||
minimize 1.0e-6 1.0e-4 1000 10000
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
fix 1 all neb 1.0
|
||||
|
||||
thermo 100
|
||||
|
||||
# run NEB for 2000 steps or to force tolerance
|
||||
|
||||
timestep 0.01
|
||||
min_style fire
|
||||
min_modify integrator verlet
|
||||
neb 0.0 0.01 100 100 10 final final.sivac
|
||||
|
|
@ -0,0 +1,80 @@
|
|||
# NEB simulation of vacancy hopping in silicon crystal
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# coordination number cutoff
|
||||
|
||||
variable r equal 2.835
|
||||
|
||||
# diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a &
|
||||
a1 1.0 0.0 0.0 &
|
||||
a2 0.0 1.0 0.0 &
|
||||
a3 0.0 0.0 1.0 &
|
||||
basis 0.0 0.0 0.0 &
|
||||
basis 0.0 0.5 0.5 &
|
||||
basis 0.5 0.0 0.5 &
|
||||
basis 0.5 0.5 0.0 &
|
||||
basis 0.25 0.25 0.25 &
|
||||
basis 0.25 0.75 0.75 &
|
||||
basis 0.75 0.25 0.75 &
|
||||
basis 0.75 0.75 0.25
|
||||
|
||||
region myreg block 0 4 &
|
||||
0 4 &
|
||||
0 4
|
||||
|
||||
#create_box 1 myreg
|
||||
#create_atoms 1 region myreg
|
||||
#mass 1 28.06
|
||||
#write_data initial.sivac
|
||||
|
||||
read_data initial.sivac
|
||||
|
||||
# make a vacancy
|
||||
|
||||
group Si type 1
|
||||
|
||||
group del id 300
|
||||
delete_atoms group del compress no
|
||||
group vacneigh id 174 175 301 304 306 331 337
|
||||
|
||||
# choose potential
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si
|
||||
|
||||
# set up neb run
|
||||
|
||||
variable u uloop 20
|
||||
|
||||
# only output atoms near vacancy
|
||||
|
||||
#dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z
|
||||
|
||||
# initial minimization to relax vacancy
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 123456
|
||||
minimize 1.0e-6 1.0e-4 1000 10000
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
fix 1 all neb 1.0
|
||||
|
||||
thermo 100
|
||||
|
||||
# run NEB for 2000 steps or to force tolerance
|
||||
|
||||
timestep 0.01
|
||||
min_style fire
|
||||
min_modify integrator eulerexplicit tmax 10.0 tmin 0.0 delaystep 5 &
|
||||
dtgrow 1.1 dtshrink 0.5 alpha0 0.1 alphashrink 0.99 &
|
||||
vdfmax 100000 halfstepback no initialdelay no
|
||||
neb 0.0 0.01 100 100 10 final final.sivac
|
||||
|
|
@ -0,0 +1,78 @@
|
|||
# NEB simulation of vacancy hopping in silicon crystal
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# coordination number cutoff
|
||||
|
||||
variable r equal 2.835
|
||||
|
||||
# diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a &
|
||||
a1 1.0 0.0 0.0 &
|
||||
a2 0.0 1.0 0.0 &
|
||||
a3 0.0 0.0 1.0 &
|
||||
basis 0.0 0.0 0.0 &
|
||||
basis 0.0 0.5 0.5 &
|
||||
basis 0.5 0.0 0.5 &
|
||||
basis 0.5 0.5 0.0 &
|
||||
basis 0.25 0.25 0.25 &
|
||||
basis 0.25 0.75 0.75 &
|
||||
basis 0.75 0.25 0.75 &
|
||||
basis 0.75 0.75 0.25
|
||||
|
||||
region myreg block 0 4 &
|
||||
0 4 &
|
||||
0 4
|
||||
|
||||
#create_box 1 myreg
|
||||
#create_atoms 1 region myreg
|
||||
#mass 1 28.06
|
||||
#write_data initial.sivac
|
||||
|
||||
read_data initial.sivac
|
||||
|
||||
# make a vacancy
|
||||
|
||||
group Si type 1
|
||||
|
||||
group del id 300
|
||||
delete_atoms group del compress no
|
||||
group vacneigh id 174 175 301 304 306 331 337
|
||||
|
||||
# choose potential
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si
|
||||
|
||||
# set up neb run
|
||||
|
||||
variable u uloop 20
|
||||
|
||||
# only output atoms near vacancy
|
||||
|
||||
#dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z
|
||||
|
||||
# initial minimization to relax vacancy
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 123456
|
||||
minimize 1.0e-6 1.0e-4 1000 10000
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
fix 1 all neb 1.0
|
||||
|
||||
thermo 100
|
||||
|
||||
# run NEB for 2000 steps or to force tolerance
|
||||
|
||||
timestep 0.01
|
||||
min_style fire/old
|
||||
|
||||
neb 0.0 0.01 100 100 10 final final.sivac
|
||||
|
|
@ -0,0 +1,78 @@
|
|||
# NEB simulation of vacancy hopping in silicon crystal
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# coordination number cutoff
|
||||
|
||||
variable r equal 2.835
|
||||
|
||||
# diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a &
|
||||
a1 1.0 0.0 0.0 &
|
||||
a2 0.0 1.0 0.0 &
|
||||
a3 0.0 0.0 1.0 &
|
||||
basis 0.0 0.0 0.0 &
|
||||
basis 0.0 0.5 0.5 &
|
||||
basis 0.5 0.0 0.5 &
|
||||
basis 0.5 0.5 0.0 &
|
||||
basis 0.25 0.25 0.25 &
|
||||
basis 0.25 0.75 0.75 &
|
||||
basis 0.75 0.25 0.75 &
|
||||
basis 0.75 0.75 0.25
|
||||
|
||||
region myreg block 0 4 &
|
||||
0 4 &
|
||||
0 4
|
||||
|
||||
#create_box 1 myreg
|
||||
#create_atoms 1 region myreg
|
||||
#mass 1 28.06
|
||||
#write_data initial.sivac
|
||||
|
||||
read_data initial.sivac
|
||||
|
||||
# make a vacancy
|
||||
|
||||
group Si type 1
|
||||
|
||||
group del id 300
|
||||
delete_atoms group del compress no
|
||||
group vacneigh id 174 175 301 304 306 331 337
|
||||
|
||||
# choose potential
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si
|
||||
|
||||
# set up neb run
|
||||
|
||||
variable u uloop 20
|
||||
|
||||
# only output atoms near vacancy
|
||||
|
||||
#dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z
|
||||
|
||||
# initial minimization to relax vacancy
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 123456
|
||||
minimize 1.0e-6 1.0e-4 1000 10000
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
fix 1 all neb 1.0
|
||||
|
||||
thermo 100
|
||||
|
||||
# run NEB for 2000 steps or to force tolerance
|
||||
|
||||
timestep 0.01
|
||||
min_style quickmin
|
||||
|
||||
neb 0.0 0.01 100 100 10 final final.sivac
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,155 @@
|
|||
LAMMPS (09 Jan 2020)
|
||||
# 2d Lennard-Jones melt and subsequent energy minimization
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box block 0 20 0 20 -0.1 0.1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 800 atoms
|
||||
create_atoms CPU = 0.000325 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 5.0 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 100 dump.min
|
||||
|
||||
#dump 2 all image 50 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 50 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 22 22 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.057 | 3.057 | 3.057 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 5 -2.461717 0 2.532033 5.0190509
|
||||
100 3.2788864 -0.74311698 0 2.5316708 15.912832
|
||||
200 3.3041082 -0.77000277 0 2.5299752 15.602653
|
||||
300 3.3840228 -0.84859211 0 2.5312006 15.188203
|
||||
400 3.3916063 -0.85694601 0 2.5304208 15.383853
|
||||
500 3.3136052 -0.77935263 0 2.5301106 15.833296
|
||||
600 3.3888915 -0.85213743 0 2.532518 15.162759
|
||||
700 3.2123675 -0.67642318 0 2.5319289 16.310565
|
||||
800 3.3016275 -0.76569171 0 2.5318087 15.639335
|
||||
900 3.4639203 -0.92788002 0 2.5317104 14.765912
|
||||
1000 3.3256788 -0.79078181 0 2.5307399 15.599298
|
||||
Loop time of 0.149596 on 1 procs for 1000 steps with 800 atoms
|
||||
|
||||
Performance: 2887777.748 tau/day, 6684.671 timesteps/s
|
||||
98.6% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.092428 | 0.092428 | 0.092428 | 0.0 | 61.79
|
||||
Neigh | 0.040435 | 0.040435 | 0.040435 | 0.0 | 27.03
|
||||
Comm | 0.003456 | 0.003456 | 0.003456 | 0.0 | 2.31
|
||||
Output | 0.000191 | 0.000191 | 0.000191 | 0.0 | 0.13
|
||||
Modify | 0.009599 | 0.009599 | 0.009599 | 0.0 | 6.42
|
||||
Other | | 0.003487 | | | 2.33
|
||||
|
||||
Nlocal: 800 ave 800 max 800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 317 ave 317 max 317 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7743 ave 7743 max 7743 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7743
|
||||
Ave neighs/atom = 9.67875
|
||||
Neighbor list builds = 203
|
||||
Dangerous builds = 0
|
||||
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
#dump_modify 1 every 25
|
||||
|
||||
thermo 50
|
||||
min_style cg
|
||||
minimize 0.0 1.0e-6 10000 10000
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.183 | 4.183 | 4.183 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
1000 3.3256788 -0.79078181 0 2.5307399 15.599298
|
||||
1050 3.3256788 -2.8361415 0 0.48538014 1.6090001
|
||||
1100 3.3256788 -2.8661626 0 0.45535906 1.6175322
|
||||
1150 3.3256788 -2.8783275 0 0.44319421 1.6293715
|
||||
1200 3.3256788 -2.8838202 0 0.43770144 1.6393211
|
||||
1250 3.3256788 -2.8956657 0 0.42585599 1.604841
|
||||
1300 3.3256788 -2.9039122 0 0.41760945 1.6594733
|
||||
1350 3.3256788 -2.9100776 0 0.4114441 1.7004165
|
||||
1400 3.3256788 -2.9131297 0 0.40839199 1.7078217
|
||||
1450 3.3256788 -2.9167506 0 0.40477104 1.7780477
|
||||
1500 3.3256788 -2.916974 0 0.4045477 1.7981449
|
||||
1550 3.3256788 -2.9169794 0 0.40454227 1.8023577
|
||||
1600 3.3256788 -2.9169795 0 0.40454213 1.8030228
|
||||
1650 3.3256788 -2.9169795 0 0.40454213 1.8030432
|
||||
1700 3.3256788 -2.9169795 0 0.40454213 1.8030396
|
||||
1750 3.3256788 -2.9169795 0 0.40454213 1.8030394
|
||||
1800 3.3256788 -2.9169795 0 0.40454213 1.8030395
|
||||
1803 3.3256788 -2.9169795 0 0.40454213 1.8030395
|
||||
Loop time of 0.293121 on 1 procs for 803 steps with 800 atoms
|
||||
|
||||
98.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = force tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-0.790781812776 -2.91697954354 -2.91697954354
|
||||
Force two-norm initial, final = 1905.47 9.82516e-07
|
||||
Force max component initial, final = 343.392 3.01878e-07
|
||||
Final line search alpha, max atom move = 1 3.01878e-07
|
||||
Iterations, force evaluations = 803 1596
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.24243 | 0.24243 | 0.24243 | 0.0 | 82.71
|
||||
Neigh | 0.016566 | 0.016566 | 0.016566 | 0.0 | 5.65
|
||||
Comm | 0.00342 | 0.00342 | 0.00342 | 0.0 | 1.17
|
||||
Output | 0.000318 | 0.000318 | 0.000318 | 0.0 | 0.11
|
||||
Modify | 0.005032 | 0.005032 | 0.005032 | 0.0 | 1.72
|
||||
Other | | 0.02536 | | | 8.65
|
||||
|
||||
Nlocal: 800 ave 800 max 800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 329 ave 329 max 329 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 6957 ave 6957 max 6957 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 6957
|
||||
Ave neighs/atom = 8.69625
|
||||
Neighbor list builds = 85
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,172 @@
|
|||
LAMMPS (09 Jan 2020)
|
||||
# 2d Lennard-Jones melt and subsequent energy minimization
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box block 0 20 0 20 -0.1 0.1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 800 atoms
|
||||
create_atoms CPU = 0.00032 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 5.0 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 100 dump.min
|
||||
|
||||
#dump 2 all image 50 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 50 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 22 22 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.057 | 3.057 | 3.057 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 5 -2.461717 0 2.532033 5.0190509
|
||||
100 3.2788864 -0.74311698 0 2.5316708 15.912832
|
||||
200 3.3041082 -0.77000277 0 2.5299752 15.602653
|
||||
300 3.3840228 -0.84859211 0 2.5312006 15.188203
|
||||
400 3.3916063 -0.85694601 0 2.5304208 15.383853
|
||||
500 3.3136052 -0.77935263 0 2.5301106 15.833296
|
||||
600 3.3888915 -0.85213743 0 2.532518 15.162759
|
||||
700 3.2123675 -0.67642318 0 2.5319289 16.310565
|
||||
800 3.3016275 -0.76569171 0 2.5318087 15.639335
|
||||
900 3.4639203 -0.92788002 0 2.5317104 14.765912
|
||||
1000 3.3256788 -0.79078181 0 2.5307399 15.599298
|
||||
Loop time of 0.148541 on 1 procs for 1000 steps with 800 atoms
|
||||
|
||||
Performance: 2908287.947 tau/day, 6732.148 timesteps/s
|
||||
99.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.090497 | 0.090497 | 0.090497 | 0.0 | 60.92
|
||||
Neigh | 0.041085 | 0.041085 | 0.041085 | 0.0 | 27.66
|
||||
Comm | 0.003431 | 0.003431 | 0.003431 | 0.0 | 2.31
|
||||
Output | 0.000188 | 0.000188 | 0.000188 | 0.0 | 0.13
|
||||
Modify | 0.009931 | 0.009931 | 0.009931 | 0.0 | 6.69
|
||||
Other | | 0.003409 | | | 2.29
|
||||
|
||||
Nlocal: 800 ave 800 max 800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 317 ave 317 max 317 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7743 ave 7743 max 7743 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7743
|
||||
Ave neighs/atom = 9.67875
|
||||
Neighbor list builds = 203
|
||||
Dangerous builds = 0
|
||||
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
#dump_modify 1 every 25
|
||||
|
||||
thermo 50
|
||||
min_style fire
|
||||
minimize 0.0 1.0e-6 10000 10000
|
||||
Parameters for fire:
|
||||
dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback relaxbox relaxbox_mod relaxbox_rate ptol
|
||||
0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.058 | 3.058 | 3.058 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
1000 0 -0.79078181 0 -0.79078181 12.79527
|
||||
1050 0.026844171 -2.7795211 0 -2.7527105 -0.87603277
|
||||
1100 0.0034822073 -2.8529023 0 -2.8494245 -1.2124257
|
||||
1150 0.00086547466 -2.868953 0 -2.8680886 -1.2359795
|
||||
1200 0.00097619081 -2.8772187 0 -2.8762437 -1.286455
|
||||
1250 0.0010932112 -2.8815244 0 -2.8804326 -1.3030012
|
||||
1300 0.00011570361 -2.8827401 0 -2.8826246 -1.3040874
|
||||
1350 0.00013328904 -2.8829838 0 -2.8828506 -1.2996017
|
||||
1400 0.00018991693 -2.8844011 0 -2.8842114 -1.2697602
|
||||
1450 0.0017139171 -2.8880702 0 -2.8863584 -1.2367621
|
||||
1500 0.00015838581 -2.891362 0 -2.8912038 -1.1688764
|
||||
1550 3.671122e-05 -2.8920253 0 -2.8919886 -1.1669644
|
||||
1600 8.5025973e-05 -2.8924697 0 -2.8923848 -1.1565595
|
||||
1650 0.00031059668 -2.8932768 0 -2.8929666 -1.1412709
|
||||
1700 8.5903751e-05 -2.8936767 0 -2.8935909 -1.1287456
|
||||
1750 5.1139269e-08 -2.8937466 0 -2.8937466 -1.1280269
|
||||
1800 1.1671203e-07 -2.893751 0 -2.8937509 -1.1269919
|
||||
1850 1.6442171e-07 -2.8937533 0 -2.8937532 -1.1269835
|
||||
1900 2.7880101e-06 -2.8937574 0 -2.8937546 -1.128914
|
||||
1950 9.7931277e-05 -2.8948559 0 -2.894758 -1.1298435
|
||||
2000 8.8954569e-06 -2.8948879 0 -2.894879 -1.1291332
|
||||
2050 1.3956548e-06 -2.8949028 0 -2.8949014 -1.1286287
|
||||
2100 4.250297e-07 -2.8949058 0 -2.8949054 -1.1286873
|
||||
2150 7.8744547e-08 -2.8949064 0 -2.8949063 -1.128789
|
||||
2200 6.1147167e-10 -2.8949064 0 -2.8949064 -1.1288611
|
||||
2250 3.0004658e-10 -2.8949064 0 -2.8949064 -1.1288707
|
||||
2300 1.2118076e-10 -2.8949064 0 -2.8949064 -1.1288784
|
||||
2350 9.1550426e-12 -2.8949064 0 -2.8949064 -1.128882
|
||||
2400 2.7467472e-14 -2.8949064 0 -2.8949064 -1.1288819
|
||||
2450 1.8628857e-14 -2.8949064 0 -2.8949064 -1.1288818
|
||||
2500 6.6730826e-15 -2.8949064 0 -2.8949064 -1.1288818
|
||||
2532 1.4818811e-15 -2.8949064 0 -2.8949064 -1.1288817
|
||||
Loop time of 0.281178 on 1 procs for 1532 steps with 800 atoms
|
||||
|
||||
98.4% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = force tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-0.790781812776 -2.89490640353 -2.89490640353
|
||||
Force two-norm initial, final = 1905.47 9.86158e-07
|
||||
Force max component initial, final = 343.392 6.07974e-07
|
||||
Final line search alpha, max atom move = 0 0
|
||||
Iterations, force evaluations = 1532 1532
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.23639 | 0.23639 | 0.23639 | 0.0 | 84.07
|
||||
Neigh | 0.011136 | 0.011136 | 0.011136 | 0.0 | 3.96
|
||||
Comm | 0.003118 | 0.003118 | 0.003118 | 0.0 | 1.11
|
||||
Output | 0.000591 | 0.000591 | 0.000591 | 0.0 | 0.21
|
||||
Modify | 0.004883 | 0.004883 | 0.004883 | 0.0 | 1.74
|
||||
Other | | 0.02506 | | | 8.91
|
||||
|
||||
Nlocal: 800 ave 800 max 800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 327 ave 327 max 327 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7012 ave 7012 max 7012 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7012
|
||||
Ave neighs/atom = 8.765
|
||||
Neighbor list builds = 55
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,161 @@
|
|||
LAMMPS (09 Jan 2020)
|
||||
# 2d Lennard-Jones melt and subsequent energy minimization
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box block 0 20 0 20 -0.1 0.1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 800 atoms
|
||||
create_atoms CPU = 0.000379 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 5.0 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 100 dump.min
|
||||
|
||||
#dump 2 all image 50 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 50 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 22 22 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.057 | 3.057 | 3.057 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 5 -2.461717 0 2.532033 5.0190509
|
||||
100 3.2788864 -0.74311698 0 2.5316708 15.912832
|
||||
200 3.3041082 -0.77000277 0 2.5299752 15.602653
|
||||
300 3.3840228 -0.84859211 0 2.5312006 15.188203
|
||||
400 3.3916063 -0.85694601 0 2.5304208 15.383853
|
||||
500 3.3136052 -0.77935263 0 2.5301106 15.833296
|
||||
600 3.3888915 -0.85213743 0 2.532518 15.162759
|
||||
700 3.2123675 -0.67642318 0 2.5319289 16.310565
|
||||
800 3.3016275 -0.76569171 0 2.5318087 15.639335
|
||||
900 3.4639203 -0.92788002 0 2.5317104 14.765912
|
||||
1000 3.3256788 -0.79078181 0 2.5307399 15.599298
|
||||
Loop time of 0.15409 on 1 procs for 1000 steps with 800 atoms
|
||||
|
||||
Performance: 2803556.363 tau/day, 6489.714 timesteps/s
|
||||
97.5% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.094416 | 0.094416 | 0.094416 | 0.0 | 61.27
|
||||
Neigh | 0.041223 | 0.041223 | 0.041223 | 0.0 | 26.75
|
||||
Comm | 0.003956 | 0.003956 | 0.003956 | 0.0 | 2.57
|
||||
Output | 0.000253 | 0.000253 | 0.000253 | 0.0 | 0.16
|
||||
Modify | 0.010146 | 0.010146 | 0.010146 | 0.0 | 6.58
|
||||
Other | | 0.004096 | | | 2.66
|
||||
|
||||
Nlocal: 800 ave 800 max 800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 317 ave 317 max 317 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7743 ave 7743 max 7743 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7743
|
||||
Ave neighs/atom = 9.67875
|
||||
Neighbor list builds = 203
|
||||
Dangerous builds = 0
|
||||
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
#dump_modify 1 every 25
|
||||
|
||||
thermo 50
|
||||
min_style fire
|
||||
min_modify alpha0 0.10 integrator verlet
|
||||
minimize 0.0 1.0e-6 10000 10000
|
||||
Parameters for fire:
|
||||
dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback relaxbox relaxbox_mod relaxbox_rate ptol
|
||||
0.1 20 1.1 0.5 0.1 0.99 10 0.02 verlet yes
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.058 | 3.058 | 3.058 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
1000 0 -0.79078181 0 -0.79078181 12.79527
|
||||
1050 0.078268931 -2.7183168 0 -2.6401457 -0.41989487
|
||||
1100 0.004111801 -2.8430419 0 -2.8389353 -1.3043522
|
||||
1150 0.005000915 -2.8768555 0 -2.8718608 -1.2706615
|
||||
1200 0.00221302 -2.8879134 0 -2.8857032 -1.2778479
|
||||
1250 0.00043036592 -2.8939906 0 -2.8935608 -1.268974
|
||||
1300 0.0014677683 -2.8992098 0 -2.8977439 -1.2905094
|
||||
1350 0.00093281043 -2.9019313 0 -2.9009996 -1.2653586
|
||||
1400 0.0005425017 -2.9060403 0 -2.9054984 -1.2368252
|
||||
1450 6.0662419e-05 -2.9065294 0 -2.9064688 -1.2376477
|
||||
1500 3.8768552e-05 -2.9066587 0 -2.9066199 -1.2235528
|
||||
1550 4.8205498e-06 -2.9066767 0 -2.9066719 -1.2267388
|
||||
1600 3.7010898e-07 -2.9066803 0 -2.90668 -1.2280952
|
||||
1650 9.3344403e-09 -2.9066807 0 -2.9066806 -1.22862
|
||||
1700 3.595307e-09 -2.9066807 0 -2.9066807 -1.2285492
|
||||
1750 2.7152688e-11 -2.9066807 0 -2.9066807 -1.2285418
|
||||
1800 2.9643465e-12 -2.9066807 0 -2.9066807 -1.2285402
|
||||
1850 8.8599324e-15 -2.9066807 0 -2.9066807 -1.2285389
|
||||
1900 8.1537037e-15 -2.9066807 0 -2.9066807 -1.2285389
|
||||
1919 1.8744314e-15 -2.9066807 0 -2.9066807 -1.2285389
|
||||
Loop time of 0.172896 on 1 procs for 919 steps with 800 atoms
|
||||
|
||||
98.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = force tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-0.790781812776 -2.90668068533 -2.90668068533
|
||||
Force two-norm initial, final = 1905.47 9.38529e-07
|
||||
Force max component initial, final = 343.392 2.3828e-07
|
||||
Final line search alpha, max atom move = 0 0
|
||||
Iterations, force evaluations = 919 919
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.14136 | 0.14136 | 0.14136 | 0.0 | 81.76
|
||||
Neigh | 0.009759 | 0.009759 | 0.009759 | 0.0 | 5.64
|
||||
Comm | 0.001941 | 0.001941 | 0.001941 | 0.0 | 1.12
|
||||
Output | 0.000313 | 0.000313 | 0.000313 | 0.0 | 0.18
|
||||
Modify | 0.002814 | 0.002814 | 0.002814 | 0.0 | 1.63
|
||||
Other | | 0.01671 | | | 9.66
|
||||
|
||||
Nlocal: 800 ave 800 max 800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 320 ave 320 max 320 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7003 ave 7003 max 7003 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7003
|
||||
Ave neighs/atom = 8.75375
|
||||
Neighbor list builds = 51
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,342 @@
|
|||
LAMMPS (09 Jan 2020)
|
||||
# 2d Lennard-Jones melt and subsequent energy minimization
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box block 0 20 0 20 -0.1 0.1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 800 atoms
|
||||
create_atoms CPU = 0.000356 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 5.0 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 100 dump.min
|
||||
|
||||
#dump 2 all image 50 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 50 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 22 22 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.057 | 3.057 | 3.057 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 5 -2.461717 0 2.532033 5.0190509
|
||||
100 3.2788864 -0.74311698 0 2.5316708 15.912832
|
||||
200 3.3041082 -0.77000277 0 2.5299752 15.602653
|
||||
300 3.3840228 -0.84859211 0 2.5312006 15.188203
|
||||
400 3.3916063 -0.85694601 0 2.5304208 15.383853
|
||||
500 3.3136052 -0.77935263 0 2.5301106 15.833296
|
||||
600 3.3888915 -0.85213743 0 2.532518 15.162759
|
||||
700 3.2123675 -0.67642318 0 2.5319289 16.310565
|
||||
800 3.3016275 -0.76569171 0 2.5318087 15.639335
|
||||
900 3.4639203 -0.92788002 0 2.5317104 14.765912
|
||||
1000 3.3256788 -0.79078181 0 2.5307399 15.599298
|
||||
Loop time of 0.149746 on 1 procs for 1000 steps with 800 atoms
|
||||
|
||||
Performance: 2884885.072 tau/day, 6677.975 timesteps/s
|
||||
98.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.091667 | 0.091667 | 0.091667 | 0.0 | 61.21
|
||||
Neigh | 0.041479 | 0.041479 | 0.041479 | 0.0 | 27.70
|
||||
Comm | 0.003516 | 0.003516 | 0.003516 | 0.0 | 2.35
|
||||
Output | 0.0002 | 0.0002 | 0.0002 | 0.0 | 0.13
|
||||
Modify | 0.009484 | 0.009484 | 0.009484 | 0.0 | 6.33
|
||||
Other | | 0.0034 | | | 2.27
|
||||
|
||||
Nlocal: 800 ave 800 max 800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 317 ave 317 max 317 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7743 ave 7743 max 7743 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7743
|
||||
Ave neighs/atom = 9.67875
|
||||
Neighbor list builds = 203
|
||||
Dangerous builds = 0
|
||||
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
#dump_modify 1 every 25
|
||||
|
||||
thermo 50
|
||||
min_style fire
|
||||
min_modify integrator eulerexplicit tmax 10.0 tmin 0.0 delaystep 5 dtgrow 1.1 dtshrink 0.5 alpha0 0.1 alphashrink 0.99 vdfmax 100000 halfstepback no initialdelay no
|
||||
minimize 0.0 1.0e-6 10000 10000
|
||||
Parameters for fire:
|
||||
dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback relaxbox relaxbox_mod relaxbox_rate ptol
|
||||
0.1 5 1.1 0.5 0.1 0.99 10 0 eulerexplicit no
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.058 | 3.058 | 3.058 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
1000 0 -0.79078181 0 -0.79078181 12.79527
|
||||
1050 0.13353902 -2.5912638 0 -2.4578917 0.5692337
|
||||
1100 0.0089379263 -2.6989463 0 -2.6900196 -0.32199212
|
||||
1150 0.0046843921 -2.759845 0 -2.7551664 -0.7652834
|
||||
1200 0.002846537 -2.789411 0 -2.7865681 -0.96589949
|
||||
1250 0.0010217747 -2.8074831 0 -2.8064626 -1.0829009
|
||||
1300 0.0053781523 -2.8242492 0 -2.8188778 -1.1318106
|
||||
1350 0.00023994777 -2.8341342 0 -2.8338945 -1.163692
|
||||
1400 0.0017009757 -2.840995 0 -2.8392962 -1.16188
|
||||
1450 0.00056400841 -2.8453557 0 -2.8447924 -1.1520067
|
||||
1500 0.00077934345 -2.8479194 0 -2.847141 -1.154398
|
||||
1550 0.00036611219 -2.8514157 0 -2.8510501 -1.172244
|
||||
1600 8.9292311e-06 -2.8527434 0 -2.8527345 -1.1747761
|
||||
1650 1.5128835e-06 -2.8542463 0 -2.8542448 -1.1844146
|
||||
1700 3.204798e-06 -2.855907 0 -2.8559038 -1.1947962
|
||||
1750 0.00074224769 -2.8571164 0 -2.8563751 -1.1985933
|
||||
1800 0.00019536702 -2.8588894 0 -2.8586943 -1.2088321
|
||||
1850 9.7569763e-05 -2.8594962 0 -2.8593988 -1.2118745
|
||||
1900 5.7320544e-05 -2.8602172 0 -2.86016 -1.2102157
|
||||
1950 4.5526736e-05 -2.8607722 0 -2.8607267 -1.2106069
|
||||
2000 2.723482e-05 -2.8615425 0 -2.8615153 -1.2116304
|
||||
2050 0.00058266182 -2.862351 0 -2.8617691 -1.2144959
|
||||
2100 6.500145e-05 -2.8634861 0 -2.8634212 -1.2196925
|
||||
2150 7.018255e-05 -2.8659666 0 -2.8658965 -1.2281308
|
||||
2200 2.7358137e-05 -2.8670193 0 -2.866992 -1.2249437
|
||||
2250 4.0619564e-05 -2.8677954 0 -2.8677549 -1.2264181
|
||||
2300 0.00037079927 -2.869037 0 -2.8686666 -1.2228396
|
||||
2350 1.7039984e-05 -2.8697054 0 -2.8696884 -1.2193694
|
||||
2400 1.1706376e-05 -2.8704557 0 -2.870444 -1.2151924
|
||||
2450 1.569166e-05 -2.8710048 0 -2.8709891 -1.2116495
|
||||
2500 1.0764974e-05 -2.8713737 0 -2.8713629 -1.2095378
|
||||
2550 0.00020637438 -2.8718339 0 -2.8716277 -1.2073921
|
||||
2600 1.3281629e-05 -2.8721042 0 -2.8720909 -1.2072822
|
||||
2650 1.6997328e-05 -2.8725439 0 -2.8725269 -1.2078205
|
||||
2700 0.00024308504 -2.8734078 0 -2.873165 -1.2083205
|
||||
2750 1.9325652e-05 -2.8742725 0 -2.8742532 -1.2086037
|
||||
2800 0.00041115503 -2.8753309 0 -2.8749202 -1.2099241
|
||||
2850 0.00016124812 -2.8763004 0 -2.8761394 -1.2100234
|
||||
2900 0.00010261801 -2.8769077 0 -2.8768052 -1.2095838
|
||||
2950 8.5284152e-05 -2.8773786 0 -2.8772935 -1.20663
|
||||
3000 3.6509277e-07 -2.8779105 0 -2.8779102 -1.2054539
|
||||
3050 0.00043346474 -2.8786802 0 -2.8782473 -1.2002574
|
||||
3100 5.5020715e-05 -2.8790024 0 -2.8789474 -1.1951741
|
||||
3150 2.1984131e-05 -2.8794335 0 -2.8794115 -1.1862473
|
||||
3200 1.6745891e-05 -2.8795341 0 -2.8795174 -1.1857447
|
||||
3250 6.7600713e-06 -2.8797504 0 -2.8797436 -1.1851768
|
||||
3300 2.5404023e-05 -2.8799202 0 -2.8798949 -1.1853619
|
||||
3350 1.4307979e-07 -2.8800767 0 -2.8800766 -1.1855388
|
||||
3400 2.3771289e-05 -2.8802876 0 -2.8802639 -1.1853283
|
||||
3450 1.5926609e-05 -2.8811779 0 -2.881162 -1.1832155
|
||||
3500 0.00023918123 -2.8816592 0 -2.8814203 -1.1795992
|
||||
3550 2.1477822e-05 -2.8818075 0 -2.881786 -1.1764183
|
||||
3600 2.4171891e-06 -2.8818685 0 -2.8818661 -1.1752634
|
||||
3650 5.1078051e-06 -2.8820201 0 -2.882015 -1.1735854
|
||||
3700 2.8288283e-06 -2.8820776 0 -2.8820748 -1.1736177
|
||||
3750 2.8261894e-05 -2.8821692 0 -2.882141 -1.1739042
|
||||
3800 2.1722286e-05 -2.8823134 0 -2.8822917 -1.174473
|
||||
3850 2.269858e-05 -2.8824364 0 -2.8824137 -1.174537
|
||||
3900 1.6463034e-06 -2.8825758 0 -2.8825741 -1.1738041
|
||||
3950 1.8888587e-05 -2.8827475 0 -2.8827287 -1.1730456
|
||||
4000 7.7137595e-07 -2.8829271 0 -2.8829263 -1.1737585
|
||||
4050 8.0218395e-06 -2.8831189 0 -2.8831108 -1.1748314
|
||||
4100 2.1775628e-07 -2.8831738 0 -2.8831736 -1.1751807
|
||||
4150 7.0972401e-06 -2.8832308 0 -2.8832237 -1.1756641
|
||||
4200 4.1552084e-07 -2.8833365 0 -2.8833361 -1.1766505
|
||||
4250 6.955018e-06 -2.8833891 0 -2.8833822 -1.1770815
|
||||
4300 0.00016095054 -2.8835126 0 -2.8833519 -1.1780786
|
||||
4350 6.2109296e-08 -2.8836037 0 -2.8836036 -1.1788493
|
||||
4400 4.9552761e-05 -2.8838275 0 -2.883778 -1.1796751
|
||||
4450 4.1572651e-06 -2.8840252 0 -2.884021 -1.1797244
|
||||
4500 4.5094019e-05 -2.8841528 0 -2.8841078 -1.1793634
|
||||
4550 1.5486277e-06 -2.8843566 0 -2.884355 -1.1786658
|
||||
4600 3.124141e-06 -2.8845241 0 -2.884521 -1.1782676
|
||||
4650 2.6550727e-06 -2.8847548 0 -2.8847521 -1.1761931
|
||||
4700 4.1414628e-05 -2.8849662 0 -2.8849249 -1.1718684
|
||||
4750 2.380964e-06 -2.8851283 0 -2.8851259 -1.1692959
|
||||
4800 8.590119e-06 -2.8852449 0 -2.8852364 -1.1685065
|
||||
4850 2.2696517e-05 -2.8854127 0 -2.88539 -1.168484
|
||||
4900 2.5100677e-05 -2.8855573 0 -2.8855322 -1.1680468
|
||||
4950 1.0901958e-05 -2.8857056 0 -2.8856947 -1.1667983
|
||||
5000 1.7660672e-05 -2.8858561 0 -2.8858385 -1.1659289
|
||||
5050 2.2115169e-05 -2.886002 0 -2.8859799 -1.1652871
|
||||
5100 6.6278908e-05 -2.8861968 0 -2.8861306 -1.1648902
|
||||
5150 6.0993884e-07 -2.8862934 0 -2.8862928 -1.1650736
|
||||
5200 0.00020333351 -2.8864792 0 -2.8862761 -1.1684121
|
||||
5250 0.00018260896 -2.8869006 0 -2.8867182 -1.1738451
|
||||
5300 5.9589204e-06 -2.8870944 0 -2.8870884 -1.1742236
|
||||
5350 3.9611705e-06 -2.8871855 0 -2.8871815 -1.1739438
|
||||
5400 1.6390307e-05 -2.8872444 0 -2.8872281 -1.1738633
|
||||
5450 1.0471949e-06 -2.8872779 0 -2.8872769 -1.173992
|
||||
5500 3.189532e-07 -2.8873146 0 -2.8873143 -1.1745333
|
||||
5550 8.5416909e-08 -2.8873521 0 -2.8873521 -1.1754741
|
||||
5600 2.8826987e-06 -2.8873622 0 -2.8873594 -1.1757461
|
||||
5650 1.4702624e-06 -2.8873706 0 -2.8873692 -1.1760765
|
||||
5700 1.569283e-07 -2.887379 0 -2.8873788 -1.1765
|
||||
5750 9.0040106e-07 -2.8873905 0 -2.8873896 -1.1767106
|
||||
5800 1.076564e-06 -2.8873972 0 -2.8873961 -1.1770001
|
||||
5850 1.1722255e-05 -2.8874127 0 -2.887401 -1.1774243
|
||||
5900 6.6748066e-06 -2.8874365 0 -2.8874298 -1.1778224
|
||||
5950 4.0946269e-07 -2.887452 0 -2.8874516 -1.1780297
|
||||
6000 6.4175894e-06 -2.8875862 0 -2.8875798 -1.1784951
|
||||
6050 2.32222e-06 -2.8878816 0 -2.8878793 -1.1754314
|
||||
6100 4.8037437e-08 -2.8879173 0 -2.8879173 -1.1743701
|
||||
6150 1.2097382e-06 -2.8879311 0 -2.8879299 -1.1736632
|
||||
6200 5.6948854e-06 -2.8879415 0 -2.8879358 -1.1733347
|
||||
6250 1.6901358e-06 -2.8879479 0 -2.8879462 -1.173324
|
||||
6300 9.6454886e-08 -2.8879494 0 -2.8879493 -1.1732735
|
||||
6350 4.8509801e-08 -2.8879504 0 -2.8879504 -1.1732669
|
||||
6400 4.4545703e-07 -2.8879518 0 -2.8879514 -1.1732436
|
||||
6450 1.2032088e-07 -2.8879532 0 -2.887953 -1.1732129
|
||||
6500 1.2605568e-08 -2.8879538 0 -2.8879538 -1.1731965
|
||||
6550 4.1040039e-10 -2.8879551 0 -2.8879551 -1.1731405
|
||||
6600 7.9776654e-08 -2.8879555 0 -2.8879554 -1.1731158
|
||||
6650 5.1675071e-08 -2.8879559 0 -2.8879559 -1.1730858
|
||||
6700 2.1758232e-08 -2.8879563 0 -2.8879562 -1.173055
|
||||
6750 2.2209691e-08 -2.8879565 0 -2.8879565 -1.1730317
|
||||
6800 1.8884076e-08 -2.8879568 0 -2.8879568 -1.1729911
|
||||
6850 7.0472036e-09 -2.8879572 0 -2.8879572 -1.1729351
|
||||
6900 6.4326889e-09 -2.8879573 0 -2.8879573 -1.172905
|
||||
6950 7.5488985e-09 -2.8879575 0 -2.8879575 -1.1728674
|
||||
7000 4.8486872e-09 -2.8879576 0 -2.8879576 -1.1728448
|
||||
7050 6.4279746e-09 -2.8879578 0 -2.8879577 -1.1727942
|
||||
7100 1.2729822e-09 -2.8879578 0 -2.8879578 -1.1727679
|
||||
7150 1.7002943e-09 -2.8879579 0 -2.8879579 -1.1727462
|
||||
7200 1.2498153e-10 -2.887958 0 -2.887958 -1.1726894
|
||||
7250 5.1498355e-08 -2.8879581 0 -2.8879581 -1.1726362
|
||||
7300 5.292335e-09 -2.8879582 0 -2.8879581 -1.1726177
|
||||
7350 2.8343246e-09 -2.8879582 0 -2.8879582 -1.1725957
|
||||
7400 1.7979847e-09 -2.8879582 0 -2.8879582 -1.1725747
|
||||
7450 1.4994133e-09 -2.8879582 0 -2.8879582 -1.1725599
|
||||
7500 1.2793921e-09 -2.8879583 0 -2.8879583 -1.1725352
|
||||
7550 5.737782e-10 -2.8879583 0 -2.8879583 -1.1725028
|
||||
7600 5.5986883e-10 -2.8879583 0 -2.8879583 -1.1724865
|
||||
7650 8.3377699e-10 -2.8879583 0 -2.8879583 -1.1724667
|
||||
7700 1.676793e-09 -2.8879583 0 -2.8879583 -1.1724537
|
||||
7750 3.7057732e-09 -2.8879583 0 -2.8879583 -1.1724393
|
||||
7800 1.2469658e-10 -2.8879584 0 -2.8879584 -1.1724136
|
||||
7850 4.2407869e-12 -2.8879584 0 -2.8879584 -1.172387
|
||||
7900 1.9275374e-11 -2.8879584 0 -2.8879584 -1.1723671
|
||||
7950 7.4412023e-10 -2.8879584 0 -2.8879584 -1.1723587
|
||||
8000 2.342806e-10 -2.8879584 0 -2.8879584 -1.1723487
|
||||
8050 1.4026755e-10 -2.8879584 0 -2.8879584 -1.1723382
|
||||
8100 1.6705221e-10 -2.8879584 0 -2.8879584 -1.1723318
|
||||
8150 1.1816748e-10 -2.8879584 0 -2.8879584 -1.172313
|
||||
8200 1.139758e-10 -2.8879584 0 -2.8879584 -1.1723053
|
||||
8250 6.2680955e-11 -2.8879584 0 -2.8879584 -1.172298
|
||||
8300 6.669349e-11 -2.8879584 0 -2.8879584 -1.172292
|
||||
8350 6.1206666e-10 -2.8879584 0 -2.8879584 -1.1722845
|
||||
8400 8.0987905e-10 -2.8879584 0 -2.8879584 -1.1722751
|
||||
8450 2.8169842e-12 -2.8879584 0 -2.8879584 -1.1722629
|
||||
8500 1.1976624e-09 -2.8879584 0 -2.8879584 -1.1722508
|
||||
8550 1.2769688e-10 -2.8879584 0 -2.8879584 -1.1722467
|
||||
8600 6.9923774e-11 -2.8879584 0 -2.8879584 -1.1722418
|
||||
8650 4.5160888e-11 -2.8879584 0 -2.8879584 -1.1722372
|
||||
8700 3.8279812e-11 -2.8879584 0 -2.8879584 -1.1722341
|
||||
8750 3.3467288e-11 -2.8879584 0 -2.8879584 -1.1722288
|
||||
8800 1.5440356e-11 -2.8879584 0 -2.8879584 -1.1722219
|
||||
8850 1.534376e-11 -2.8879584 0 -2.8879584 -1.1722185
|
||||
8900 2.3131183e-11 -2.8879584 0 -2.8879584 -1.1722144
|
||||
8950 4.6772726e-11 -2.8879584 0 -2.8879584 -1.1722117
|
||||
9000 1.0577837e-10 -2.8879584 0 -2.8879584 -1.1722087
|
||||
9050 3.6207287e-12 -2.8879584 0 -2.8879584 -1.1722035
|
||||
9100 1.2802863e-13 -2.8879584 0 -2.8879584 -1.1721981
|
||||
9150 5.8887842e-13 -2.8879584 0 -2.8879584 -1.1721941
|
||||
9200 2.300678e-11 -2.8879584 0 -2.8879584 -1.1721924
|
||||
9250 7.3278771e-12 -2.8879584 0 -2.8879584 -1.1721904
|
||||
9300 4.4157433e-12 -2.8879584 0 -2.8879584 -1.1721883
|
||||
9350 5.3075512e-12 -2.8879584 0 -2.8879584 -1.172187
|
||||
9400 3.8604199e-12 -2.8879584 0 -2.8879584 -1.1721833
|
||||
9450 3.7145253e-12 -2.8879584 0 -2.8879584 -1.1721818
|
||||
9500 2.0563961e-12 -2.8879584 0 -2.8879584 -1.1721804
|
||||
9550 2.1953054e-12 -2.8879584 0 -2.8879584 -1.1721792
|
||||
9600 2.0292485e-11 -2.8879584 0 -2.8879584 -1.1721777
|
||||
9650 2.7040181e-11 -2.8879584 0 -2.8879584 -1.1721759
|
||||
9700 9.5405566e-14 -2.8879584 0 -2.8879584 -1.1721735
|
||||
9750 4.0766333e-11 -2.8879584 0 -2.8879584 -1.1721712
|
||||
9800 4.3804922e-12 -2.8879584 0 -2.8879584 -1.1721704
|
||||
9850 2.4094174e-12 -2.8879584 0 -2.8879584 -1.1721695
|
||||
9900 1.5618924e-12 -2.8879584 0 -2.8879584 -1.1721686
|
||||
9950 1.3276948e-12 -2.8879584 0 -2.8879584 -1.172168
|
||||
10000 1.1661354e-12 -2.8879584 0 -2.8879584 -1.172167
|
||||
10050 5.4130138e-13 -2.8879584 0 -2.8879584 -1.1721656
|
||||
10100 5.3930245e-13 -2.8879584 0 -2.8879584 -1.172165
|
||||
10150 8.1475776e-13 -2.8879584 0 -2.8879584 -1.1721642
|
||||
10200 1.6498249e-12 -2.8879584 0 -2.8879584 -1.1721637
|
||||
10250 3.7458971e-12 -2.8879584 0 -2.8879584 -1.1721631
|
||||
10300 1.285673e-13 -2.8879584 0 -2.8879584 -1.1721621
|
||||
10350 4.5812377e-15 -2.8879584 0 -2.8879584 -1.1721611
|
||||
10400 2.1117455e-14 -2.8879584 0 -2.8879584 -1.1721603
|
||||
10450 8.2667409e-13 -2.8879584 0 -2.8879584 -1.17216
|
||||
10500 2.6385234e-13 -2.8879584 0 -2.8879584 -1.1721596
|
||||
10550 1.5919509e-13 -2.8879584 0 -2.8879584 -1.1721592
|
||||
10600 1.9165062e-13 -2.8879584 0 -2.8879584 -1.172159
|
||||
10650 1.3972041e-13 -2.8879584 0 -2.8879584 -1.1721583
|
||||
10700 1.3469994e-13 -2.8879584 0 -2.8879584 -1.172158
|
||||
10750 7.4707625e-14 -2.8879584 0 -2.8879584 -1.1721577
|
||||
10800 7.9795578e-14 -2.8879584 0 -2.8879584 -1.1721575
|
||||
10850 7.3860559e-13 -2.8879584 0 -2.8879584 -1.1721572
|
||||
10900 9.8555453e-13 -2.8879584 0 -2.8879584 -1.1721569
|
||||
10950 3.487218e-15 -2.8879584 0 -2.8879584 -1.1721564
|
||||
11000 1.4915771e-12 -2.8879584 0 -2.8879584 -1.172156
|
||||
Loop time of 1.75996 on 1 procs for 10000 steps with 800 atoms
|
||||
|
||||
98.4% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
-0.790781812776 -2.88795843023 -2.88795843023
|
||||
Force two-norm initial, final = 1905.47 9.60915e-05
|
||||
Force max component initial, final = 343.392 3.71774e-05
|
||||
Final line search alpha, max atom move = 0 0
|
||||
Iterations, force evaluations = 10000 10000
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.5377 | 1.5377 | 1.5377 | 0.0 | 87.37
|
||||
Neigh | 0.012664 | 0.012664 | 0.012664 | 0.0 | 0.72
|
||||
Comm | 0.015656 | 0.015656 | 0.015656 | 0.0 | 0.89
|
||||
Output | 0.004186 | 0.004186 | 0.004186 | 0.0 | 0.24
|
||||
Modify | 0.02968 | 0.02968 | 0.02968 | 0.0 | 1.69
|
||||
Other | | 0.16 | | | 9.09
|
||||
|
||||
Nlocal: 800 ave 800 max 800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 311 ave 311 max 311 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7009 ave 7009 max 7009 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7009
|
||||
Ave neighs/atom = 8.76125
|
||||
Neighbor list builds = 66
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
|
|
@ -0,0 +1,338 @@
|
|||
LAMMPS (09 Jan 2020)
|
||||
# 2d Lennard-Jones melt and subsequent energy minimization
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box block 0 20 0 20 -0.1 0.1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 800 atoms
|
||||
create_atoms CPU = 0.000345 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 5.0 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 100 dump.min
|
||||
|
||||
#dump 2 all image 50 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 50 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 22 22 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.057 | 3.057 | 3.057 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 5 -2.461717 0 2.532033 5.0190509
|
||||
100 3.2788864 -0.74311698 0 2.5316708 15.912832
|
||||
200 3.3041082 -0.77000277 0 2.5299752 15.602653
|
||||
300 3.3840228 -0.84859211 0 2.5312006 15.188203
|
||||
400 3.3916063 -0.85694601 0 2.5304208 15.383853
|
||||
500 3.3136052 -0.77935263 0 2.5301106 15.833296
|
||||
600 3.3888915 -0.85213743 0 2.532518 15.162759
|
||||
700 3.2123675 -0.67642318 0 2.5319289 16.310565
|
||||
800 3.3016275 -0.76569171 0 2.5318087 15.639335
|
||||
900 3.4639203 -0.92788002 0 2.5317104 14.765912
|
||||
1000 3.3256788 -0.79078181 0 2.5307399 15.599298
|
||||
Loop time of 0.14894 on 1 procs for 1000 steps with 800 atoms
|
||||
|
||||
Performance: 2900496.844 tau/day, 6714.113 timesteps/s
|
||||
99.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.091005 | 0.091005 | 0.091005 | 0.0 | 61.10
|
||||
Neigh | 0.040404 | 0.040404 | 0.040404 | 0.0 | 27.13
|
||||
Comm | 0.003588 | 0.003588 | 0.003588 | 0.0 | 2.41
|
||||
Output | 0.000226 | 0.000226 | 0.000226 | 0.0 | 0.15
|
||||
Modify | 0.010077 | 0.010077 | 0.010077 | 0.0 | 6.77
|
||||
Other | | 0.00364 | | | 2.44
|
||||
|
||||
Nlocal: 800 ave 800 max 800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 317 ave 317 max 317 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7743 ave 7743 max 7743 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7743
|
||||
Ave neighs/atom = 9.67875
|
||||
Neighbor list builds = 203
|
||||
Dangerous builds = 0
|
||||
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
#dump_modify 1 every 25
|
||||
|
||||
thermo 50
|
||||
min_style fire/old
|
||||
minimize 0.0 1.0e-6 10000 10000
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.058 | 3.058 | 3.058 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
1000 0 -0.79078181 0 -0.79078181 12.79527
|
||||
1050 0.15078629 -2.5003801 0 -2.3497823 1.2721061
|
||||
1100 0.00074837835 -2.7050909 0 -2.7043434 -0.37905868
|
||||
1150 0.0063037865 -2.7509932 0 -2.7446973 -0.71482554
|
||||
1200 0.00034408524 -2.7960993 0 -2.7957557 -1.0263545
|
||||
1250 0.00085176575 -2.8126463 0 -2.8117956 -1.1021125
|
||||
1300 0.00033628622 -2.8280448 0 -2.8277089 -1.1471915
|
||||
1350 0.00026177536 -2.8357089 0 -2.8354474 -1.1676514
|
||||
1400 0.0011622998 -2.8431054 0 -2.8419446 -1.1596473
|
||||
1450 0.0010839093 -2.8457268 0 -2.8446442 -1.1518499
|
||||
1500 0.00024665053 -2.8480136 0 -2.8477672 -1.1520869
|
||||
1550 7.831216e-05 -2.849584 0 -2.8495057 -1.1506084
|
||||
1600 3.2759808e-05 -2.8511231 0 -2.8510904 -1.1497061
|
||||
1650 3.9272607e-05 -2.8526234 0 -2.8525841 -1.1511215
|
||||
1700 5.5569128e-05 -2.8538287 0 -2.8537732 -1.1497192
|
||||
1750 7.4734101e-05 -2.8558245 0 -2.8557498 -1.1480928
|
||||
1800 5.8181251e-05 -2.8575248 0 -2.8574667 -1.1518976
|
||||
1850 2.7589109e-05 -2.8585475 0 -2.85852 -1.1511439
|
||||
1900 0.00024942163 -2.8595367 0 -2.8592876 -1.1467285
|
||||
1950 0.00015592998 -2.8607519 0 -2.8605962 -1.1436241
|
||||
2000 0.00028229354 -2.8619889 0 -2.861707 -1.1439985
|
||||
2050 0.00024971806 -2.8634866 0 -2.8632372 -1.1509204
|
||||
2100 0.00021986576 -2.8646023 0 -2.8643827 -1.1564575
|
||||
2150 0.00011079739 -2.8664318 0 -2.8663211 -1.1525135
|
||||
2200 4.968224e-05 -2.8676285 0 -2.8675789 -1.1577511
|
||||
2250 0.00072993169 -2.8690151 0 -2.868286 -1.1626387
|
||||
2300 0.00036359157 -2.8707132 0 -2.87035 -1.1659444
|
||||
2350 9.6832406e-06 -2.871387 0 -2.8713773 -1.1678889
|
||||
2400 9.1595369e-05 -2.8719934 0 -2.8719019 -1.168413
|
||||
2450 0.00026776536 -2.8727209 0 -2.8724535 -1.1717116
|
||||
2500 3.7718609e-05 -2.8731223 0 -2.8730846 -1.172836
|
||||
2550 9.6791591e-05 -2.8738124 0 -2.8737157 -1.1743997
|
||||
2600 7.2536654e-05 -2.8742543 0 -2.8741818 -1.1746239
|
||||
2650 1.8893154e-06 -2.8749235 0 -2.8749216 -1.1766016
|
||||
2700 2.8723983e-07 -2.8753101 0 -2.8753099 -1.1802186
|
||||
2750 5.7708673e-05 -2.8758588 0 -2.8758012 -1.1854027
|
||||
2800 4.5723463e-07 -2.8762504 0 -2.87625 -1.188637
|
||||
2850 0.00040742553 -2.8770574 0 -2.8766505 -1.1889095
|
||||
2900 0.00019261386 -2.8775383 0 -2.8773459 -1.1935269
|
||||
2950 9.2541507e-06 -2.8779083 0 -2.8778991 -1.1971015
|
||||
3000 4.0734432e-05 -2.8780621 0 -2.8780214 -1.1981841
|
||||
3050 2.6984859e-05 -2.8783255 0 -2.8782986 -1.2005265
|
||||
3100 0.00037203153 -2.8787959 0 -2.8784243 -1.2041583
|
||||
3150 3.7451961e-05 -2.8793384 0 -2.879301 -1.2063399
|
||||
3200 0.00028165903 -2.8799668 0 -2.8796855 -1.2040089
|
||||
3250 9.6738762e-06 -2.880449 0 -2.8804394 -1.1972021
|
||||
3300 2.9461217e-06 -2.8806905 0 -2.8806875 -1.1939943
|
||||
3350 3.5642952e-05 -2.880824 0 -2.8807884 -1.193625
|
||||
3400 6.0881141e-07 -2.8810003 0 -2.8809997 -1.1933965
|
||||
3450 2.3583108e-05 -2.8811075 0 -2.8810839 -1.1928363
|
||||
3500 1.8866811e-05 -2.8813124 0 -2.8812936 -1.1887048
|
||||
3550 4.4326159e-06 -2.8815176 0 -2.8815132 -1.1868378
|
||||
3600 3.7260058e-05 -2.8818335 0 -2.8817963 -1.184903
|
||||
3650 4.5577822e-05 -2.8821473 0 -2.8821018 -1.1851718
|
||||
3700 3.8004179e-05 -2.8824225 0 -2.8823846 -1.1835832
|
||||
3750 4.4633061e-05 -2.8826141 0 -2.8825695 -1.1832413
|
||||
3800 0.00021888149 -2.8832209 0 -2.8830023 -1.1831072
|
||||
3850 6.0865074e-05 -2.8840206 0 -2.8839598 -1.1854745
|
||||
3900 8.5323757e-05 -2.8850341 0 -2.8849489 -1.1854657
|
||||
3950 6.8711987e-07 -2.8858208 0 -2.8858201 -1.1860154
|
||||
4000 0.00013494811 -2.8863852 0 -2.8862504 -1.1781078
|
||||
4050 1.8129952e-05 -2.886732 0 -2.8867139 -1.177396
|
||||
4100 3.8263774e-05 -2.8879089 0 -2.8878707 -1.1752856
|
||||
4150 3.658559e-05 -2.8890262 0 -2.8889897 -1.1734493
|
||||
4200 0.00012015214 -2.8893467 0 -2.8892267 -1.1760827
|
||||
4250 0.00018767456 -2.889917 0 -2.8897296 -1.1786237
|
||||
4300 0.00012637647 -2.8915235 0 -2.8913973 -1.1816011
|
||||
4350 8.2492648e-06 -2.8922133 0 -2.8922051 -1.1808514
|
||||
4400 5.1940315e-05 -2.892508 0 -2.8924562 -1.180161
|
||||
4450 2.4116793e-05 -2.8928525 0 -2.8928284 -1.175724
|
||||
4500 1.7213569e-06 -2.8929309 0 -2.8929292 -1.1774283
|
||||
4550 5.9338191e-06 -2.8929979 0 -2.892992 -1.1770692
|
||||
4600 3.5756493e-06 -2.8930523 0 -2.8930487 -1.1768106
|
||||
4650 6.4365391e-08 -2.8931003 0 -2.8931002 -1.1764066
|
||||
4700 1.9109163e-05 -2.8931378 0 -2.8931187 -1.1761873
|
||||
4750 1.6360653e-06 -2.8931854 0 -2.8931837 -1.1758258
|
||||
4800 2.588147e-06 -2.8932194 0 -2.8932168 -1.1755478
|
||||
4850 2.2695812e-06 -2.893236 0 -2.8932337 -1.1755321
|
||||
4900 8.6290019e-07 -2.893252 0 -2.8932511 -1.1755463
|
||||
4950 5.9986079e-06 -2.8932768 0 -2.8932708 -1.1757398
|
||||
5000 2.7886685e-06 -2.8932946 0 -2.8932919 -1.1759759
|
||||
5050 3.4895687e-07 -2.8933085 0 -2.8933082 -1.176161
|
||||
5100 3.0956189e-07 -2.893326 0 -2.8933257 -1.176581
|
||||
5150 3.6248707e-07 -2.893338 0 -2.8933377 -1.1769306
|
||||
5200 7.8502109e-07 -2.893349 0 -2.8933482 -1.1771957
|
||||
5250 2.0163751e-06 -2.893358 0 -2.893356 -1.1774764
|
||||
5300 1.5694813e-06 -2.8933681 0 -2.8933665 -1.1778313
|
||||
5350 1.6087226e-07 -2.8933778 0 -2.8933776 -1.1781241
|
||||
5400 1.3237298e-06 -2.8933861 0 -2.8933848 -1.1784213
|
||||
5450 4.6902744e-07 -2.8933924 0 -2.8933919 -1.1786315
|
||||
5500 3.4438648e-08 -2.8933991 0 -2.893399 -1.1788989
|
||||
5550 2.7042583e-06 -2.8934069 0 -2.8934042 -1.1794234
|
||||
5600 1.6439602e-06 -2.8934192 0 -2.8934176 -1.1800027
|
||||
5650 3.0743987e-08 -2.8934232 0 -2.8934232 -1.1801474
|
||||
5700 3.9527406e-07 -2.8934289 0 -2.8934285 -1.1803286
|
||||
5750 1.225525e-08 -2.8934371 0 -2.8934371 -1.1807575
|
||||
5800 4.9916581e-06 -2.8934455 0 -2.8934405 -1.181139
|
||||
5850 1.9695167e-07 -2.8934483 0 -2.8934481 -1.1813037
|
||||
5900 9.7192688e-09 -2.8934527 0 -2.8934527 -1.1814006
|
||||
5950 1.6382372e-07 -2.8934559 0 -2.8934557 -1.181466
|
||||
6000 1.6672305e-07 -2.8934582 0 -2.893458 -1.1815167
|
||||
6050 2.1385354e-06 -2.8934621 0 -2.89346 -1.1817115
|
||||
6100 2.1134327e-07 -2.8934647 0 -2.8934644 -1.1817726
|
||||
6150 1.0776963e-07 -2.8934666 0 -2.8934665 -1.1818243
|
||||
6200 1.1340092e-07 -2.8934698 0 -2.8934697 -1.1817959
|
||||
6250 4.8193492e-08 -2.8934719 0 -2.8934718 -1.1818113
|
||||
6300 2.7200421e-07 -2.8934757 0 -2.8934755 -1.1818626
|
||||
6350 5.2129576e-07 -2.8934777 0 -2.8934772 -1.1818984
|
||||
6400 4.274711e-07 -2.8934796 0 -2.8934792 -1.181939
|
||||
6450 3.9574056e-07 -2.8934809 0 -2.8934805 -1.1819686
|
||||
6500 1.4771033e-08 -2.8934829 0 -2.8934829 -1.1820179
|
||||
6550 1.9994259e-09 -2.8934848 0 -2.8934848 -1.182073
|
||||
6600 2.1220811e-09 -2.8934858 0 -2.8934858 -1.1821061
|
||||
6650 9.8083547e-08 -2.8934867 0 -2.8934866 -1.1821395
|
||||
6700 4.8492273e-07 -2.8934877 0 -2.8934872 -1.182221
|
||||
6750 8.9996832e-08 -2.8934884 0 -2.8934883 -1.1823243
|
||||
6800 6.4333635e-08 -2.8934896 0 -2.8934895 -1.1824575
|
||||
6850 7.1095413e-08 -2.8934904 0 -2.8934903 -1.1825552
|
||||
6900 5.2266462e-08 -2.8934909 0 -2.8934909 -1.1825847
|
||||
6950 3.2973112e-08 -2.8934918 0 -2.8934918 -1.1826705
|
||||
7000 3.8926793e-08 -2.8934924 0 -2.8934924 -1.1827266
|
||||
7050 6.0657306e-08 -2.893493 0 -2.8934929 -1.1827998
|
||||
7100 2.1552835e-08 -2.8934937 0 -2.8934937 -1.1828681
|
||||
7150 2.3988432e-08 -2.893494 0 -2.893494 -1.1829117
|
||||
7200 5.0100549e-07 -2.8934949 0 -2.8934944 -1.1831237
|
||||
7250 5.1293833e-07 -2.8934961 0 -2.8934956 -1.1832769
|
||||
7300 4.9193885e-08 -2.8934978 0 -2.8934978 -1.1834501
|
||||
7350 1.7704457e-07 -2.8935041 0 -2.8935039 -1.1838658
|
||||
7400 1.0705432e-05 -2.8935219 0 -2.8935112 -1.1843004
|
||||
7450 7.1746118e-05 -2.8936326 0 -2.893561 -1.1849502
|
||||
7500 3.1813929e-06 -2.8938743 0 -2.8938711 -1.1832931
|
||||
7550 6.3043396e-07 -2.8939295 0 -2.8939289 -1.1820798
|
||||
7600 5.2150405e-07 -2.8939502 0 -2.8939497 -1.1820883
|
||||
7650 4.7517449e-07 -2.8939658 0 -2.8939653 -1.1819437
|
||||
7700 4.4885882e-07 -2.8939757 0 -2.8939752 -1.1817119
|
||||
7750 4.6725067e-07 -2.8939842 0 -2.8939837 -1.1813933
|
||||
7800 4.582757e-07 -2.8939901 0 -2.8939896 -1.1809685
|
||||
7850 5.6014095e-07 -2.8939959 0 -2.8939954 -1.1803629
|
||||
7900 4.9239111e-07 -2.8940002 0 -2.8939997 -1.1799761
|
||||
7950 5.8652837e-07 -2.8940042 0 -2.8940036 -1.179493
|
||||
8000 5.2119991e-07 -2.894007 0 -2.8940065 -1.1792154
|
||||
8050 5.6171299e-07 -2.8940096 0 -2.8940091 -1.1789381
|
||||
8100 5.1588922e-07 -2.8940115 0 -2.894011 -1.1788465
|
||||
8150 5.8224721e-07 -2.8940133 0 -2.8940127 -1.1786473
|
||||
8200 4.734318e-07 -2.8940145 0 -2.894014 -1.1784863
|
||||
8250 6.5262092e-07 -2.8940158 0 -2.8940151 -1.1783061
|
||||
8300 6.1708016e-07 -2.8940165 0 -2.8940159 -1.1781777
|
||||
8350 6.8388448e-08 -2.8940173 0 -2.8940172 -1.1779926
|
||||
8400 8.4463536e-08 -2.8940181 0 -2.894018 -1.177889
|
||||
8450 3.9363627e-07 -2.8940188 0 -2.8940184 -1.1777552
|
||||
8500 3.0541987e-10 -2.8940193 0 -2.8940193 -1.1776655
|
||||
8550 2.9629605e-09 -2.8940199 0 -2.8940199 -1.1774346
|
||||
8600 2.6219397e-09 -2.8940203 0 -2.8940203 -1.1772429
|
||||
8650 7.2863159e-09 -2.8940208 0 -2.8940208 -1.1771118
|
||||
8700 5.3112415e-09 -2.8940212 0 -2.8940211 -1.1770375
|
||||
8750 1.0799289e-08 -2.8940216 0 -2.8940216 -1.1769494
|
||||
8800 1.0335141e-08 -2.894022 0 -2.894022 -1.1768857
|
||||
8850 7.8517969e-07 -2.8940229 0 -2.8940221 -1.176868
|
||||
8900 1.200945e-06 -2.8940245 0 -2.8940233 -1.1767465
|
||||
8950 2.0266151e-08 -2.8940265 0 -2.8940264 -1.1766326
|
||||
9000 8.393891e-08 -2.8940288 0 -2.8940288 -1.1764556
|
||||
9050 4.3322427e-08 -2.894035 0 -2.894035 -1.1757866
|
||||
9100 5.558366e-08 -2.8940416 0 -2.8940416 -1.1748494
|
||||
9150 5.6153929e-08 -2.8940464 0 -2.8940464 -1.1741107
|
||||
9200 3.3093925e-08 -2.8940495 0 -2.8940494 -1.1734613
|
||||
9250 2.5678554e-08 -2.8940507 0 -2.8940507 -1.1732185
|
||||
9300 1.960171e-08 -2.8940512 0 -2.8940512 -1.1731441
|
||||
9350 6.8264475e-10 -2.8940516 0 -2.8940516 -1.1730971
|
||||
9400 3.9755331e-09 -2.8940518 0 -2.8940518 -1.1730732
|
||||
9450 6.6819447e-09 -2.894052 0 -2.894052 -1.1730593
|
||||
9500 2.8570816e-08 -2.8940521 0 -2.8940521 -1.1730524
|
||||
9550 8.7433449e-10 -2.8940522 0 -2.8940522 -1.1730474
|
||||
9600 1.2024295e-09 -2.8940523 0 -2.8940523 -1.1731417
|
||||
9650 4.3992465e-09 -2.8940524 0 -2.8940524 -1.1731584
|
||||
9700 6.9801912e-09 -2.8940524 0 -2.8940524 -1.1731609
|
||||
9750 2.0127261e-09 -2.8940525 0 -2.8940525 -1.1731647
|
||||
9800 1.9820186e-09 -2.8940525 0 -2.8940525 -1.1731771
|
||||
9850 2.0267793e-09 -2.8940525 0 -2.8940525 -1.1731899
|
||||
9900 2.5623826e-09 -2.8940526 0 -2.8940526 -1.1732135
|
||||
9950 2.7321573e-09 -2.8940526 0 -2.8940526 -1.1732373
|
||||
10000 3.7027158e-09 -2.8940526 0 -2.8940526 -1.1732798
|
||||
10050 6.7838458e-09 -2.8940527 0 -2.8940527 -1.1733257
|
||||
10100 1.6635632e-08 -2.8940528 0 -2.8940527 -1.1734128
|
||||
10150 4.5898574e-08 -2.8940529 0 -2.8940529 -1.173554
|
||||
10200 1.8171023e-07 -2.8940534 0 -2.8940532 -1.173811
|
||||
10250 1.4919312e-06 -2.8940568 0 -2.8940553 -1.1744943
|
||||
10300 1.1909136e-05 -2.8940907 0 -2.8940789 -1.1762331
|
||||
10350 1.807619e-05 -2.8949091 0 -2.894891 -1.1819669
|
||||
10400 2.8045001e-05 -2.8954967 0 -2.8954687 -1.1834846
|
||||
10450 1.1453554e-05 -2.8956053 0 -2.8955939 -1.1848261
|
||||
10500 3.3687864e-06 -2.8956525 0 -2.8956491 -1.1850246
|
||||
10550 1.9367666e-06 -2.8956863 0 -2.8956844 -1.1846614
|
||||
10600 1.2782114e-07 -2.8956995 0 -2.8956994 -1.1843742
|
||||
10650 6.6195319e-07 -2.8957052 0 -2.8957045 -1.1841825
|
||||
10700 4.7437869e-07 -2.8957078 0 -2.8957074 -1.1840626
|
||||
10750 1.7270059e-07 -2.8957124 0 -2.8957122 -1.1840153
|
||||
10800 1.1015125e-07 -2.8957137 0 -2.8957136 -1.1839328
|
||||
10850 7.0349976e-08 -2.8957147 0 -2.8957146 -1.1838699
|
||||
10900 6.837958e-08 -2.8957152 0 -2.8957151 -1.1838349
|
||||
10950 6.4194728e-08 -2.8957156 0 -2.8957156 -1.1838001
|
||||
11000 4.9879507e-08 -2.8957159 0 -2.8957158 -1.1837799
|
||||
Loop time of 1.74349 on 1 procs for 10000 steps with 800 atoms
|
||||
|
||||
98.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
-0.790781812776 -2.89571584656 -2.89571585284
|
||||
Force two-norm initial, final = 1905.47 0.0695855
|
||||
Force max component initial, final = 343.392 0.0295536
|
||||
Final line search alpha, max atom move = 0 0
|
||||
Iterations, force evaluations = 10000 10000
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.5154 | 1.5154 | 1.5154 | 0.0 | 86.92
|
||||
Neigh | 0.014633 | 0.014633 | 0.014633 | 0.0 | 0.84
|
||||
Comm | 0.017629 | 0.017629 | 0.017629 | 0.0 | 1.01
|
||||
Output | 0.00418 | 0.00418 | 0.00418 | 0.0 | 0.24
|
||||
Modify | 0.030156 | 0.030156 | 0.030156 | 0.0 | 1.73
|
||||
Other | | 0.1615 | | | 9.26
|
||||
|
||||
Nlocal: 800 ave 800 max 800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 318 ave 318 max 318 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7003 ave 7003 max 7003 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7003
|
||||
Ave neighs/atom = 8.75375
|
||||
Neighbor list builds = 74
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
|
|
@ -0,0 +1,15 @@
|
|||
LAMMPS (09 Jan 2020)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.33333333 -2212.7428 0.66666667 -2212.2247 1 -2211.7959
|
||||
10 0.82975832 0.151496 0.051405637 0.82975832 0.82890942 0.44110237 0.38602248 1.6383945 0 -2213.336 0.34232243 -2212.9441 0.67673819 -2212.8949 1 -2213.2809
|
||||
20 0.1352153 0.017969594 0.028869242 0.1352153 0.71343115 0.41634032 0.41253973 1.7292177 0 -2213.3368 0.32696596 -2212.9588 0.6532446 -2212.9204 1 -2213.333
|
||||
30 0.040631856 0.0047789392 0.0035943777 0.040631856 0.77848301 0.38922096 0.38909328 1.7666107 0 -2213.3374 0.33479277 -2212.9482 0.66840762 -2212.9544 1 -2213.3373
|
||||
40 0.010021333 0.00094141903 0.0026779237 0.010021333 0.78047283 0.38807503 0.38804134 1.765797 0 -2213.3374 0.33414241 -2212.9493 0.66764466 -2212.9529 1 -2213.3374
|
||||
41 0.0085585955 0.00080485818 0.0024573847 0.0085585955 0.78063064 0.38800164 0.38797632 1.7656661 0 -2213.3374 0.33413244 -2212.9494 0.66759535 -2212.9527 1 -2213.3374
|
||||
Climbing replica = 2
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
41 0.78063064 0.31131254 0.0024573847 0.0085585955 0.78063064 0.38800164 0.38797632 1.7656661 0 -2213.3374 0.33413244 -2212.9494 0.66759535 -2212.9527 1 -2213.3374
|
||||
51 0.077404428 0.031367667 0.0011842934 0.0024342976 0.019465249 0.51014525 0.51014291 1.761094 0 -2213.3374 0.49613471 -2212.8272 0.72707246 -2213.0479 1 -2213.3374
|
||||
61 0.012232045 0.0032274471 0.00078574104 0.0014332303 0.008388584 0.51009811 0.51009738 1.7611503 0 -2213.3374 0.49457348 -2212.8273 0.74541597 -2213.0782 1 -2213.3374
|
||||
62 0.0089103916 0.0024842796 0.00072806474 0.0014932704 0.0083939608 0.51009995 0.51009934 1.7610284 0 -2213.3374 0.49503069 -2212.8273 0.74593364 -2213.079 1 -2213.3374
|
||||
|
|
@ -0,0 +1,14 @@
|
|||
LAMMPS (09 Jan 2020)
|
||||
Running on 8 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.14285714 -2213.1848 0.28571429 -2212.8577 0.42857143 -2212.5353 0.57142857 -2212.3131 0.71428571 -2212.192 0.85714286 -2212.0797 1 -2211.7959
|
||||
10 0.83279099 0.15218551 0.051457912 0.83279099 0.51294565 0.51146911 0.45623003 1.6449446 0 -2213.336 0.14840724 -2213.2346 0.29535615 -2213.0138 0.4417452 -2212.8419 0.58719049 -2212.8245 0.73204589 -2212.9629 0.8720532 -2213.1643 1 -2213.2807
|
||||
20 0.13499135 0.025513623 0.028873652 0.13499135 0.31173673 0.49652505 0.49272333 1.751414 0 -2213.3368 0.14539729 -2213.243 0.28705892 -2213.024 0.42611693 -2212.854 0.56353342 -2212.8403 0.69946058 -2212.9846 0.83838557 -2213.203 1 -2213.333
|
||||
30 0.045307583 0.0061820354 0.0037366106 0.042519391 0.32123848 0.49279844 0.49266844 1.8063132 0 -2213.3374 0.14088843 -2213.2542 0.28088573 -2213.0379 0.41966614 -2212.859 0.55987626 -2212.8446 0.7049047 -2213.0136 0.85267772 -2213.2453 1 -2213.3373
|
||||
40 0.01020258 0.0024688055 0.0028587701 0.01020258 0.32691899 0.49208236 0.49204824 1.8050507 0 -2213.3374 0.14078995 -2213.2543 0.2808158 -2213.038 0.42032863 -2212.8585 0.56121469 -2212.8453 0.70535554 -2213.0139 0.85229608 -2213.2444 1 -2213.3373
|
||||
41 0.008663273 0.0023142496 0.0026407777 0.008633887 0.32859141 0.49188737 0.49186145 1.8049682 0 -2213.3374 0.14071905 -2213.2544 0.28075314 -2213.0381 0.42045231 -2212.8585 0.56155466 -2212.8455 0.70564189 -2213.0143 0.85237894 -2213.2445 1 -2213.3374
|
||||
Climbing replica = 5
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
41 0.32859141 0.13237876 0.0026407777 0.008633887 0.32859141 0.49188737 0.49186145 1.8049682 0 -2213.3374 0.14071905 -2213.2544 0.28075314 -2213.0381 0.42045231 -2212.8585 0.56155466 -2212.8455 0.70564189 -2213.0143 0.85237894 -2213.2445 1 -2213.3374
|
||||
51 0.040958022 0.016469867 0.0005521899 0.0016920665 0.040958022 0.50982635 0.50982533 1.8022601 0 -2213.3374 0.13880123 -2213.2577 0.26695723 -2213.0629 0.37347534 -2212.9058 0.4947259 -2212.8276 0.66038346 -2212.9436 0.8406605 -2213.2262 1 -2213.3374
|
||||
60 0.0086936374 0.0031014459 0.00019536798 0.0014152883 0.0028728935 0.51009384 0.5100937 1.8047724 0 -2213.3374 0.12947154 -2213.2696 0.25490265 -2213.0841 0.37918482 -2212.8998 0.502053 -2212.8273 0.66626732 -2212.9516 0.83109228 -2213.2129 1 -2213.3374
|
||||
|
|
@ -0,0 +1,13 @@
|
|||
LAMMPS (09 Jan 2020)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.33333333 -2212.7428 0.66666667 -2212.2247 1 -2211.7959
|
||||
10 0.48320283 0.070875032 0.038616783 0.48320283 0.73566671 0.43244307 0.41490356 1.6995075 0 -2213.3364 0.32902356 -2212.9569 0.65268687 -2212.904 1 -2213.3189
|
||||
20 0.04588662 0.0059014273 0.013607587 0.04588662 0.7620294 0.39621211 0.39588855 1.754979 0 -2213.3372 0.32672928 -2212.9586 0.66103382 -2212.941 1 -2213.3369
|
||||
30 0.012046386 0.0023677314 0.0024864261 0.012046386 0.77394417 0.390621 0.39059583 1.7683216 0 -2213.3374 0.33656712 -2212.9468 0.66993108 -2212.956 1 -2213.3374
|
||||
32 0.0082265111 0.002338617 0.0024204614 0.0082265111 0.77424743 0.39048139 0.39045939 1.7683165 0 -2213.3374 0.33645819 -2212.9469 0.66981988 -2212.9558 1 -2213.3374
|
||||
Climbing replica = 2
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
32 0.77424743 0.30840645 0.0024204614 0.0082265111 0.77424743 0.39048139 0.39045939 1.7683165 0 -2213.3374 0.33645819 -2212.9469 0.66981988 -2212.9558 1 -2213.3374
|
||||
42 0.10894394 0.044043242 0.0013210541 0.0029131753 0.021916453 0.5102364 0.51023223 1.7634332 0 -2213.3374 0.49598665 -2212.8272 0.71765441 -2213.0326 1 -2213.3374
|
||||
50 0.0068513242 0.0010095684 0.00065625863 0.001215472 0.0066965947 0.51011571 0.51011496 1.7619971 0 -2213.3374 0.49559669 -2212.8273 0.74807431 -2213.0827 1 -2213.3374
|
||||
|
|
@ -0,0 +1,14 @@
|
|||
LAMMPS (09 Jan 2020)
|
||||
Running on 8 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.14285714 -2213.1848 0.28571429 -2212.8577 0.42857143 -2212.5353 0.57142857 -2212.3131 0.71428571 -2212.192 0.85714286 -2212.0797 1 -2211.7959
|
||||
10 0.48475755 0.071114508 0.038599753 0.48475755 0.37640584 0.50318641 0.48560785 1.7145875 0 -2213.3364 0.1447689 -2213.2412 0.28627124 -2213.0244 0.42632938 -2212.8531 0.56539552 -2212.8332 0.7032047 -2212.9696 0.83935165 -2213.178 1 -2213.3188
|
||||
20 0.046926614 0.006867162 0.013743996 0.046926614 0.28004989 0.49743548 0.49710086 1.7876287 0 -2213.3372 0.142513 -2213.2504 0.28233628 -2213.034 0.41881659 -2212.8597 0.55388168 -2212.8398 0.69295642 -2212.9888 0.84301311 -2213.2259 1 -2213.3369
|
||||
30 0.012933981 0.0025468388 0.0021659256 0.012933981 0.33105878 0.49161235 0.49157812 1.8094495 0 -2213.3374 0.13877456 -2213.2574 0.2776974 -2213.0439 0.41817927 -2212.8603 0.5617581 -2212.8458 0.70750491 -2213.0183 0.85397925 -2213.2476 1 -2213.3374
|
||||
32 0.0094719828 0.002190111 0.0020531136 0.0094719828 0.33155635 0.49154859 0.49152008 1.8093908 0 -2213.3374 0.13875933 -2213.2574 0.2777511 -2213.0437 0.41830977 -2212.8602 0.56184682 -2212.8458 0.70752982 -2213.0184 0.8539532 -2213.2475 1 -2213.3374
|
||||
Climbing replica = 5
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
32 0.33155635 0.13350858 0.0020531136 0.0094719828 0.33155635 0.49154859 0.49152008 1.8093908 0 -2213.3374 0.13875933 -2213.2574 0.2777511 -2213.0437 0.41830977 -2212.8602 0.56184682 -2212.8458 0.70752982 -2213.0184 0.8539532 -2213.2475 1 -2213.3374
|
||||
42 0.054183917 0.021868092 0.00037963557 0.0016877522 0.054183917 0.50961909 0.50961819 1.8035718 0 -2213.3374 0.13834505 -2213.2584 0.26708756 -2213.0628 0.37311054 -2212.9062 0.49221559 -2212.8278 0.660749 -2212.9444 0.84197285 -2213.2284 1 -2213.3374
|
||||
52 0.022191714 0.0081097792 0.00012251534 0.00045278336 0.018020069 0.51004165 0.51004156 1.806295 0 -2213.3374 0.11858703 -2213.2817 0.2484601 -2213.0953 0.37835084 -2212.9009 0.49927321 -2212.8273 0.66777338 -2212.9539 0.83280212 -2213.2156 1 -2213.3374
|
||||
61 0.0083637188 0.0032627544 8.8875493e-05 0.00028087968 0.0034720486 0.51009259 0.51009255 1.8057964 0 -2213.3374 0.12337729 -2213.2765 0.24928935 -2213.0938 0.37439488 -2212.9054 0.50189879 -2212.8273 0.66754201 -2212.9535 0.83596085 -2213.22 1 -2213.3374
|
||||
|
|
@ -0,0 +1,23 @@
|
|||
LAMMPS (09 Jan 2020)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.33333333 -2212.7428 0.66666667 -2212.2247 1 -2211.7959
|
||||
10 1.3693388 0.28041646 0.070738081 1.3693388 1.0855833 0.49695052 0.30796931 1.5832462 0 -2213.3353 0.35022053 -2212.92 0.69816488 -2212.8384 1 -2213.1464
|
||||
20 1.1002508 0.21873472 0.049142357 1.1002508 0.96650653 0.44246122 0.38196494 1.6785075 0 -2213.3362 0.34083391 -2212.9409 0.66986112 -2212.8937 1 -2213.2757
|
||||
30 0.51368685 0.060842471 0.039205784 0.51368685 0.75179947 0.42112286 0.40449278 1.7009906 0 -2213.3364 0.33411939 -2212.9506 0.66142227 -2212.9153 1 -2213.3198
|
||||
40 0.35823734 0.045892314 0.033965264 0.35823734 0.73284549 0.41639462 0.4075633 1.7148522 0 -2213.3366 0.33138373 -2212.9538 0.65884796 -2212.9202 1 -2213.3278
|
||||
50 0.41165748 0.076994838 0.021380826 0.41165748 0.78427738 0.40229169 0.39779205 1.7632679 0 -2213.3371 0.32419234 -2212.9593 0.65452671 -2212.9348 1 -2213.3326
|
||||
60 0.076915443 0.010958664 0.016926588 0.076915443 0.75408409 0.39957497 0.39862604 1.7606518 0 -2213.3372 0.32519215 -2212.9591 0.65667393 -2212.9376 1 -2213.3362
|
||||
70 0.10481382 0.015447066 0.014548011 0.10481382 0.76748189 0.39515902 0.3946702 1.7555947 0 -2213.3372 0.32808712 -2212.9568 0.66188046 -2212.9421 1 -2213.3367
|
||||
80 0.080915257 0.008490983 0.012981317 0.080915257 0.76868863 0.39409972 0.39377313 1.7563219 0 -2213.3373 0.32892342 -2212.9557 0.6623966 -2212.9432 1 -2213.3369
|
||||
90 0.03261844 0.0036037258 0.010975647 0.03261844 0.77019393 0.39275317 0.39258035 1.7570762 0 -2213.3373 0.33001491 -2212.9544 0.66324116 -2212.9445 1 -2213.3371
|
||||
100 0.053370763 0.0072724044 0.009243639 0.053370763 0.77457554 0.39117385 0.391031 1.7582617 0 -2213.3373 0.33114311 -2212.9531 0.66427428 -2212.9461 1 -2213.3372
|
||||
Climbing replica = 3
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
100 0.77457554 0.30675535 0.009243639 0.053370763 0.77457554 0.39117385 0.391031 1.7582617 0 -2213.3373 0.33114311 -2212.9531 0.66427428 -2212.9461 1 -2213.3372
|
||||
110 0.25585774 0.10268695 0.0070464547 0.0681587 0.14797757 0.50920581 0.50909423 1.7558262 0 -2213.3374 0.31405087 -2212.9805 0.48492192 -2212.8281 1 -2213.3372
|
||||
120 0.11790673 0.046047759 0.0056305403 0.032412928 0.073256467 0.51011765 0.51007105 1.7564765 0 -2213.3374 0.28119336 -2213.0335 0.49788361 -2212.8272 1 -2213.3373
|
||||
130 0.070383648 0.012735737 0.0040321557 0.011560639 0.070383648 0.51017901 0.51016087 1.7586689 0 -2213.3374 0.25054735 -2213.0848 0.50803649 -2212.8272 1 -2213.3374
|
||||
140 0.031165303 0.0054585981 0.0037609991 0.0081879563 0.031165303 0.51010628 0.51009071 1.7588792 0 -2213.3374 0.2509652 -2213.084 0.50725262 -2212.8273 1 -2213.3374
|
||||
150 0.032102393 0.0051272026 0.0029882352 0.0078487546 0.032102393 0.51012806 0.51011832 1.7587138 0 -2213.3374 0.25247871 -2213.081 0.50452467 -2212.8273 1 -2213.3374
|
||||
153 0.0098882985 0.0021249062 0.0028642357 0.0047391334 0.0068711217 0.51010879 0.51009999 1.7588126 0 -2213.3374 0.25247357 -2213.0811 0.50451804 -2212.8273 1 -2213.3374
|
||||
|
|
@ -0,0 +1,25 @@
|
|||
LAMMPS (09 Jan 2020)
|
||||
Running on 8 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.14285714 -2213.1848 0.28571429 -2212.8577 0.42857143 -2212.5353 0.57142857 -2212.3131 0.71428571 -2212.192 0.85714286 -2212.0797 1 -2211.7959
|
||||
10 1.3733952 0.28091862 0.070816258 1.3733952 0.8486803 0.56001239 0.3703372 1.585382 0 -2213.3353 0.1507806 -2213.2252 0.30063588 -2212.994 0.45029991 -2212.8095 0.59994263 -2212.7753 0.7496139 -2212.8912 0.89858029 -2213.0683 1 -2213.1457
|
||||
20 1.092582 0.20848565 0.049208846 1.092582 0.67749217 0.51312948 0.45351955 1.6893895 0 -2213.3362 0.14936576 -2213.2335 0.29517709 -2213.0109 0.44023761 -2212.8383 0.58433586 -2212.823 0.72824623 -2212.9685 0.86563155 -2213.1656 1 -2213.2765
|
||||
30 0.51394672 0.065440154 0.039324493 0.51394672 0.3958278 0.49724388 0.48072013 1.7159739 0 -2213.3364 0.14741033 -2213.2378 0.29093102 -2213.0178 0.43329455 -2212.8488 0.57560149 -2212.8391 0.71699492 -2212.9908 0.85518626 -2213.2019 1 -2213.3199
|
||||
40 0.3585576 0.049551349 0.034062896 0.3585576 0.35880033 0.49523368 0.48643307 1.7331908 0 -2213.3366 0.1468741 -2213.2401 0.28995894 -2213.0199 0.43116537 -2212.8509 0.57200904 -2212.8414 0.71172557 -2212.9933 0.85019682 -2213.2079 1 -2213.3278
|
||||
50 0.44071315 0.082631584 0.022058757 0.44071315 0.37223078 0.49368273 0.48892253 1.798835 0 -2213.3371 0.14570064 -2213.2457 0.28667681 -2213.0242 0.42410363 -2212.8534 0.55976055 -2212.8434 0.69487743 -2212.9955 0.83779975 -2213.2217 1 -2213.3324
|
||||
60 0.077895494 0.011715318 0.01696469 0.077895494 0.32663094 0.49291962 0.49197362 1.7955425 0 -2213.3372 0.1454209 -2213.2463 0.2868202 -2213.0251 0.42463425 -2212.854 0.56068056 -2212.8442 0.69668441 -2212.9982 0.84064029 -2213.2268 1 -2213.3362
|
||||
70 0.11340967 0.020267586 0.014639143 0.11200288 0.32902721 0.49268033 0.49216997 1.7893615 0 -2213.3372 0.14432947 -2213.2481 0.28644798 -2213.0271 0.42527709 -2212.8546 0.56239953 -2212.8445 0.70115891 -2213.0022 0.84751195 -2213.2328 1 -2213.3367
|
||||
80 0.059890228 0.0072324994 0.013525373 0.058536736 0.32663552 0.49254358 0.49222746 1.7897234 0 -2213.3372 0.14416888 -2213.2483 0.28619681 -2213.0275 0.42510701 -2212.8548 0.5624421 -2212.8447 0.70158835 -2213.0031 0.84785092 -2213.2336 1 -2213.3369
|
||||
90 0.046425179 0.0085878339 0.012661487 0.044701202 0.32705463 0.49239983 0.49214608 1.7902988 0 -2213.3373 0.14397996 -2213.2486 0.28591514 -2213.0281 0.42492825 -2212.8549 0.56254967 -2212.8449 0.70215415 -2213.0043 0.84829939 -2213.2344 1 -2213.337
|
||||
100 0.10492073 0.011902365 0.0086596336 0.098577447 0.33783582 0.49131393 0.49111204 1.7952617 0 -2213.3373 0.14284709 -2213.2507 0.28418505 -2213.0317 0.42398447 -2212.8559 0.5637284 -2212.846 0.70592525 -2213.0117 0.85128864 -2213.2397 1 -2213.3371
|
||||
Climbing replica = 5
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
100 0.33783582 0.13401694 0.0086596336 0.098577447 0.33783582 0.49131393 0.49111204 1.7952617 0 -2213.3373 0.14284709 -2213.2507 0.28418505 -2213.0317 0.42398447 -2212.8559 0.5637284 -2212.846 0.70592525 -2213.0117 0.85128864 -2213.2397 1 -2213.3371
|
||||
110 0.18587506 0.036451754 0.010634469 0.17023192 0.096871396 0.51011217 0.50966159 1.7980162 0 -2213.3374 0.14250254 -2213.2514 0.28367135 -2213.0327 0.42003349 -2212.8588 0.50682002 -2212.8272 0.70273624 -2213.0073 0.85172992 -2213.241 1 -2213.3369
|
||||
120 0.10027564 0.032272806 0.0066799491 0.069972769 0.04600783 0.51006637 0.50996326 1.7980446 0 -2213.3374 0.14245419 -2213.2516 0.28333857 -2213.0334 0.41656844 -2212.8616 0.50571617 -2212.8273 0.69946889 -2213.0023 0.85165952 -2213.2413 1 -2213.3373
|
||||
130 0.061140793 0.022612825 0.0051287229 0.035432028 0.023420936 0.51012054 0.51007667 1.79856 0 -2213.3374 0.14224093 -2213.252 0.28182793 -2213.0361 0.40850953 -2212.8685 0.50337537 -2212.8272 0.69184303 -2212.9904 0.85074583 -2213.2402 1 -2213.3373
|
||||
140 0.034227221 0.013436677 0.0033777969 0.012466833 0.012341194 0.51010526 0.5100916 1.7997532 0 -2213.3374 0.14115179 -2213.254 0.27552835 -2213.0474 0.39134491 -2212.8853 0.50005108 -2212.8273 0.67579228 -2212.9658 0.84597693 -2213.2336 1 -2213.3374
|
||||
150 0.031519482 0.012310467 0.003215866 0.0067823368 0.0094298698 0.51010745 0.51009621 1.799913 0 -2213.3374 0.1407836 -2213.2545 0.27442232 -2213.0493 0.39094764 -2212.8858 0.50040612 -2212.8273 0.67547004 -2212.9653 0.84498145 -2213.2322 1 -2213.3374
|
||||
160 0.02145751 0.006224623 0.0025005459 0.015465641 0.009264856 0.51010724 0.51009839 1.8012956 0 -2213.3374 0.13767881 -2213.2589 0.26720429 -2213.0621 0.38791572 -2212.8894 0.50222367 -2212.8273 0.67294161 -2212.9614 0.83875897 -2213.2236 1 -2213.3374
|
||||
170 0.066130312 0.0055647193 0.0038237308 0.038908839 0.020979589 0.51009997 0.51007791 1.8039701 0 -2213.3374 0.13100945 -2213.2676 0.25738978 -2213.0796 0.3821429 -2212.8962 0.50312597 -2212.8273 0.66833145 -2212.9546 0.83201742 -2213.2142 1 -2213.3374
|
||||
175 0.008829511 0.0032927835 0.00089755332 0.0014591785 0.0043357949 0.51009467 0.51009389 1.8039465 0 -2213.3374 0.13086052 -2213.2678 0.2573384 -2213.0797 0.38201967 -2212.8964 0.50305513 -2212.8273 0.66828977 -2212.9546 0.83216025 -2213.2144 1 -2213.3374
|
||||
|
|
@ -0,0 +1,23 @@
|
|||
LAMMPS (09 Jan 2020)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.33333333 -2212.7428 0.66666667 -2212.2247 1 -2211.7959
|
||||
10 1.3693388 0.28041646 0.070738081 1.3693388 1.0855833 0.49695052 0.30796931 1.5832462 0 -2213.3353 0.35022053 -2212.92 0.69816488 -2212.8384 1 -2213.1464
|
||||
20 1.1002508 0.21873472 0.049142357 1.1002508 0.96650653 0.44246122 0.38196494 1.6785075 0 -2213.3362 0.34083391 -2212.9409 0.66986112 -2212.8937 1 -2213.2757
|
||||
30 0.51368685 0.060842471 0.039205784 0.51368685 0.75179947 0.42112286 0.40449278 1.7009906 0 -2213.3364 0.33411939 -2212.9506 0.66142227 -2212.9153 1 -2213.3198
|
||||
40 0.35823734 0.045892314 0.033965264 0.35823734 0.73284549 0.41639462 0.4075633 1.7148522 0 -2213.3366 0.33138373 -2212.9538 0.65884796 -2212.9202 1 -2213.3278
|
||||
50 0.41165748 0.076994838 0.021380826 0.41165748 0.78427738 0.40229169 0.39779205 1.7632679 0 -2213.3371 0.32419234 -2212.9593 0.65452671 -2212.9348 1 -2213.3326
|
||||
60 0.076915443 0.010958664 0.016926588 0.076915443 0.75408409 0.39957497 0.39862604 1.7606518 0 -2213.3372 0.32519215 -2212.9591 0.65667393 -2212.9376 1 -2213.3362
|
||||
70 0.10481382 0.015447066 0.014548011 0.10481382 0.76748189 0.39515902 0.3946702 1.7555947 0 -2213.3372 0.32808712 -2212.9568 0.66188046 -2212.9421 1 -2213.3367
|
||||
80 0.080915257 0.008490983 0.012981317 0.080915257 0.76868863 0.39409972 0.39377313 1.7563219 0 -2213.3373 0.32892342 -2212.9557 0.6623966 -2212.9432 1 -2213.3369
|
||||
90 0.03261844 0.0036037258 0.010975647 0.03261844 0.77019393 0.39275317 0.39258035 1.7570762 0 -2213.3373 0.33001491 -2212.9544 0.66324116 -2212.9445 1 -2213.3371
|
||||
100 0.053370763 0.0072724044 0.009243639 0.053370763 0.77457554 0.39117385 0.391031 1.7582617 0 -2213.3373 0.33114311 -2212.9531 0.66427428 -2212.9461 1 -2213.3372
|
||||
Climbing replica = 3
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
100 0.77457554 0.30675535 0.009243639 0.053370763 0.77457554 0.39117385 0.391031 1.7582617 0 -2213.3373 0.33114311 -2212.9531 0.66427428 -2212.9461 1 -2213.3372
|
||||
110 0.25585774 0.10268695 0.0070464547 0.0681587 0.14797757 0.50920581 0.50909423 1.7558262 0 -2213.3374 0.31405087 -2212.9805 0.48492192 -2212.8281 1 -2213.3372
|
||||
120 0.11790673 0.046047759 0.0056305403 0.032412928 0.073256467 0.51011765 0.51007105 1.7564765 0 -2213.3374 0.28119336 -2213.0335 0.49788361 -2212.8272 1 -2213.3373
|
||||
130 0.070383648 0.012735737 0.0040321557 0.011560639 0.070383648 0.51017901 0.51016087 1.7586689 0 -2213.3374 0.25054735 -2213.0848 0.50803649 -2212.8272 1 -2213.3374
|
||||
140 0.031165303 0.0054585981 0.0037609991 0.0081879563 0.031165303 0.51010628 0.51009071 1.7588792 0 -2213.3374 0.2509652 -2213.084 0.50725262 -2212.8273 1 -2213.3374
|
||||
150 0.032102393 0.0051272026 0.0029882352 0.0078487546 0.032102393 0.51012806 0.51011832 1.7587138 0 -2213.3374 0.25247871 -2213.081 0.50452467 -2212.8273 1 -2213.3374
|
||||
153 0.0098882985 0.0021249062 0.0028642357 0.0047391334 0.0068711217 0.51010879 0.51009999 1.7588126 0 -2213.3374 0.25247357 -2213.0811 0.50451804 -2212.8273 1 -2213.3374
|
||||
|
|
@ -0,0 +1,25 @@
|
|||
LAMMPS (09 Jan 2020)
|
||||
Running on 8 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.14285714 -2213.1848 0.28571429 -2212.8577 0.42857143 -2212.5353 0.57142857 -2212.3131 0.71428571 -2212.192 0.85714286 -2212.0797 1 -2211.7959
|
||||
10 1.3733952 0.28091862 0.070816258 1.3733952 0.8486803 0.56001239 0.3703372 1.585382 0 -2213.3353 0.1507806 -2213.2252 0.30063588 -2212.994 0.45029991 -2212.8095 0.59994263 -2212.7753 0.7496139 -2212.8912 0.89858029 -2213.0683 1 -2213.1457
|
||||
20 1.092582 0.20848565 0.049208846 1.092582 0.67749217 0.51312948 0.45351955 1.6893895 0 -2213.3362 0.14936576 -2213.2335 0.29517709 -2213.0109 0.44023761 -2212.8383 0.58433586 -2212.823 0.72824623 -2212.9685 0.86563155 -2213.1656 1 -2213.2765
|
||||
30 0.51394672 0.065440154 0.039324493 0.51394672 0.3958278 0.49724388 0.48072013 1.7159739 0 -2213.3364 0.14741033 -2213.2378 0.29093102 -2213.0178 0.43329455 -2212.8488 0.57560149 -2212.8391 0.71699492 -2212.9908 0.85518626 -2213.2019 1 -2213.3199
|
||||
40 0.3585576 0.049551349 0.034062896 0.3585576 0.35880033 0.49523368 0.48643307 1.7331908 0 -2213.3366 0.1468741 -2213.2401 0.28995894 -2213.0199 0.43116537 -2212.8509 0.57200904 -2212.8414 0.71172557 -2212.9933 0.85019682 -2213.2079 1 -2213.3278
|
||||
50 0.44071315 0.082631584 0.022058757 0.44071315 0.37223078 0.49368273 0.48892253 1.798835 0 -2213.3371 0.14570064 -2213.2457 0.28667681 -2213.0242 0.42410363 -2212.8534 0.55976055 -2212.8434 0.69487743 -2212.9955 0.83779975 -2213.2217 1 -2213.3324
|
||||
60 0.077895494 0.011715318 0.01696469 0.077895494 0.32663094 0.49291962 0.49197362 1.7955425 0 -2213.3372 0.1454209 -2213.2463 0.2868202 -2213.0251 0.42463425 -2212.854 0.56068056 -2212.8442 0.69668441 -2212.9982 0.84064029 -2213.2268 1 -2213.3362
|
||||
70 0.11340967 0.020267586 0.014639143 0.11200288 0.32902721 0.49268033 0.49216997 1.7893615 0 -2213.3372 0.14432947 -2213.2481 0.28644798 -2213.0271 0.42527709 -2212.8546 0.56239953 -2212.8445 0.70115891 -2213.0022 0.84751195 -2213.2328 1 -2213.3367
|
||||
80 0.059890228 0.0072324994 0.013525373 0.058536736 0.32663552 0.49254358 0.49222746 1.7897234 0 -2213.3372 0.14416888 -2213.2483 0.28619681 -2213.0275 0.42510701 -2212.8548 0.5624421 -2212.8447 0.70158835 -2213.0031 0.84785092 -2213.2336 1 -2213.3369
|
||||
90 0.046425179 0.0085878339 0.012661487 0.044701202 0.32705463 0.49239983 0.49214608 1.7902988 0 -2213.3373 0.14397996 -2213.2486 0.28591514 -2213.0281 0.42492825 -2212.8549 0.56254967 -2212.8449 0.70215415 -2213.0043 0.84829939 -2213.2344 1 -2213.337
|
||||
100 0.10492073 0.011902365 0.0086596336 0.098577447 0.33783582 0.49131393 0.49111204 1.7952617 0 -2213.3373 0.14284709 -2213.2507 0.28418505 -2213.0317 0.42398447 -2212.8559 0.5637284 -2212.846 0.70592525 -2213.0117 0.85128864 -2213.2397 1 -2213.3371
|
||||
Climbing replica = 5
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
100 0.33783582 0.13401694 0.0086596336 0.098577447 0.33783582 0.49131393 0.49111204 1.7952617 0 -2213.3373 0.14284709 -2213.2507 0.28418505 -2213.0317 0.42398447 -2212.8559 0.5637284 -2212.846 0.70592525 -2213.0117 0.85128864 -2213.2397 1 -2213.3371
|
||||
110 0.18587506 0.036451754 0.010634469 0.17023192 0.096871396 0.51011217 0.50966159 1.7980162 0 -2213.3374 0.14250254 -2213.2514 0.28367135 -2213.0327 0.42003349 -2212.8588 0.50682002 -2212.8272 0.70273624 -2213.0073 0.85172992 -2213.241 1 -2213.3369
|
||||
120 0.10027564 0.032272806 0.0066799491 0.069972769 0.04600783 0.51006637 0.50996326 1.7980446 0 -2213.3374 0.14245419 -2213.2516 0.28333857 -2213.0334 0.41656844 -2212.8616 0.50571617 -2212.8273 0.69946889 -2213.0023 0.85165952 -2213.2413 1 -2213.3373
|
||||
130 0.061140793 0.022612825 0.0051287229 0.035432028 0.023420936 0.51012054 0.51007667 1.79856 0 -2213.3374 0.14224093 -2213.252 0.28182793 -2213.0361 0.40850953 -2212.8685 0.50337537 -2212.8272 0.69184303 -2212.9904 0.85074583 -2213.2402 1 -2213.3373
|
||||
140 0.034227221 0.013436677 0.0033777969 0.012466833 0.012341194 0.51010526 0.5100916 1.7997532 0 -2213.3374 0.14115179 -2213.254 0.27552835 -2213.0474 0.39134491 -2212.8853 0.50005108 -2212.8273 0.67579228 -2212.9658 0.84597693 -2213.2336 1 -2213.3374
|
||||
150 0.031519482 0.012310467 0.003215866 0.0067823368 0.0094298698 0.51010745 0.51009621 1.799913 0 -2213.3374 0.1407836 -2213.2545 0.27442232 -2213.0493 0.39094764 -2212.8858 0.50040612 -2212.8273 0.67547004 -2212.9653 0.84498145 -2213.2322 1 -2213.3374
|
||||
160 0.02145751 0.006224623 0.0025005459 0.015465641 0.009264856 0.51010724 0.51009839 1.8012956 0 -2213.3374 0.13767881 -2213.2589 0.26720429 -2213.0621 0.38791572 -2212.8894 0.50222367 -2212.8273 0.67294161 -2212.9614 0.83875897 -2213.2236 1 -2213.3374
|
||||
170 0.066130312 0.0055647193 0.0038237308 0.038908839 0.020979589 0.51009997 0.51007791 1.8039701 0 -2213.3374 0.13100945 -2213.2676 0.25738978 -2213.0796 0.3821429 -2212.8962 0.50312597 -2212.8273 0.66833145 -2212.9546 0.83201742 -2213.2142 1 -2213.3374
|
||||
175 0.008829511 0.0032927835 0.00089755332 0.0014591785 0.0043357949 0.51009467 0.51009389 1.8039465 0 -2213.3374 0.13086052 -2213.2678 0.2573384 -2213.0797 0.38201967 -2212.8964 0.50305513 -2212.8273 0.66828977 -2212.9546 0.83216025 -2213.2144 1 -2213.3374
|
||||
|
|
@ -0,0 +1,18 @@
|
|||
LAMMPS (09 Jan 2020)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.33333333 -2212.7428 0.66666667 -2212.2247 1 -2211.7959
|
||||
10 0.24005275 0.036502104 0.036483049 0.24005275 0.68351722 0.42916118 0.41794425 1.6989349 0 -2213.3365 0.32909183 -2212.9587 0.65386736 -2212.9073 1 -2213.3253
|
||||
20 0.07940898 0.016398055 0.024706844 0.07940898 0.71637784 0.41387872 0.41157886 1.7343662 0 -2213.3369 0.32478734 -2212.9621 0.65348766 -2212.923 1 -2213.3346
|
||||
30 0.094973707 0.0083631681 0.015145947 0.035267404 0.7535772 0.40072717 0.40024605 1.7504612 0 -2213.3372 0.32705584 -2212.9584 0.65894506 -2212.9365 1 -2213.3367
|
||||
40 0.027727472 0.0044528145 0.011618173 0.022562656 0.76133752 0.39614635 0.39591731 1.7547519 0 -2213.3373 0.32873163 -2212.9562 0.66124255 -2212.9411 1 -2213.337
|
||||
50 0.01942935 0.0030110281 0.0087135562 0.015391975 0.76952681 0.39274846 0.3926388 1.7578616 0 -2213.3373 0.33022595 -2212.9543 0.66307279 -2212.9446 1 -2213.3372
|
||||
60 0.019000226 0.0016228054 0.0053426183 0.0086165952 0.77759608 0.3893686 0.38933362 1.7610433 0 -2213.3374 0.33187548 -2212.9523 0.66497618 -2212.948 1 -2213.3373
|
||||
63 0.0097473558 0.0012728697 0.004778276 0.0076133796 0.7786505 0.38888835 0.38886103 1.7615288 0 -2213.3374 0.33212079 -2212.952 0.66525353 -2212.9485 1 -2213.3373
|
||||
Climbing replica = 3
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
63 0.7786505 0.31085887 0.004778276 0.0076133796 0.7786505 0.38888835 0.38886103 1.7615288 0 -2213.3374 0.33212079 -2212.952 0.66525353 -2212.9485 1 -2213.3373
|
||||
73 0.098492019 0.033618082 0.0027887232 0.0042741347 0.036396293 0.51024836 0.51023981 1.7607191 0 -2213.3374 0.27571995 -2213.0417 0.50430689 -2212.8271 1 -2213.3374
|
||||
83 0.032231558 0.012626629 0.0020833883 0.0031571731 0.010051365 0.51014599 0.51014135 1.7602543 0 -2213.3374 0.26039027 -2213.0673 0.5035489 -2212.8272 1 -2213.3374
|
||||
93 0.010620711 0.0034681655 0.0014722232 0.0022089665 0.0056709673 0.5101128 0.51011054 1.7601229 0 -2213.3374 0.25434046 -2213.0777 0.50383318 -2212.8273 1 -2213.3374
|
||||
94 0.0096723674 0.0031191785 0.0014334811 0.002149467 0.0054516532 0.51011153 0.51010939 1.7601211 0 -2213.3374 0.25413802 -2213.078 0.50385902 -2212.8273 1 -2213.3374
|
||||
|
|
@ -0,0 +1,21 @@
|
|||
LAMMPS (09 Jan 2020)
|
||||
Running on 8 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.14285714 -2213.1848 0.28571429 -2212.8577 0.42857143 -2212.5353 0.57142857 -2212.3131 0.71428571 -2212.192 0.85714286 -2212.0797 1 -2211.7959
|
||||
10 0.45237221 0.062369106 0.043713415 0.45237221 0.33984237 0.50434364 0.47974444 1.681593 0 -2213.3362 0.145972 -2213.2393 0.28963267 -2213.0224 0.43234899 -2212.8512 0.57436617 -2212.8319 0.71564291 -2212.9699 0.85294239 -2213.1766 1 -2213.3116
|
||||
20 0.17466055 0.019608542 0.027733064 0.16054263 0.29142661 0.49877454 0.49547267 1.7524163 0 -2213.3369 0.14387205 -2213.2456 0.28439667 -2213.0291 0.42233932 -2212.8573 0.5588361 -2212.8381 0.69513708 -2212.9781 0.83702043 -2213.2011 1 -2213.3336
|
||||
30 0.045422642 0.010354266 0.01818213 0.045422642 0.28112975 0.49759387 0.49675173 1.7746784 0 -2213.3371 0.14290957 -2213.2488 0.28281709 -2213.0326 0.41989281 -2212.859 0.55582211 -2212.8395 0.69368801 -2212.9853 0.83973606 -2213.2161 1 -2213.3363
|
||||
40 0.038021578 0.0077863453 0.013142053 0.027303941 0.28657705 0.49667648 0.49635337 1.7848045 0 -2213.3372 0.1420496 -2213.2509 0.28169834 -2213.0351 0.41895631 -2212.8598 0.55576002 -2212.8406 0.69554601 -2212.9918 0.84293215 -2213.2247 1 -2213.3369
|
||||
50 0.023478387 0.0050438726 0.0094370881 0.017117841 0.2948129 0.4956627 0.49552819 1.7913648 0 -2213.3373 0.14130551 -2213.2524 0.28080367 -2213.0371 0.41862494 -2212.8601 0.55666336 -2212.8417 0.69796419 -2212.9977 0.84561062 -2213.2308 1 -2213.3372
|
||||
60 0.015568349 0.0036585595 0.0065356733 0.010880239 0.30476692 0.49454143 0.49448589 1.7961707 0 -2213.3374 0.14069048 -2213.2537 0.28018046 -2213.0385 0.41875119 -2212.86 0.55806463 -2212.8428 0.70047903 -2213.0032 0.84789117 -2213.2356 1 -2213.3373
|
||||
70 0.011117037 0.002930771 0.0046665969 0.0074340459 0.31343722 0.4935777 0.49355166 1.7991441 0 -2213.3374 0.14033265 -2213.2544 0.27992696 -2213.0392 0.41915513 -2212.8596 0.55940642 -2212.8438 0.70245129 -2213.0073 0.8494878 -2213.2387 1 -2213.3373
|
||||
77 0.0095031741 0.0025470028 0.0037787977 0.0059130847 0.31843202 0.4930196 0.49300314 1.8005357 0 -2213.3374 0.14019726 -2213.2547 0.27989276 -2213.0394 0.41949004 -2212.8594 0.56021118 -2212.8444 0.7035183 -2213.0094 0.85030235 -2213.2402 1 -2213.3374
|
||||
Climbing replica = 5
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
77 0.31843202 0.12858086 0.0037787977 0.0059130847 0.31843202 0.4930196 0.49300314 1.8005357 0 -2213.3374 0.14019726 -2213.2547 0.27989276 -2213.0394 0.41949004 -2212.8594 0.56021118 -2212.8444 0.7035183 -2213.0094 0.85030235 -2213.2402 1 -2213.3374
|
||||
87 0.068485358 0.020416571 0.0025906821 0.0039654836 0.024981085 0.51001438 0.51000702 1.8017658 0 -2213.3374 0.13988537 -2213.2554 0.2781578 -2213.0427 0.40602784 -2212.8709 0.50551349 -2212.8274 0.69111931 -2212.99 0.8499171 -2213.2398 1 -2213.3374
|
||||
97 0.031476072 0.0123593 0.0020332076 0.0030835531 0.0070061038 0.51009654 0.51009211 1.8020357 0 -2213.3374 0.13898543 -2213.2569 0.27381812 -2213.0504 0.39685543 -2212.8798 0.50256086 -2212.8273 0.68246582 -2212.9764 0.84621512 -2213.2346 1 -2213.3374
|
||||
107 0.028460125 0.0067640875 0.0014194664 0.0021303377 0.0026454458 0.51009858 0.51009648 1.8028 0 -2213.3374 0.13646 -2213.2604 0.26764336 -2213.0614 0.38930317 -2212.8879 0.50193579 -2212.8273 0.67546861 -2212.9656 0.8411568 -2213.2275 1 -2213.3374
|
||||
117 0.014824889 0.0055517464 0.0010985753 0.0016392459 0.0019892141 0.51009713 0.51009589 1.8033322 0 -2213.3374 0.13447899 -2213.263 0.26412103 -2213.0676 0.38617147 -2212.8914 0.5020058 -2212.8273 0.67278941 -2212.9615 0.83870093 -2213.224 1 -2213.3374
|
||||
127 0.011626205 0.00404434 0.00078110388 0.0011582058 0.0014475679 0.51009594 0.51009533 1.8039369 0 -2213.3374 0.13219331 -2213.266 0.26054642 -2213.074 0.38339139 -2212.8946 0.50214085 -2212.8273 0.67071709 -2212.9584 0.83665693 -2213.2211 1 -2213.3374
|
||||
132 0.0089531814 0.0035807918 0.00069218572 0.0010244011 0.0012955882 0.51009566 0.51009518 1.8041186 0 -2213.3374 0.13150535 -2213.2669 0.2595308 -2213.0758 0.38264847 -2212.8955 0.50218195 -2212.8273 0.67024326 -2212.9576 0.83617539 -2213.2204 1 -2213.3374
|
||||
75
src/min.cpp
75
src/min.cpp
|
|
@ -58,6 +58,18 @@ Min::Min(LAMMPS *lmp) : Pointers(lmp)
|
|||
linestyle = 1;
|
||||
normstyle = TWO;
|
||||
|
||||
delaystep = 20;
|
||||
dtgrow = 1.1;
|
||||
dtshrink = 0.5;
|
||||
alpha0 = 0.25;
|
||||
alphashrink = 0.99;
|
||||
tmax = 10.0;
|
||||
tmin = 0.02;
|
||||
integrator = 0;
|
||||
halfstepback_flag = 1;
|
||||
delaystep_start_flag = 1;
|
||||
max_vdotf_negatif = 2000;
|
||||
|
||||
elist_global = elist_atom = NULL;
|
||||
vlist_global = vlist_atom = cvlist_atom = NULL;
|
||||
|
||||
|
|
@ -184,6 +196,10 @@ void Min::init()
|
|||
neighbor->dist_check = 1;
|
||||
|
||||
niter = neval = 0;
|
||||
|
||||
// store timestep size (important for variable timestep minimizer)
|
||||
|
||||
dtinit = update->dt;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
@ -473,6 +489,10 @@ void Min::cleanup()
|
|||
|
||||
modify->delete_fix("MINIMIZE");
|
||||
domain->box_too_small_check();
|
||||
|
||||
// reset timestep size (important for variable timestep minimizer)
|
||||
|
||||
update->dt = dtinit;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
@ -658,6 +678,58 @@ void Min::modify_params(int narg, char **arg)
|
|||
if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command");
|
||||
dmax = force->numeric(FLERR,arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"delaystep") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command");
|
||||
delaystep = force->numeric(FLERR,arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"dtgrow") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command");
|
||||
dtgrow = force->numeric(FLERR,arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"dtshrink") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command");
|
||||
dtshrink = force->numeric(FLERR,arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"alpha0") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command");
|
||||
alpha0 = force->numeric(FLERR,arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"alphashrink") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command");
|
||||
alphashrink = force->numeric(FLERR,arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"tmax") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command");
|
||||
tmax = force->numeric(FLERR,arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"tmin") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command");
|
||||
tmin = force->numeric(FLERR,arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"halfstepback") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command");
|
||||
if (strcmp(arg[iarg+1],"yes") == 0) halfstepback_flag = 1;
|
||||
else if (strcmp(arg[iarg+1],"no") == 0) halfstepback_flag = 0;
|
||||
else error->all(FLERR,"Illegal min_modify command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"initialdelay") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command");
|
||||
if (strcmp(arg[iarg+1],"yes") == 0) delaystep_start_flag = 1;
|
||||
else if (strcmp(arg[iarg+1],"no") == 0) delaystep_start_flag = 0;
|
||||
else error->all(FLERR,"Illegal min_modify command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"vdfmax") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command");
|
||||
max_vdotf_negatif = force->numeric(FLERR,arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"integrator") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command");
|
||||
if (strcmp(arg[iarg+1],"eulerimplicit") == 0) integrator = 0;
|
||||
else if (strcmp(arg[iarg+1],"verlet") == 0) integrator = 1;
|
||||
else if (strcmp(arg[iarg+1],"leapfrog") == 0) integrator = 2;
|
||||
else if (strcmp(arg[iarg+1],"eulerexplicit") == 0) integrator = 3;
|
||||
else error->all(FLERR,"Illegal min_modify command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"line") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command");
|
||||
if (strcmp(arg[iarg+1],"backtrack") == 0) linestyle = 0;
|
||||
|
|
@ -999,6 +1071,7 @@ char *Min::stopstrings(int n)
|
|||
"quadratic factors are zero",
|
||||
"trust region too small",
|
||||
"HFTN minimizer error",
|
||||
"walltime limit reached"};
|
||||
"walltime limit reached",
|
||||
"max iterations with v.f negative"};
|
||||
return (char *) strings[n];
|
||||
}
|
||||
|
|
|
|||
14
src/min.h
14
src/min.h
|
|
@ -57,7 +57,7 @@ class Min : protected Pointers {
|
|||
|
||||
// possible return values of iterate() method
|
||||
enum{MAXITER,MAXEVAL,ETOL,FTOL,DOWNHILL,ZEROALPHA,ZEROFORCE,
|
||||
ZEROQUAD,TRSMALL,INTERROR,TIMEOUT};
|
||||
ZEROQUAD,TRSMALL,INTERROR,TIMEOUT,MAXVDOTF};
|
||||
|
||||
protected:
|
||||
int eflag,vflag; // flags for energy/virial computation
|
||||
|
|
@ -70,6 +70,18 @@ class Min : protected Pointers {
|
|||
|
||||
int normstyle; // TWO, MAX or INF flag for force norm evaluation
|
||||
|
||||
double dtinit; // store the default timestep
|
||||
|
||||
// only for minimize style fire2
|
||||
int delaystep; // minium steps of dynamics
|
||||
double dtgrow,dtshrink; // timestep increase, decrease
|
||||
double alpha0,alphashrink; // mixing velocities+forces coefficient
|
||||
double tmax,tmin; // timestep multiplicators max, min
|
||||
int integrator; // Newton integration: euler, leapfrog, verlet...
|
||||
int halfstepback_flag; // half step backward when v.f <= 0.0
|
||||
int delaystep_start_flag; // delay the initial dt_shrink
|
||||
int max_vdotf_negatif; // maximum iteration with v.f > 0.0
|
||||
|
||||
int nelist_global,nelist_atom; // # of PE,virial computes to check
|
||||
int nvlist_global,nvlist_atom,ncvlist_atom;
|
||||
class Compute **elist_global; // lists of PE,virial Computes
|
||||
|
|
|
|||
339
src/min_fire.cpp
339
src/min_fire.cpp
|
|
@ -11,16 +11,26 @@
|
|||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "min_fire.h"
|
||||
#include <mpi.h>
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing authors: Julien Guénolé, CNRS and
|
||||
Erik Bitzek, FAU Erlangen-Nuernberg
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <cmath>
|
||||
#include "min_fire.h"
|
||||
#include "universe.h"
|
||||
#include "atom.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "update.h"
|
||||
#include "output.h"
|
||||
#include "timer.h"
|
||||
#include "error.h"
|
||||
#include "variable.h"
|
||||
#include "modify.h"
|
||||
#include "compute.h"
|
||||
#include "domain.h"
|
||||
#include "neighbor.h"
|
||||
#include "comm.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -28,13 +38,6 @@ using namespace LAMMPS_NS;
|
|||
|
||||
#define EPS_ENERGY 1.0e-8
|
||||
|
||||
#define DELAYSTEP 5
|
||||
#define DT_GROW 1.1
|
||||
#define DT_SHRINK 0.5
|
||||
#define ALPHA0 0.1
|
||||
#define ALPHA_SHRINK 0.99
|
||||
#define TMAX 10.0
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
MinFire::MinFire(LAMMPS *lmp) : Min(lmp) {}
|
||||
|
|
@ -45,10 +48,18 @@ void MinFire::init()
|
|||
{
|
||||
Min::init();
|
||||
|
||||
// simple parameters validation
|
||||
|
||||
if (tmax < tmin) error->all(FLERR,"tmax has to be larger than tmin");
|
||||
if (dtgrow < 1.0) error->all(FLERR,"dtgrow has to be larger than 1.0");
|
||||
if (dtshrink > 1.0) error->all(FLERR,"dtshrink has to be smaller than 1.0");
|
||||
|
||||
dt = update->dt;
|
||||
dtmax = TMAX * dt;
|
||||
alpha = ALPHA0;
|
||||
last_negative = update->ntimestep;
|
||||
dtmax = tmax * dt;
|
||||
dtmin = tmin * dt;
|
||||
alpha = alpha0;
|
||||
last_negative = ntimestep_start = update->ntimestep;
|
||||
vdotf_negatif = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
|
@ -58,6 +69,22 @@ void MinFire::setup_style()
|
|||
double **v = atom->v;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
// print the parameters used within fire into the log
|
||||
|
||||
const char *s1[] = {"eulerimplicit","verlet","leapfrog","eulerexplicit"};
|
||||
const char *s2[] = {"no","yes"};
|
||||
|
||||
if (comm->me == 0 && logfile) {
|
||||
fprintf(logfile," Parameters for fire: \n"
|
||||
" dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin "
|
||||
" integrator halfstepback \n"
|
||||
" %4g %9i %6g %8g %6g %11g %4g %4g %13s %12s \n",
|
||||
dmax, delaystep, dtgrow, dtshrink, alpha0, alphashrink, tmax, tmin,
|
||||
s1[integrator], s2[halfstepback_flag]);
|
||||
}
|
||||
|
||||
// initialize the velocities
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
v[i][0] = v[i][1] = v[i][2] = 0.0;
|
||||
}
|
||||
|
|
@ -88,6 +115,39 @@ int MinFire::iterate(int maxiter)
|
|||
|
||||
alpha_final = 0.0;
|
||||
|
||||
// Leap Frog integration initialization
|
||||
|
||||
if (integrator == 2) {
|
||||
|
||||
double **f = atom->f;
|
||||
double **v = atom->v;
|
||||
double *rmass = atom->rmass;
|
||||
double *mass = atom->mass;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
energy_force(0);
|
||||
neval++;
|
||||
|
||||
dtf = -0.5 * dt * force->ftm2v;
|
||||
|
||||
if (rmass) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
dtfm = dtf / rmass[i];
|
||||
v[i][0] = dtfm * f[i][0];
|
||||
v[i][1] = dtfm * f[i][1];
|
||||
v[i][2] = dtfm * f[i][2];
|
||||
}
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
dtfm = dtf / mass[type[i]];
|
||||
v[i][0] = dtfm * f[i][0];
|
||||
v[i][1] = dtfm * f[i][1];
|
||||
v[i][2] = dtfm * f[i][2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
for (int iter = 0; iter < maxiter; iter++) {
|
||||
|
||||
if (timer->check_timeout(niter))
|
||||
|
|
@ -96,11 +156,17 @@ int MinFire::iterate(int maxiter)
|
|||
ntimestep = ++update->ntimestep;
|
||||
niter++;
|
||||
|
||||
// vdotfall = v dot f
|
||||
// pointers
|
||||
|
||||
int nlocal = atom->nlocal;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
int nlocal = atom->nlocal;
|
||||
double **x = atom->x;
|
||||
double *rmass = atom->rmass;
|
||||
double *mass = atom->mass;
|
||||
int *type = atom->type;
|
||||
|
||||
// vdotfall = v dot f
|
||||
|
||||
vdotf = 0.0;
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
|
|
@ -118,11 +184,14 @@ int MinFire::iterate(int maxiter)
|
|||
// if (v dot f) > 0:
|
||||
// v = (1-alpha) v + alpha |v| Fhat
|
||||
// |v| = length of v, Fhat = unit f
|
||||
// if more than DELAYSTEP since v dot f was negative:
|
||||
// increase timestep and decrease alpha
|
||||
// Only: (1-alpha) and alpha |v| Fhat is calculated here
|
||||
// the modificatin of v is made wihtin the integration, after v update
|
||||
// if more than delaystep since v dot f was negative:
|
||||
// increase timestep, update global timestep and decrease alpha
|
||||
|
||||
if (vdotfall > 0.0) {
|
||||
vdotv = 0.0;
|
||||
vdotf_negatif = 0;
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
vdotv += v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
|
||||
MPI_Allreduce(&vdotv,&vdotvall,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
|
@ -149,36 +218,59 @@ int MinFire::iterate(int maxiter)
|
|||
}
|
||||
|
||||
scale1 = 1.0 - alpha;
|
||||
if (fdotfall == 0.0) scale2 = 0.0;
|
||||
if (fdotfall <= 1e-20) scale2 = 0.0;
|
||||
else scale2 = alpha * sqrt(vdotvall/fdotfall);
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
v[i][0] = scale1*v[i][0] + scale2*f[i][0];
|
||||
v[i][1] = scale1*v[i][1] + scale2*f[i][1];
|
||||
v[i][2] = scale1*v[i][2] + scale2*f[i][2];
|
||||
|
||||
if (ntimestep - last_negative > delaystep) {
|
||||
dt = MIN(dt*dtgrow,dtmax);
|
||||
update->dt = dt;
|
||||
alpha *= alphashrink;
|
||||
}
|
||||
|
||||
if (ntimestep - last_negative > DELAYSTEP) {
|
||||
dt = MIN(dt*DT_GROW,dtmax);
|
||||
alpha *= ALPHA_SHRINK;
|
||||
}
|
||||
|
||||
// else (v dot f) <= 0:
|
||||
// decrease timestep, reset alpha, set v = 0
|
||||
// else (v dot f) <= 0
|
||||
// if more than delaystep since starting the relaxation:
|
||||
// reset alpha
|
||||
// if dt*dtshrink > dtmin:
|
||||
// decrease timestep
|
||||
// update global timestep (for thermo output)
|
||||
// half step back within the dynamics: x(t) = x(t-0.5*dt)
|
||||
// reset velocities: v = 0
|
||||
|
||||
} else {
|
||||
last_negative = ntimestep;
|
||||
dt *= DT_SHRINK;
|
||||
alpha = ALPHA0;
|
||||
int delayflag = 1;
|
||||
if (ntimestep - ntimestep_start < delaystep && delaystep_start_flag)
|
||||
delayflag = 0;
|
||||
if (delayflag) {
|
||||
alpha = alpha0;
|
||||
if (dt*dtshrink >= dtmin) {
|
||||
dt *= dtshrink;
|
||||
update->dt = dt;
|
||||
}
|
||||
}
|
||||
|
||||
// stopping criterion while stuck in a local bassin of the PES
|
||||
|
||||
vdotf_negatif++;
|
||||
if (max_vdotf_negatif > 0 && vdotf_negatif > max_vdotf_negatif)
|
||||
return MAXVDOTF;
|
||||
|
||||
// inertia correction
|
||||
|
||||
if (halfstepback_flag) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
x[i][0] -= 0.5 * dtv * v[i][0];
|
||||
x[i][1] -= 0.5 * dtv * v[i][1];
|
||||
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;
|
||||
}
|
||||
|
||||
// limit timestep so no particle moves further than dmax
|
||||
|
||||
double *rmass = atom->rmass;
|
||||
double *mass = atom->mass;
|
||||
int *type = atom->type;
|
||||
|
||||
dtvone = dt;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
|
|
@ -186,6 +278,7 @@ int MinFire::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
|
||||
|
|
@ -196,43 +289,161 @@ int MinFire::iterate(int maxiter)
|
|||
MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,universe->uworld);
|
||||
}
|
||||
|
||||
dtf = dtv * force->ftm2v;
|
||||
// Dynamic integration scheme:
|
||||
// 0: semi-implicit Euler
|
||||
// 1: velocity Verlet
|
||||
// 2: leapfrog (initial half step before the iteration loop)
|
||||
// 3: explicit Euler
|
||||
|
||||
// Euler integration step
|
||||
// Semi-implicit Euler OR Leap Frog integration
|
||||
|
||||
double **x = atom->x;
|
||||
if (integrator == 0 || integrator == 2) {
|
||||
|
||||
if (rmass) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
dtfm = dtf / rmass[i];
|
||||
x[i][0] += dtv * v[i][0];
|
||||
x[i][1] += dtv * v[i][1];
|
||||
x[i][2] += dtv * v[i][2];
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
dtf = dtv * force->ftm2v;
|
||||
|
||||
if (rmass) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
dtfm = dtf / rmass[i];
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
if (vdotfall > 0.0) {
|
||||
v[i][0] = scale1*v[i][0] + scale2*f[i][0];
|
||||
v[i][1] = scale1*v[i][1] + scale2*f[i][1];
|
||||
v[i][2] = scale1*v[i][2] + scale2*f[i][2];
|
||||
}
|
||||
x[i][0] += dtv * v[i][0];
|
||||
x[i][1] += dtv * v[i][1];
|
||||
x[i][2] += dtv * v[i][2];
|
||||
}
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
dtfm = dtf / mass[type[i]];
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
if (vdotfall > 0.0) {
|
||||
v[i][0] = scale1*v[i][0] + scale2*f[i][0];
|
||||
v[i][1] = scale1*v[i][1] + scale2*f[i][1];
|
||||
v[i][2] = scale1*v[i][2] + scale2*f[i][2];
|
||||
}
|
||||
x[i][0] += dtv * v[i][0];
|
||||
x[i][1] += dtv * v[i][1];
|
||||
x[i][2] += dtv * v[i][2];
|
||||
}
|
||||
}
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
dtfm = dtf / mass[type[i]];
|
||||
x[i][0] += dtv * v[i][0];
|
||||
x[i][1] += dtv * v[i][1];
|
||||
x[i][2] += dtv * v[i][2];
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
|
||||
eprevious = ecurrent;
|
||||
ecurrent = energy_force(0);
|
||||
neval++;
|
||||
|
||||
// Velocity Verlet integration
|
||||
|
||||
} else if (integrator == 1) {
|
||||
|
||||
dtf = 0.5 * dtv * force->ftm2v;
|
||||
|
||||
if (rmass) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
dtfm = dtf / rmass[i];
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
if (vdotfall > 0.0) {
|
||||
v[i][0] = scale1*v[i][0] + scale2*f[i][0];
|
||||
v[i][1] = scale1*v[i][1] + scale2*f[i][1];
|
||||
v[i][2] = scale1*v[i][2] + scale2*f[i][2];
|
||||
}
|
||||
x[i][0] += dtv * v[i][0];
|
||||
x[i][1] += dtv * v[i][1];
|
||||
x[i][2] += dtv * v[i][2];
|
||||
}
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
dtfm = dtf / mass[type[i]];
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
if (vdotfall > 0.0) {
|
||||
v[i][0] = scale1*v[i][0] + scale2*f[i][0];
|
||||
v[i][1] = scale1*v[i][1] + scale2*f[i][1];
|
||||
v[i][2] = scale1*v[i][2] + scale2*f[i][2];
|
||||
}
|
||||
x[i][0] += dtv * v[i][0];
|
||||
x[i][1] += dtv * v[i][1];
|
||||
x[i][2] += dtv * v[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
eprevious = ecurrent;
|
||||
ecurrent = energy_force(0);
|
||||
neval++;
|
||||
|
||||
if (rmass) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
dtfm = dtf / rmass[i];
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
}
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
dtfm = dtf / mass[type[i]];
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
// Standard Euler integration
|
||||
|
||||
} else if (integrator == 3) {
|
||||
|
||||
dtf = dtv * force->ftm2v;
|
||||
|
||||
if (rmass) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
dtfm = dtf / rmass[i];
|
||||
if (vdotfall > 0.0) {
|
||||
v[i][0] = scale1*v[i][0] + scale2*f[i][0];
|
||||
v[i][1] = scale1*v[i][1] + scale2*f[i][1];
|
||||
v[i][2] = scale1*v[i][2] + scale2*f[i][2];
|
||||
}
|
||||
x[i][0] += dtv * v[i][0];
|
||||
x[i][1] += dtv * v[i][1];
|
||||
x[i][2] += dtv * v[i][2];
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
}
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
dtfm = dtf / mass[type[i]];
|
||||
if (vdotfall > 0.0) {
|
||||
v[i][0] = scale1*v[i][0] + scale2*f[i][0];
|
||||
v[i][1] = scale1*v[i][1] + scale2*f[i][1];
|
||||
v[i][2] = scale1*v[i][2] + scale2*f[i][2];
|
||||
}
|
||||
x[i][0] += dtv * v[i][0];
|
||||
x[i][1] += dtv * v[i][1];
|
||||
x[i][2] += dtv * v[i][2];
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
eprevious = ecurrent;
|
||||
ecurrent = energy_force(0);
|
||||
neval++;
|
||||
}
|
||||
|
||||
eprevious = ecurrent;
|
||||
ecurrent = energy_force(0);
|
||||
neval++;
|
||||
|
||||
// energy tolerance criterion
|
||||
// only check after DELAYSTEP elapsed since velocties reset to 0
|
||||
// only check after delaystep elapsed since velocties reset to 0
|
||||
// sync across replicas if running multi-replica minimization
|
||||
// reset the timestep to the initial value
|
||||
|
||||
if (update->etol > 0.0 && ntimestep-last_negative > DELAYSTEP) {
|
||||
if (update->etol > 0.0 && ntimestep-last_negative > delaystep) {
|
||||
if (update->multireplica == 0) {
|
||||
if (fabs(ecurrent-eprevious) <
|
||||
update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
|
||||
|
|
@ -243,12 +454,14 @@ int MinFire::iterate(int maxiter)
|
|||
flag = 0;
|
||||
else flag = 1;
|
||||
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
|
||||
if (flagall == 0) return ETOL;
|
||||
if (flagall == 0)
|
||||
return ETOL;
|
||||
}
|
||||
}
|
||||
|
||||
// force tolerance criterion
|
||||
// sync across replicas if running multi-replica minimization
|
||||
// reset the timestep to the initial value
|
||||
|
||||
fdotf = 0.0;
|
||||
if (update->ftol > 0.0) {
|
||||
|
|
|
|||
|
|
@ -34,9 +34,10 @@ class MinFire : public Min {
|
|||
int iterate(int);
|
||||
|
||||
private:
|
||||
double dt,dtmax;
|
||||
double dt,dtmax,dtmin;
|
||||
double alpha;
|
||||
bigint last_negative;
|
||||
bigint last_negative,ntimestep_start;
|
||||
int vdotf_negatif;
|
||||
};
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,279 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "min_fire_old.h"
|
||||
#include <mpi.h>
|
||||
#include <cmath>
|
||||
#include "universe.h"
|
||||
#include "atom.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "update.h"
|
||||
#include "output.h"
|
||||
#include "timer.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
// EPS_ENERGY = minimum normalization for energy tolerance
|
||||
|
||||
#define EPS_ENERGY 1.0e-8
|
||||
|
||||
#define DELAYSTEP 5
|
||||
#define DT_GROW 1.1
|
||||
#define DT_SHRINK 0.5
|
||||
#define ALPHA0 0.1
|
||||
#define ALPHA_SHRINK 0.99
|
||||
#define TMAX 10.0
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
MinFireOld::MinFireOld(LAMMPS *lmp) : Min(lmp) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void MinFireOld::init()
|
||||
{
|
||||
Min::init();
|
||||
|
||||
dt = update->dt;
|
||||
dtmax = TMAX * dt;
|
||||
alpha = ALPHA0;
|
||||
last_negative = update->ntimestep;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void MinFireOld::setup_style()
|
||||
{
|
||||
double **v = atom->v;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
v[i][0] = v[i][1] = v[i][2] = 0.0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set current vector lengths and pointers
|
||||
called after atoms have migrated
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void MinFireOld::reset_vectors()
|
||||
{
|
||||
// atomic dof
|
||||
|
||||
nvec = 3 * atom->nlocal;
|
||||
if (nvec) xvec = atom->x[0];
|
||||
if (nvec) fvec = atom->f[0];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int MinFireOld::iterate(int maxiter)
|
||||
{
|
||||
bigint ntimestep;
|
||||
double vmax,vdotf,vdotfall,vdotv,vdotvall,fdotf,fdotfall;
|
||||
double scale1,scale2;
|
||||
double dtvone,dtv,dtf,dtfm;
|
||||
int flag,flagall;
|
||||
|
||||
alpha_final = 0.0;
|
||||
|
||||
for (int iter = 0; iter < maxiter; iter++) {
|
||||
|
||||
if (timer->check_timeout(niter))
|
||||
return TIMEOUT;
|
||||
|
||||
ntimestep = ++update->ntimestep;
|
||||
niter++;
|
||||
|
||||
// vdotfall = v dot f
|
||||
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
vdotf = 0.0;
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
vdotf += v[i][0]*f[i][0] + v[i][1]*f[i][1] + v[i][2]*f[i][2];
|
||||
MPI_Allreduce(&vdotf,&vdotfall,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
// sum vdotf over replicas, if necessary
|
||||
// this communicator would be invalid for multiprocess replicas
|
||||
|
||||
if (update->multireplica == 1) {
|
||||
vdotf = vdotfall;
|
||||
MPI_Allreduce(&vdotf,&vdotfall,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
|
||||
}
|
||||
|
||||
// if (v dot f) > 0:
|
||||
// v = (1-alpha) v + alpha |v| Fhat
|
||||
// |v| = length of v, Fhat = unit f
|
||||
// if more than DELAYSTEP since v dot f was negative:
|
||||
// increase timestep and decrease alpha
|
||||
|
||||
if (vdotfall > 0.0) {
|
||||
vdotv = 0.0;
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
vdotv += v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
|
||||
MPI_Allreduce(&vdotv,&vdotvall,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
// sum vdotv over replicas, if necessary
|
||||
// this communicator would be invalid for multiprocess replicas
|
||||
|
||||
if (update->multireplica == 1) {
|
||||
vdotv = vdotvall;
|
||||
MPI_Allreduce(&vdotv,&vdotvall,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
|
||||
}
|
||||
|
||||
fdotf = 0.0;
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
fdotf += f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2];
|
||||
MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
// sum fdotf over replicas, if necessary
|
||||
// this communicator would be invalid for multiprocess replicas
|
||||
|
||||
if (update->multireplica == 1) {
|
||||
fdotf = fdotfall;
|
||||
MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
|
||||
}
|
||||
|
||||
scale1 = 1.0 - alpha;
|
||||
if (fdotfall == 0.0) scale2 = 0.0;
|
||||
else scale2 = alpha * sqrt(vdotvall/fdotfall);
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
v[i][0] = scale1*v[i][0] + scale2*f[i][0];
|
||||
v[i][1] = scale1*v[i][1] + scale2*f[i][1];
|
||||
v[i][2] = scale1*v[i][2] + scale2*f[i][2];
|
||||
}
|
||||
|
||||
if (ntimestep - last_negative > DELAYSTEP) {
|
||||
dt = MIN(dt*DT_GROW,dtmax);
|
||||
alpha *= ALPHA_SHRINK;
|
||||
}
|
||||
|
||||
// else (v dot f) <= 0:
|
||||
// decrease timestep, reset alpha, set v = 0
|
||||
|
||||
} else {
|
||||
last_negative = ntimestep;
|
||||
dt *= DT_SHRINK;
|
||||
alpha = ALPHA0;
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
v[i][0] = v[i][1] = v[i][2] = 0.0;
|
||||
}
|
||||
|
||||
// limit timestep so no particle moves further than dmax
|
||||
|
||||
double *rmass = atom->rmass;
|
||||
double *mass = atom->mass;
|
||||
int *type = atom->type;
|
||||
|
||||
dtvone = dt;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
vmax = MAX(fabs(v[i][0]),fabs(v[i][1]));
|
||||
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
|
||||
// this communicator would be invalid for multiprocess replicas
|
||||
|
||||
if (update->multireplica == 1) {
|
||||
dtvone = dtv;
|
||||
MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,universe->uworld);
|
||||
}
|
||||
|
||||
dtf = dtv * force->ftm2v;
|
||||
|
||||
// Euler integration step
|
||||
|
||||
double **x = atom->x;
|
||||
|
||||
if (rmass) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
dtfm = dtf / rmass[i];
|
||||
x[i][0] += dtv * v[i][0];
|
||||
x[i][1] += dtv * v[i][1];
|
||||
x[i][2] += dtv * v[i][2];
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
}
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
dtfm = dtf / mass[type[i]];
|
||||
x[i][0] += dtv * v[i][0];
|
||||
x[i][1] += dtv * v[i][1];
|
||||
x[i][2] += dtv * v[i][2];
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
eprevious = ecurrent;
|
||||
ecurrent = energy_force(0);
|
||||
neval++;
|
||||
|
||||
// energy tolerance criterion
|
||||
// only check after DELAYSTEP elapsed since velocties reset to 0
|
||||
// sync across replicas if running multi-replica minimization
|
||||
|
||||
if (update->etol > 0.0 && ntimestep-last_negative > DELAYSTEP) {
|
||||
if (update->multireplica == 0) {
|
||||
if (fabs(ecurrent-eprevious) <
|
||||
update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
|
||||
return ETOL;
|
||||
} else {
|
||||
if (fabs(ecurrent-eprevious) <
|
||||
update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
|
||||
flag = 0;
|
||||
else flag = 1;
|
||||
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
|
||||
if (flagall == 0) return ETOL;
|
||||
}
|
||||
}
|
||||
|
||||
// force tolerance criterion
|
||||
// sync across replicas if running multi-replica minimization
|
||||
|
||||
fdotf = 0.0;
|
||||
if (update->ftol > 0.0) {
|
||||
if (normstyle == MAX) fdotf = fnorm_max(); // max force norm
|
||||
else if (normstyle == INF) fdotf = fnorm_inf(); // inf force norm
|
||||
else if (normstyle == TWO) fdotf = fnorm_sqr(); // Euclidean force 2-norm
|
||||
else error->all(FLERR,"Illegal min_modify command");
|
||||
if (update->multireplica == 0) {
|
||||
if (fdotf < update->ftol*update->ftol) return FTOL;
|
||||
} else {
|
||||
if (fdotf < update->ftol*update->ftol) flag = 0;
|
||||
else flag = 1;
|
||||
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
|
||||
if (flagall == 0) return FTOL;
|
||||
}
|
||||
}
|
||||
|
||||
// output for thermo, dump, restart files
|
||||
|
||||
if (output->next == ntimestep) {
|
||||
timer->stamp();
|
||||
output->write(ntimestep);
|
||||
timer->stamp(Timer::OUTPUT);
|
||||
}
|
||||
}
|
||||
|
||||
return MAXITER;
|
||||
}
|
||||
|
|
@ -0,0 +1,45 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef MINIMIZE_CLASS
|
||||
|
||||
MinimizeStyle(fire/old,MinFireOld)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_MIN_FIRE_OLD_H
|
||||
#define LMP_MIN_FIRE_OLD_H
|
||||
|
||||
#include "min.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class MinFireOld : public Min {
|
||||
public:
|
||||
MinFireOld(class LAMMPS *);
|
||||
~MinFireOld() {}
|
||||
void init();
|
||||
void setup_style();
|
||||
void reset_vectors();
|
||||
int iterate(int);
|
||||
|
||||
private:
|
||||
double dt,dtmax;
|
||||
double alpha;
|
||||
bigint last_negative;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
Loading…
Reference in New Issue