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Merge pull request #3392 from akohlmey/minimize-neighbor-check

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Update test for neighbor list settings during minimization
This commit is contained in:
Axel Kohlmeyer
2022-08-17 20:55:23 -04:00
committed by GitHub
parent c3f57037e6 d1e0af7ef5
commit 1b979be939
3 changed files with 92 additions and 63 deletions
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116
doc/src/minimize.rst
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@ -32,30 +32,51 @@ Description
Perform an energy minimization of the system, by iteratively adjusting
atom coordinates. Iterations are terminated when one of the stopping
criteria is satisfied. At that point the configuration will hopefully
be in local potential energy minimum. More precisely, the
be in a local potential energy minimum. More precisely, the
configuration should approximate a critical point for the objective
function (see below), which may or may not be a local minimum.
The minimization algorithm used is set by the
:doc:`min_style <min_style>` command. Other options are set by the
:doc:`min_modify <min_modify>` command. Minimize commands can be
interspersed with :doc:`run <run>` commands to alternate between
relaxation and dynamics. The minimizers bound the distance atoms move
in one iteration, so that you can relax systems with highly overlapped
atoms (large energies and forces) by pushing the atoms off of each
other.
The minimization algorithm used is set by the :doc:`min_style
<min_style>` command. Other options are set by the :doc:`min_modify
<min_modify>` command. Minimize commands can be interspersed with
:doc:`run <run>` commands to alternate between relaxation and dynamics.
The minimizers bound the distance atoms may move in one iteration, so
that you can relax systems with highly overlapped atoms (large energies
and forces) by pushing the atoms off of each other.
Alternate means of relaxing a system are to run dynamics with a small
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.
.. admonition:: Neighbor list update settings
:class: note
The distance that atoms can move during individual minimization steps
can be quite large, especially at the beginning of a minimization.
Thus `neighbor list settings <neigh_modify>` of *every = 1* and
*delay = 0* are **required**. This may be combined with either
*check = no* (always update the neighbor list) or *check = yes* (only
update the neighbor list if at least one atom has moved more than
half the `neighbor list skin <neighbor>` distance since the last
reneighboring). Using *check = yes* is recommended since it avoids
unneeded reneighboring steps when the system is closer to the minimum
and thus atoms move only small distances. Using *check = no* may
be required for debugging or when coupling LAMMPS with external
codes that require a predictable sequence of neighbor list updates.
If the settings are **not** *every = 1* and *delay = 0*, LAMMPS
will temporarily apply a `neigh_modify every 1 delay 0 check yes
<neigh_modify>` setting during the minimization and restore the
original setting at the end of the minimization. A corresponding
message will be printed to the screen and log file, if this happens.
Alternate means of relaxing a system are to run dynamics with a small 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.
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 0.0 0.0
0.0 <fix_setforce>` to the other atoms. See a more detailed discussion
of :ref:`using fixes while minimizing below <fix_minimize>`.
The :doc:`minimization styles <min_style>` *cg*, *sd*, and *hftn*
involves an outer iteration loop which sets the search direction along
@ -74,10 +95,11 @@ 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.
The damped dynamic minimizer algorithms will use the timestep you
have defined via the :doc:`timestep <timestep>` command or its
default value. Often they will converge more quickly if you use a
timestep about 10x larger than you would normally use for regular
molecular dynamics simulations.
----------
@ -210,34 +232,42 @@ The iterations and force evaluation values are what is checked by the
.. note::
There are several force fields in LAMMPS which have
discontinuities or other approximations which may prevent you from
performing an energy minimization to high tolerances. For example,
you should use a :doc:`pair style <pair_style>` that goes to 0.0 at the
cutoff distance when performing minimization (even if you later change
it when running dynamics). If you do not do this, the total energy of
There are several force fields in LAMMPS which have discontinuities
or other approximations which may prevent you from performing an
energy minimization to tight tolerances. For example, you should use
a :doc:`pair style <pair_style>` that goes to 0.0 at the cutoff
distance when performing minimization (even if you later change it
when running dynamics). If you do not do this, the total energy of
the system will have discontinuities when the relative distance
between any pair of atoms changes from cutoff+epsilon to
cutoff-epsilon and the minimizer may behave poorly. Some of the
many-body potentials use splines and other internal cutoffs that
inherently have this problem. The :doc:`long-range Coulombic styles <kspace_style>` (PPPM, Ewald) are approximate to within the
user-specified tolerance, which means their energy and forces may not
agree to a higher precision than the Kspace-specified tolerance. In
all these cases, the minimizer may give up and stop before finding a
minimum to the specified energy or force tolerance.
between any pair of atoms changes from cutoff *plus* epsilon to
cutoff *minus* epsilon and the minimizer may thus behave poorly.
Some of the many-body potentials use splines and other internal
cutoffs that inherently have this problem. The :doc:`long-range
Coulombic styles <kspace_style>` (PPPM, Ewald) are approximate to
within the user-specified tolerance, which means their energy and
forces may not agree to a higher precision than the Kspace-specified
tolerance. This agreement is further reduced when using tabulation
to speed up the computation of the real-space part of the Coulomb
interactions, which is enabled by default. In all these cases, the
minimizer may give up and stop before finding a minimum to the
specified energy or force tolerance.
Note that a cutoff Lennard-Jones potential (and others) can be shifted
so that its energy is 0.0 at the cutoff via the
:doc:`pair_modify <pair_modify>` command. See the doc pages for
individual :doc:`pair styles <pair_style>` for details. Note that
Coulombic potentials always have a cutoff, unless versions with a
long-range component are used (e.g. :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`). The CHARMM potentials go to 0.0 at
the cutoff (e.g. :doc:`pair_style lj/charmm/coul/charmm <pair_charmm>`),
as do the GROMACS potentials (e.g. :doc:`pair_style lj/gromacs <pair_gromacs>`).
so that its energy is 0.0 at the cutoff via the :doc:`pair_modify
<pair_modify>` command. See the doc pages for individual :doc:`pair
styles <pair_style>` for details. Note that most Coulombic potentials
have a cutoff, unless versions with a long-range component are used
(e.g. :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`) or some
other damping/smoothing schemes are used. The CHARMM potentials go to
0.0 at the cutoff (e.g. :doc:`pair_style lj/charmm/coul/charmm
<pair_charmm>`), as do the GROMACS potentials (e.g. :doc:`pair_style
lj/gromacs <pair_gromacs>`).
If a soft potential (:doc:`pair_style soft <pair_soft>`) is used the
Astop value is used for the prefactor (no time dependence).
.. _fix_minimize:
The :doc:`fix box/relax <fix_box_relax>` command can be used to apply an
external pressure to the simulation box and allow it to shrink/expand
during the minimization.

37
src/min.cpp
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@ -94,13 +94,13 @@ Min::Min(LAMMPS *lmp) : Pointers(lmp)
Min::~Min()
{
delete [] elist_global;
delete [] elist_atom;
delete [] vlist_global;
delete [] vlist_atom;
delete [] cvlist_atom;
delete[] elist_global;
delete[] elist_atom;
delete[] vlist_global;
delete[] vlist_atom;
delete[] cvlist_atom;
delete [] fextra;
delete[] fextra;
memory->sfree(xextra_atom);
memory->sfree(fextra_atom);
@ -128,7 +128,7 @@ void Min::init()
// can then add vectors to fix_minimize in setup()
nextra_global = 0;
delete [] fextra;
delete[] fextra;
fextra = nullptr;
nextra_atom = 0;
@ -182,16 +182,15 @@ void Min::init()
neigh_delay = neighbor->delay;
neigh_dist_check = neighbor->dist_check;
if (neigh_every != 1 || neigh_delay != 0 || neigh_dist_check != 1) {
if ((neigh_every != 1) || (neigh_delay != 0)) {
if (comm->me == 0)
error->warning(FLERR, "Using 'neigh_modify every 1 delay 0 check"
" yes' setting during minimization");
utils::logmesg(lmp, "Switching to 'neigh_modify every 1 delay 0 check yes' "
"setting during minimization\n");
neighbor->every = 1;
neighbor->delay = 0;
neighbor->dist_check = 1;
}
neighbor->every = 1;
neighbor->delay = 0;
neighbor->dist_check = 1;
niter = neval = 0;
// store timestep size (important for variable timestep minimizer)
@ -751,11 +750,11 @@ void Min::modify_params(int narg, char **arg)
void Min::ev_setup()
{
delete [] elist_global;
delete [] elist_atom;
delete [] vlist_global;
delete [] vlist_atom;
delete [] cvlist_atom;
delete[] elist_global;
delete[] elist_atom;
delete[] vlist_global;
delete[] vlist_atom;
delete[] cvlist_atom;
elist_global = elist_atom = nullptr;
vlist_global = vlist_atom = cvlist_atom = nullptr;

2
src/neighbor.cpp
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@ -1713,7 +1713,7 @@ void Neighbor::print_pairwise_info()
}
std::string out = "Neighbor list info ...\n";
out += fmt::format(" update every {} steps, delay {} steps, check {}\n",
out += fmt::format(" update: every = {} steps, delay = {} steps, check = {}\n",
every,delay,dist_check ? "yes" : "no");
out += fmt::format(" max neighbors/atom: {}, page size: {}\n",
oneatom, pgsize);