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Merge pull request #1860 from akohlmey/collected-small-changes

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Collected small changes for next patch release
This commit is contained in:
Axel Kohlmeyer
2020-01-31 12:21:17 -05:00
committed by GitHub
parent 39188da85b 6424883daf
commit 56ff70de70
7 changed files with 144 additions and 136 deletions
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240
doc/src/pair_modify.rst
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@ -13,18 +13,14 @@ Syntax
* one or more keyword/value pairs may be listed
* keyword = *pair* or *shift* or *mix* or *table* or *table/disp* or *tabinner*
or *tabinner/disp* or *tail* or *compute* or *nofdotr*
or *tabinner/disp* or *tail* or *compute* or *nofdotr* or *special* or
*compute/tally*
.. parsed-literal::
*pair* values = sub-style N *special* which wt1 wt2 wt3
or sub-style N *compute/tally* flag
*pair* value = sub-style N
sub-style = sub-style of :doc:`pair hybrid <pair_hybrid>`
N = which instance of sub-style (only if sub-style is used multiple times)
*special* which wt1 wt2 wt3 = override *special_bonds* settings (optional)
which = *lj/coul* or *lj* or *coul*
w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive
*compute/tally* flag = *yes* or *no*
N = which instance of sub-style (1 to M), only specify if sub-style is used multiple times
*mix* value = *geometric* or *arithmetic* or *sixthpower*
*shift* value = *yes* or *no*
*table* value = N
@ -37,8 +33,11 @@ Syntax
cutoff = inner cutoff at which to begin table (distance units)
*tail* value = *yes* or *no*
*compute* value = *yes* or *no*
*nofdotr*
*nofdotr* value = none
*special* values = which wt1 wt2 wt3
which = *lj/coul* or *lj* or *coul*
w1,w2,w3 = 1-2, 1-3, 1-4 weights from 0.0 to 1.0 inclusive
*compute/tally* value = *yes* or *no*
Examples
@ -53,47 +52,41 @@ Examples
pair_modify pair lj/cut compute no
pair_modify pair tersoff compute/tally no
pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0
pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5 special coul 0.0 0.0 0.8333333
Description
"""""""""""
Modify the parameters of the currently defined pair style. Not all
parameters are relevant to all pair styles.
Modify the parameters of the currently defined pair style. If the
pair style is :doc:`hybrid or hybrid/overlay <pair_hybrid>`, then the
specified parameters are by default modified for all the hybrid sub-styles.
If used, the *pair* keyword must appear first in the list of keywords.
It can only be used with the :doc:`hybrid and hybrid/overlay <pair_hybrid>` pair styles. It means that all the
following parameters will only be modified for the specified
sub-style. If the sub-style is defined multiple times, then an
additional numeric argument *N* must also be specified, which is a
number from 1 to M where M is the number of times the sub-style was
listed in the :doc:`pair_style hybrid <pair_hybrid>` command. The extra
number indicates which instance of the sub-style the remaining
keywords will be applied to. Note that if the *pair* keyword is not
used, and the pair style is *hybrid* or *hybrid/overlay*\ , then all the
specified keywords will be applied to all sub-styles.
.. note::
The *special* and *compute/tally* keywords can **only** be used in
conjunction with the *pair* keyword and must directly follow it.
*special* allows to override the
:doc:`special_bonds <special_bonds>` settings for the specified sub-style.
*compute/tally* allows to disable or enable registering
:doc:`compute \*/tally <compute_tally>` computes for a given sub-style.
More details are given below.
The behavior for hybrid pair styles can be changed by using the *pair*
keyword, which allows selection of a specific sub-style to apply all
remaining keywords to.
The *special* and *compute/tally* keywords can **only** be
used in conjunction with the *pair* keyword. See further details about
these 3 keywords below.
The *mix* keyword affects pair coefficients for interactions between
atoms of type I and J, when I != J and the coefficients are not
explicitly set in the input script. Note that coefficients for I = J
must be set explicitly, either in the input script via the
"pair\_coeff" command or in the "Pair Coeffs" section of the :doc:`data file <read_data>`. For some pair styles it is not necessary to
specify coefficients when I != J, since a "mixing" rule will create
them from the I,I and J,J settings. The pair\_modify *mix* value
determines what formulas are used to compute the mixed coefficients.
In each case, the cutoff distance is mixed the same way as sigma.
:doc:`pair_coeff <pair_coeff>` command or in the "Pair Coeffs" section of the
:doc:`data file <read_data>`. For some pair styles it is not
necessary to specify coefficients when I != J, since a "mixing" rule
will create them from the I,I and J,J settings. The pair\_modify
*mix* value determines what formulas are used to compute the mixed
coefficients. In each case, the cutoff distance is mixed the same way
as sigma.
Note that not all pair styles support mixing. Also, some mix options
are not available for certain pair styles. See the doc page for
individual pair styles for those restrictions. Note also that the
:doc:`pair_coeff <pair_coeff>` command also can be to directly set
Note that not all pair styles support mixing and some mix options
are not available for certain pair styles. Also, there are additional
restrictions when using :doc:`pair style hybrid or hybrid/overlay <pair_hybrid>`.
See the doc page for individual pair styles for those restrictions. Note also that the
:doc:`pair_coeff <pair_coeff>` command also can be used to directly set
coefficients for a specific I != J pairing, in which case no mixing is
performed.
@ -135,10 +128,11 @@ see the doc page for individual styles to see which potentials support
these options. If N is non-zero, a table of length 2\^N is
pre-computed for forces and energies, which can shrink their
computational cost by up to a factor of 2. The table is indexed via a
bit-mapping technique :ref:`(Wolff) <Wolff1>` and a linear interpolation is
performed between adjacent table values. In our experiments with
different table styles (lookup, linear, spline), this method typically
gave the best performance in terms of speed and accuracy.
bit-mapping technique :ref:`(Wolff) <Wolff1>` and a linear
interpolation is performed between adjacent table values. In our
experiments with different table styles (lookup, linear, spline), this
method typically gave the best performance in terms of speed and
accuracy.
The choice of table length is a tradeoff in accuracy versus speed. A
larger N yields more accurate force computations, but requires more
@ -162,27 +156,28 @@ pairwise interactions are computed via table lookup for simulations
with "real" units, but some close pairs may be computed directly
(non-table) for simulations with "lj" units.
When the *tail* keyword is set to *yes*\ , certain pair styles will add
a long-range VanderWaals tail "correction" to the energy and pressure.
These corrections are bookkeeping terms which do not affect dynamics,
unless a constant-pressure simulation is being performed. See the doc
page for individual styles to see which support this option. These
corrections are included in the calculation and printing of
thermodynamic quantities (see the :doc:`thermo_style <thermo_style>`
command). Their effect will also be included in constant NPT or NPH
simulations where the pressure influences the simulation box
dimensions (e.g. the :doc:`fix npt <fix_nh>` and :doc:`fix nph <fix_nh>`
commands). The formulas used for the long-range corrections come from
equation 5 of :ref:`(Sun) <Sun>`.
When the *tail* keyword is set to *yes*\ , certain pair styles will
add a long-range VanderWaals tail "correction" to the energy and
pressure. These corrections are bookkeeping terms which do not affect
dynamics, unless a constant-pressure simulation is being performed.
See the doc page for individual styles to see which support this
option. These corrections are included in the calculation and
printing of thermodynamic quantities (see the :doc:`thermo_style
<thermo_style>` command). Their effect will also be included in
constant NPT or NPH simulations where the pressure influences the
simulation box dimensions (e.g. the :doc:`fix npt <fix_nh>` and
:doc:`fix nph <fix_nh>` commands). The formulas used for the
long-range corrections come from equation 5 of :ref:`(Sun) <Sun>`.
.. note::
The tail correction terms are computed at the beginning of each
run, using the current atom counts of each atom type. If atoms are
deleted (or lost) or created during a simulation, e.g. via the :doc:`fix gcmc <fix_gcmc>` command, the correction factors are not
re-computed. If you expect the counts to change dramatically, you can
break a run into a series of shorter runs so that the correction
factors are re-computed more frequently.
deleted (or lost) or created during a simulation, e.g. via the
:doc:`fix gcmc <fix_gcmc>` command, the correction factors are not
re-computed. If you expect the counts to change dramatically, you
can break a run into a series of shorter runs so that the
correction factors are re-computed more frequently.
Several additional assumptions are inherent in using tail corrections,
including the following:
@ -191,26 +186,27 @@ including the following:
should not be used for systems that are non-liquid, 2d, have a slab
geometry (only 2d periodic), or inhomogeneous.
* G(r), the radial distribution function (rdf), is unity beyond the
cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for an
LJ fluid), and it is probably a good idea to verify this assumption by
checking the rdf. The rdf is not exactly unity beyond the cutoff for
each pair of interaction types, so the tail correction is necessarily
an approximation.
cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for
an LJ fluid), and it is probably a good idea to verify this
assumption by checking the rdf. The rdf is not exactly unity beyond
the cutoff for each pair of interaction types, so the tail
correction is necessarily an approximation.
The tail corrections are computed at the beginning of each simulation
run. If the number of atoms changes during the run, e.g. due to atoms
leaving the simulation domain, or use of the :doc:`fix gcmc <fix_gcmc>`
command, then the corrections are not updated to reflect the changed
atom count. If this is a large effect in your simulation, you should
break the long run into several short runs, so that the correction
factors are re-computed multiple times.
The tail corrections are computed at the beginning of each
simulation run. If the number of atoms changes during the run,
e.g. due to atoms leaving the simulation domain, or use of the
:doc:`fix gcmc <fix_gcmc>` command, then the corrections are not
updated to reflect the changed atom count. If this is a large
effect in your simulation, you should break the long run into
several short runs, so that the correction factors are re-computed
multiple times.
* Thermophysical properties obtained from calculations with this option
enabled will not be thermodynamically consistent with the truncated
force-field that was used. In other words, atoms do not feel any LJ
pair interactions beyond the cutoff, but the energy and pressure
reported by the simulation include an estimated contribution from
those interactions.
* Thermophysical properties obtained from calculations with this
option enabled will not be thermodynamically consistent with the
truncated force-field that was used. In other words, atoms do not
feel any LJ pair interactions beyond the cutoff, but the energy and
pressure reported by the simulation include an estimated
contribution from those interactions.
The *compute* keyword allows pairwise computations to be turned off,
@ -225,53 +221,73 @@ a simulation with :doc:`pair_style hybrid <pair_hybrid>` with only a
subset of the hybrid sub-styles enabled. Second, this option allows
you to perform a simulation with only long-range interactions but no
short-range pairwise interactions. Doing this by simply not defining
a pair style will not work, because the
:doc:`kspace_style <kspace_style>` command requires a Kspace-compatible
pair style be defined.
a pair style will not work, because the :doc:`kspace_style
<kspace_style>` command requires a Kspace-compatible pair style be
defined.
The *nofdotr* keyword allows to disable an optimization that computes
the global stress tensor from the total forces and atom positions rather
than from summing forces between individual pairs of atoms.
the global stress tensor from the total forces and atom positions
rather than from summing forces between individual pairs of atoms.
----------
The *pair* keyword can only be used with the :doc:`hybrid and
hybrid/overlay <pair_hybrid>` pair styles. If used, it must appear
first in the list of keywords.
The *special* keyword allows to override the 1-2, 1-3, and 1-4
exclusion settings for individual sub-styles of a
:doc:`hybrid pair style <pair_hybrid>`. It requires 4 arguments similar
to the :doc:`special_bonds <special_bonds>` command, *which* and
wt1,wt2,wt3. The *which* argument can be *lj* to change the
Lennard-Jones settings, *coul* to change the Coulombic settings,
or *lj/coul* to change both to the same set of 3 values. The wt1,wt2,wt3
values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
1-3, and 1-4 bond topology neighbors, respectively. The *special*
keyword can only be used in conjunction with the *pair* keyword
and has to directly follow it. This option is not compatible with
pair styles from the GPU or the USER-INTEL package and attempting
it will cause an error.
Its meaning is that all the following parameters will only be modified
for the specified sub-style. If the sub-style is defined multiple
times, then an additional numeric argument *N* must also be specified,
which is a number from 1 to M where M is the number of times the
sub-style was listed in the :doc:`pair_style hybrid <pair_hybrid>`
command. The extra number indicates which instance of the sub-style
the remaining keywords will be applied to.
The *special* and *compute/tally* keywords can **only** be used in
conjunction with the *pair* keyword and they must directly follow it.
I.e. any other keyword, must appear after *pair*, *special*, and
*compute/tally*.
The *special* keyword overrides the global :doc:`special_bonds <special_bonds>`
1-2, 1-3, 1-4 exclusion settings (weights) for the sub-style selected
by the *pair* keyword.
Similar to the :doc:`special_bonds <special_bonds>` command, it takes
4 arguments. The *which* argument can be *lj* to change only the
non-Coulomb weights (e.g. Lennard-Jones or Buckingham), *coul* to change
only the Coulombic settings, or *lj/coul* to change both to the same
values. The *wt1,wt2,wt3* values are numeric weights from 0.0 to 1.0
inclusive, for the 1-2, 1-3, and 1-4 bond topology neighbors, respectively.
The *special* keyword can be used multiple times, e.g. to set the *lj*
and *coul* settings to different values.
.. note::
The global settings specified by the
:doc:`special_bonds <special_bonds>` command affect the construction of
neighbor lists. Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors)
exclude those pairs from the neighbor list entirely. Weights of 1.0
store the neighbor with no weighting applied. Thus only global values
different from exactly 0.0 or 1.0 can be overridden and an error is
generated if the requested setting is not compatible with the global
setting. Substituting 1.0e-10 for 0.0 and 0.9999999999 for 1.0 is
usually a sufficient workaround in this case without causing a
significant error.
The *compute/tally* keyword takes exactly 1 argument (\ *no* or *yes*\ ),
and allows to selectively disable or enable processing of the various
:doc:`compute \*/tally <compute_tally>` styles for a given
:doc:`pair hybrid or hybrid/overlay <pair_hybrid>` sub-style.
The *special* keyword is not compatible with pair styles from the
GPU or the USER-INTEL package and attempting to use it will cause
an error.
.. note::
Any "pair\_modify pair compute/tally" command must be issued
Weights of exactly 0.0 or 1.0 in the :doc:`special_bonds <special_bonds>`
command have implications on the neighbor list construction, which
means that they cannot be overridden by using the *special* keyword.
One workaround for this restriction is to use the :doc:`special_bonds <special_bonds>`
command with weights like 1.0e-10 or 0.999999999 instead of 0.0 or 1.0,
respectively, which enables to reset each them to any value between 0.0
and 1.0 inclusively. Otherwise you can set **all** global weights to
an arbitrary number between 0.0 or 1.0, like 0.5, and then you have
to override **all** *special* settings for **all** sub-styles which use
the 1-2, 1-3, and 1-4 exclusion weights in their force/energy computation.
The *compute/tally* keyword disables or enables registering :doc:`compute
\*/tally <compute_tally>` computes for the sub-style specified by
the *pair* keyword. Use *no* to disable, or *yes* to enable.
.. note::
The "pair_modify pair compute/tally" command must be issued
**before** the corresponding compute style is defined.
@ -290,7 +306,7 @@ Related commands
""""""""""""""""
:doc:`pair_style <pair_style>`, :doc:`pair_style hybrid <pair_hybrid>`,
pair\_coeff"_pair\_coeff.html, :doc:`thermo_style <thermo_style>`,
:doc:`pair_coeff <pair_coeff>`, :doc:`thermo_style <thermo_style>`,
:doc:`compute \*/tally <compute_tally>`
Default

6
doc/src/set.rst
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@ -359,9 +359,9 @@ particles must be ellipsoids as defined by the :doc:`atom_style ellipsoid <atom_
of the particles is set to the 3 specified components.
Keyword *omega* sets the angular velocity of selected atoms. The
particles must be spheres as defined by the "atom\_style sphere"_
atom\_style.html command. The angular velocity vector of the particles
is set to the 3 specified components.
particles must be spheres as defined by the
:doc:`atom_style sphere <atom_style>` command. The angular velocity
vector of the particles is set to the 3 specified components.
Keyword *mass* sets the mass of all selected particles. The particles
must have a per-atom mass attribute, as defined by the

2
src/kspace.cpp
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@ -286,7 +286,7 @@ void KSpace::qsum_qsq(int warning_flag)
double qsum_local(0.0), qsqsum_local(0.0);
#if defined(_OPENMP)
#pragma omp parallel for default(none) reduction(+:qsum_local,qsqsum_local)
#pragma omp parallel for default(shared) reduction(+:qsum_local,qsqsum_local)
#endif
for (int i = 0; i < nlocal; i++) {
qsum_local += q[i];

7
src/neighbor.cpp
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@ -402,13 +402,6 @@ void Neighbor::init()
}
}
// maxwt = max multiplicative factor on atom indices stored in neigh list
maxwt = 0;
if (special_flag[1] == 2) maxwt = 2;
if (special_flag[2] == 2) maxwt = 3;
if (special_flag[3] == 2) maxwt = 4;
// ------------------------------------------------------------------
// xhold array

1
src/neighbor.h
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@ -166,7 +166,6 @@ class Neighbor : protected Pointers {
int maxatom; // max size of atom-based NeighList arrays
int maxrequest; // max size of NeighRequest list
int maxwt; // max weighting factor applied + 1
// info for other Neigh classes: NBin,NStencil,NPair,NTopo

15
src/pair_hybrid.cpp
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@ -859,14 +859,17 @@ void PairHybrid::modify_params(int narg, char **arg)
iarg = 3;
}
// if 2nd keyword (after pair) is special:
// invoke modify_special() for the sub-style
// keywords "special" and "compute/tally" have to be listed directly
// after "pair" but can be given multiple times
again:
if (iarg < narg && strcmp(arg[iarg],"special") == 0) {
if (narg < iarg+5)
error->all(FLERR,"Illegal pair_modify special command");
modify_special(m,narg-iarg,&arg[iarg+1]);
iarg += 5;
goto again;
}
// if 2nd keyword (after pair) is compute/tally:
@ -881,11 +884,13 @@ void PairHybrid::modify_params(int narg, char **arg)
compute_tally[m] = 0;
} else error->all(FLERR,"Illegal pair_modify compute/tally command");
iarg += 2;
goto again;
}
// apply the remaining keywords to the base pair style itself and the
// sub-style except for "pair" and "special".
// the former is important for some keywords like "tail" or "compute"
// apply the remaining keywords to the base pair style itself and
// the sub-style except for "pair" and "special" or "compute/tally"
// and their arguments. the former is important for some keywords
// like "tail" or "compute"
if (narg-iarg > 0) {
Pair::modify_params(narg-iarg,&arg[iarg]);

9
src/random_mars.cpp
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@ -183,7 +183,7 @@ void RanMars::select_subset(bigint ntarget, int nmine, int *mark, int *next)
int mode,index,oldindex,newvalue,nflip,which,niter;
int active[2],first[2],last[2];
int newactive[2],newfirst[2],newlast[2];
bigint nmark,nactive,nactiveall,nflipall,bnflip;
bigint nmark,nflipall;
bigint activeall[2],bsum[3],bsumall[3];
double thresh;
@ -210,15 +210,12 @@ void RanMars::select_subset(bigint ntarget, int nmine, int *mark, int *next)
// choose to ADD or SUBTRACT from current nmark
// thresh = desired flips / size of active set
// nactive = size of current active set, only for debug output below
if (ntarget-nmark > 0) {
mode = ADD;
// nactive = active[mode];
thresh = 1.0 * (ntarget-nmark) / activeall[mode];
} else {
mode = SUBTRACT;
// nactive = active[mode];
thresh = 1.0 * (nmark-ntarget) / activeall[mode];
}
@ -278,12 +275,10 @@ void RanMars::select_subset(bigint ntarget, int nmine, int *mark, int *next)
bsum[0] = nflip;
bsum[1] = active[0];
bsum[2] = active[1];
bsum[3] = nactive;
MPI_Allreduce(&bsum,&bsumall,4,MPI_LMP_BIGINT,MPI_SUM,world);
MPI_Allreduce(&bsum,&bsumall,3,MPI_LMP_BIGINT,MPI_SUM,world);
nflipall = bsumall[0];
activeall[0] = bsumall[1];
activeall[1] = bsumall[2];
nactiveall = bsumall[3];
if (mode == ADD) nmark += nflipall;
else if (mode == SUBTRACT) nmark -= nflipall;