Merge pull request #3607 from akohlmey/no-inn-sewer-ants

Getting out of the insurance business :-)
This commit is contained in:
Axel Kohlmeyer
2023-01-23 21:02:53 -05:00
committed by GitHub
312 changed files with 453 additions and 448 deletions

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@ -63,7 +63,7 @@ In the src directory, there is one top-level Makefile and several
low-level machine-specific files named Makefile.xxx where xxx = the
machine name. If a low-level Makefile exists for your platform, you do
not need to edit the top-level Makefile. However you should check the
system-specific section of the low-level Makefile to insure the
system-specific section of the low-level Makefile to ensure the
various paths are correct for your environment. If a low-level
Makefile does not exist for your platform, you will need to add a
suitable target to the top-level Makefile. You will also need to

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@ -1206,7 +1206,7 @@ this command is not typically needed if the "nonbond style" and "
an exception to this is if a short cutoff is used initially,
but a longer cutoff will be used for a subsequent run (in the same
input script), in this case the "maximum cutoff" command should be
used to insure enough memory is allocated for the later run
used to ensure enough memory is allocated for the later run
note that a restart file contains nonbond cutoffs (so it is not necessary
to use a "nonbond style" command before "read restart"), but LAMMPS
still needs to know what the maximum cutoff will be before the

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@ -533,7 +533,7 @@ processor's ghost cells extend further than nearest neighbor
processors.
This can be checked by callers who have the option to change the
global grid size to insure more efficient nearest-neighbor-only
global grid size to ensure more efficient nearest-neighbor-only
communication if they wish. In this case, they instantiate a grid of
a given size (resolution), then invoke *setup_comm()* followed by
*ghost_adjacent()*. If the ghost cells are not adjacent, they destroy
@ -753,7 +753,7 @@ their input script syntax, as described on the :doc:`Howto_grid
* f_ID:gname:dname
* f_ID:gname:dname[I]
Each grid a command instantiates has a unique *gname*, defined by the
Each grid command instantiates has a unique *gname*, defined by the
command. Likewise each grid cell data structure (scalar or vector)
associated with a grid has a unique *dname*, also defined by the
command.
@ -784,8 +784,7 @@ The *get_grid_by_index()* method is called after the
*get_grid_by_name()* method, using the grid index it returned as its
argument. This method will return a pointer to the Grid2d or Grid3d
class. The caller can use this to query grid attributes, such as the
global size of the grid. The :doc:`dump grid <dump>` to insure each
its grid reference arguments are for grids of the same size.
global size of the grid, to ensure it is of the expected size.
The *get_griddata_by_name()* method takes a grid index *igrid* and a
data name as input. It returns two values. The *ncol* argument is

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@ -113,7 +113,7 @@ LAMMPS output, something is wrong with your simulation. If you
suspect this is happening, it is a good idea to print out
thermodynamic info frequently (e.g. every timestep) via the
:doc:`thermo <thermo>` so you can monitor what is happening.
Visualizing the atom movement is also a good idea to insure your model
Visualizing the atom movement is also a good idea to ensure your model
is behaving as you expect.
In parallel, one way LAMMPS can hang is due to how different MPI

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@ -6092,7 +6092,7 @@ keyword to allow for additional bonds to be formed
after a read_data, read_restart, or create_box command.
*Next command must list all universe and uloop variables*
This is to insure they stay in sync.
This is to ensure they stay in sync.
*No Kspace style defined for compute group/group*
Self-explanatory.
@ -7231,7 +7231,7 @@ keyword to allow for additional bonds to be formed
*Replacing a fix, but new style != old style*
A fix ID can be used a second time, but only if the style matches the
previous fix. In this case it is assumed you with to reset a fix's
previous fix. In this case it is assumed you want to reset a fix's
parameters. This error may mean you are mistakenly re-using a fix ID
when you do not intend to.
@ -7337,7 +7337,7 @@ keyword to allow for additional bonds to be formed
*Rigid body atoms %d %d missing on proc %d at step %ld*
This means that an atom cannot find the atom that owns the rigid body
it is part of, or vice versa. The solution is to use the communicate
cutoff command to insure ghost atoms are acquired from far enough away
cutoff command to ensure ghost atoms are acquired from far enough away
to encompass the max distance printed when the fix rigid/small command
was invoked.

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@ -351,7 +351,7 @@ This will most likely cause errors in kinetic fluctuations.
Self-explanatory.
*Kspace_modify slab param < 2.0 may cause unphysical behavior*
The kspace_modify slab parameter should be larger to insure periodic
The kspace_modify slab parameter should be larger to ensure periodic
grids padded with empty space do not overlap.
*Less insertions than requested*
@ -491,7 +491,7 @@ This will most likely cause errors in kinetic fluctuations.
*Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies*
This is because excluding specific pair interactions also excludes
them from long-range interactions which may not be the desired effect.
The special_bonds command handles this consistently by insuring
The special_bonds command handles this consistently by ensuring
excluded (or weighted) 1-2, 1-3, 1-4 interactions are treated
consistently by both the short-range pair style and the long-range
solver. This is not done for exclusions of charged atom pairs via the
@ -545,7 +545,7 @@ This will most likely cause errors in kinetic fluctuations.
If there are other fixes that act immediately after the initial stage
of time integration within a timestep (i.e. after atoms move), then
the command that sets up the dynamic group should appear after those
fixes. This will insure that dynamic group assignments are made
fixes. This will ensure that dynamic group assignments are made
after all atoms have moved.
*One or more respa levels compute no forces*

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@ -22,7 +22,7 @@ atom in the file, assign a z coordinate so it falls inside the
z-boundaries of the box - e.g. 0.0.
Use the :doc:`fix enforce2d <fix_enforce2d>` command as the last
defined fix to insure that the z-components of velocities and forces
defined fix to ensure that the z-components of velocities and forces
are zeroed out every timestep. The reason to make it the last fix is
so that any forces induced by other fixes will be zeroed out.

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@ -111,7 +111,7 @@ Therefore it is typically desirable to decouple the relative motion of
the core/shell pair, which is an imaginary degree of freedom, from the
real physical system. To do that, the :doc:`compute temp/cs <compute_temp_cs>` command can be used, in conjunction with
any of the thermostat fixes, such as :doc:`fix nvt <fix_nh>` or :doc:`fix langevin <fix_langevin>`. This compute uses the center-of-mass velocity
of the core/shell pairs to calculate a temperature, and insures that
of the core/shell pairs to calculate a temperature, and ensures that
velocity is what is rescaled for thermostatting purposes. This
compute also works for a system with both core/shell pairs and
non-polarized ions (ions without an attached satellite particle). The

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@ -93,7 +93,7 @@ Some of the pair styles used to compute pairwise interactions between
finite-size particles also compute the correct interaction with point
particles as well, e.g. the interaction between a point particle and a
finite-size particle or between two point particles. If necessary,
:doc:`pair_style hybrid <pair_hybrid>` can be used to insure the correct
:doc:`pair_style hybrid <pair_hybrid>` can be used to ensure the correct
interactions are computed for the appropriate style of interactions.
Likewise, using groups to partition particles (ellipsoids versus
spheres versus point particles) will allow you to use the appropriate

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@ -70,7 +70,7 @@ single processor outputs, mpi4py is not working correctly.
Also note that once you import the mpi4py module, mpi4py initializes MPI
for you, and you can use MPI calls directly in your Python script, as
described in the mpi4py documentation. The last line of your Python
script should be ``MPI.finalize()``, to insure MPI is shut down
script should be ``MPI.finalize()``, to ensure MPI is shut down
correctly.

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@ -362,10 +362,10 @@ Reorder the processors in the MPI communicator used to instantiate
LAMMPS, in one of several ways. The original MPI communicator ranks
all P processors from 0 to P-1. The mapping of these ranks to
physical processors is done by MPI before LAMMPS begins. It may be
useful in some cases to alter the rank order. E.g. to insure that
useful in some cases to alter the rank order. E.g. to ensure that
cores within each node are ranked in a desired order. Or when using
the :doc:`run_style verlet/split <run_style>` command with 2 partitions
to insure that a specific Kspace processor (in the second partition) is
to ensure that a specific Kspace processor (in the second partition) is
matched up with a specific set of processors in the first partition.
See the :doc:`General tips <Speed_tips>` page for more details.
@ -398,7 +398,7 @@ so that the processors in each partition will be
0 1 2 4 5 6 8 9 10
3 7 11
See the "processors" command for how to insure processors from each
See the "processors" command for how to ensure processors from each
partition could then be grouped optimally for quad-core nodes.
If the keyword is *custom*, then a file that specifies a permutation

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@ -122,7 +122,7 @@ potentially *dangerous* rebuilds. If atom movement triggered neighbor
list rebuilding (see the :doc:`neigh_modify <neigh_modify>` command),
then dangerous reneighborings are those that were triggered on the
first timestep atom movement was checked for. If this count is
non-zero you may wish to reduce the delay factor to insure no force
non-zero you may wish to reduce the delay factor to ensure no force
interactions are missed by atoms moving beyond the neighbor skin
distance before a rebuild takes place.

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@ -282,7 +282,7 @@ showing the use of the *template* atom style versus *molecular*.
.. note::
When using the *template* style with a :doc:`molecule template
<molecule>` that contains multiple molecules, you should insure the
<molecule>` that contains multiple molecules, you should ensure the
atom types, bond types, angle_types, etc in all the molecules are
consistent. E.g. if one molecule represents H2O and another CO2,
then you probably do not want each molecule file to define 2 atom

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@ -148,7 +148,7 @@ In the last scenario, a :doc:`fix <fix>` or :doc:`compute <compute>` or
:doc:`pairwise potential <pair_style>` needs to calculate with ghost
atoms beyond the normal pairwise cutoff for some computation it
performs (e.g. locate neighbors of ghost atoms in a manybody pair
potential). Setting the ghost cutoff appropriately can insure it will
potential). Setting the ghost cutoff appropriately can ensure it will
find the needed atoms.
.. note::

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@ -75,7 +75,7 @@ neighbor atom in each requested ADF.
If you request any outer cutoff *Router* > force cutoff, or if no
pair style is defined, e.g. the :doc:`rerun <rerun>` command is being used to
post-process a dump file of snapshots you must insure ghost atom information
post-process a dump file of snapshots you must ensure ghost atom information
out to the largest value of *Router* + *skin* is communicated, via the
:doc:`comm_modify cutoff <comm_modify>` command, else the ADF computation
cannot be performed, and LAMMPS will give an error message. The *skin* value

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@ -43,7 +43,7 @@ compute group. Note that normally a CNA calculation should only be
performed on mono-component systems.
The CNA calculation can be sensitive to the specified cutoff value.
You should insure the appropriate nearest neighbors of an atom are
You should ensure the appropriate nearest neighbors of an atom are
found within the cutoff distance for the presumed crystal structure
(e.g., 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest
neighbors for perfect BCC crystals). These formulas can be used to

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@ -58,7 +58,7 @@ are adding atoms or molecules to the system (see the :doc:`fix pour
<fix_pour>`, :doc:`fix deposit <fix_deposit>`, and :doc:`fix gcmc
<fix_gcmc>` commands) or expect atoms or molecules to be lost
(e.g. due to exiting the simulation box or via :doc:`fix evaporate
<fix_evaporate>`), then this option should be used to insure the
<fix_evaporate>`), then this option should be used to ensure the
temperature is correctly normalized.
.. note::

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@ -74,7 +74,7 @@ compute command was first invoked.
This compute stores the original position (of the
center-of-mass) of each chunk. When a displacement is calculated on a
later timestep, it is assumed that the same atoms are assigned to the
same chunk ID. However LAMMPS has no simple way to insure this is the
same chunk ID. However LAMMPS has no simple way to ensure this is the
case, though you can use the *ids once* option when specifying the
:doc:`compute chunk/atom <compute_chunk_atom>` command. Note that if
this is not the case, the MSD calculation does not have a sensible

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@ -82,7 +82,7 @@ distance specified.
every timestep this command is invoked (or every reneighboring
timestep, whichever is less frequent), which is inefficient. LAMMPS
will warn you if this is the case. If you specify a *Rcut* > force
cutoff, you must insure ghost atom information out to *Rcut* + *skin*
cutoff, you must ensure ghost atom information out to *Rcut* + *skin*
is communicated, via the :doc:`comm_modify cutoff <comm_modify>`
command, else the RDF computation cannot be performed, and LAMMPS will
give an error message. The *skin* value is what is specified with the

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@ -108,7 +108,7 @@ atom types 1, 2, and 3, then each created molecule will have atom types
For the *box* style, the create_atoms command fills the entire
simulation box with particles on the lattice. If your simulation box
is periodic, you should insure its size is a multiple of the lattice
is periodic, you should ensure its size is a multiple of the lattice
spacings, to avoid unwanted atom overlaps at the box boundaries. If
your box is periodic and a multiple of the lattice spacing in a
particular dimension, LAMMPS is careful to put exactly one particle at
@ -121,7 +121,7 @@ and also consistent with the region volume. See the :doc:`region
that its "volume" is either inside or outside its geometric boundary.
Also note that if a region is the same size as a periodic simulation
box (in some dimension), LAMMPS does NOT implement the same logic
described above for the *box* style, to insure exactly one particle at
described above for the *box* style, to ensure exactly one particle at
periodic boundaries. If this is desired, you should either use the
*box* style, or tweak the region size to get precisely the particles
you want.
@ -222,7 +222,7 @@ to the simulation. For example, grain boundaries can be created, by
interleaving the create_atoms command with :doc:`lattice <lattice>`
commands specifying different orientations.
When this command is used, care should be taken to insure the
When this command is used, care should be taken to ensure the
resulting system does not contain particles that are highly
overlapped. Such overlaps will cause many interatomic potentials to
compute huge energies and forces, leading to bad dynamics. There are
@ -316,7 +316,7 @@ inserting particles, which may be limited by the *region* style or the
fraction of them (:math:`0 \le f \le 1`) will be assigned particles.
For the *subset* keyword only the specified *Nsubset* of them will be
assigned particles. In both cases the assigned lattice sites are
chosen randomly. An iterative algorithm is used that insures the
chosen randomly. An iterative algorithm is used that ensures the
correct number of particles are inserted, in a perfectly random
fashion. Which lattice sites are selected will change with the number
of processors used.

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@ -130,7 +130,7 @@ a distance that encompasses the *rmax* for new bonds to create.
If you want to create bonds between pairs of 1--3 or 1--4 atoms in
the current bond topology, then you need to use :doc:`special_bonds
lj 0 1 1 <special_bonds>` to insure those pairs appear in the
lj 0 1 1 <special_bonds>` to ensure those pairs appear in the
neighbor list. They will not appear with the default special_bonds
settings, which are zero for 1--2, 1--3, and 1--4 atoms. 1--3 or 1--4
atoms are those which are two hops or three hops apart in the bond

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@ -193,7 +193,7 @@ are then used as described above, when computing energy and force for
individual dihedral angles and their atoms. This means that if you
want the interpolation tables of length *Ntable* to match exactly what
is in the tabulated file (with effectively nopreliminary
interpolation), you should set *Ntable* = *Nfile*\ . To insure the
interpolation), you should set *Ntable* = *Nfile*\ . To ensure the
nodal points in the user's file are aligned with the interpolated
table entries, the angles in the table should be integer multiples of
360/\ *Ntable* degrees, or 2\*PI/\ *Ntable* radians (depending on your

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@ -596,7 +596,7 @@ then one file per snapshot is written and the "\*" character is
replaced with the timestep value. For example, tmp.dump.\* becomes
tmp.dump.0, tmp.dump.10000, tmp.dump.20000, etc. This option is not
available for the *dcd* and *xtc* styles. Note that the
:doc:`dump_modify pad <dump_modify>` command can be used to insure all
:doc:`dump_modify pad <dump_modify>` command can be used to ensure all
timestep numbers are the same length (e.g., 00010), which can make it
easier to read a series of dump files in order with some
post-processing tools.

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@ -255,7 +255,7 @@ one image file per snapshot is written. The "\*" character is replaced
with the timestep value. For example, tmp.dump.\*.jpg becomes
tmp.dump.0.jpg, tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc. Note
that the :doc:`dump_modify pad <dump_modify>` command can be used to
insure all timestep numbers are the same length (e.g., 00010), which
ensure all timestep numbers are the same length (e.g., 00010), which
can make it easier to convert a series of images into a movie in the
correct ordering.

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@ -410,7 +410,7 @@ command is invoked.
----------
The *flush* keyword determines whether a flush operation is invoked
after a dump snapshot is written to the dump file. A flush insures
after a dump snapshot is written to the dump file. A flush ensures
the output in that file is current (no buffering by the OS), even if
LAMMPS halts before the simulation completes. Flushes cannot be
performed with dump style *xtc*\ .

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@ -130,7 +130,7 @@ character appears in the filename, then one file per snapshot is
written and the "\*" character is replaced with the timestep value.
For example, tmp.dump\*.vtk becomes tmp.dump0.vtk, tmp.dump10000.vtk,
tmp.dump20000.vtk, etc. Note that the :doc:`dump_modify pad <dump_modify>`
command can be used to insure all timestep numbers are the same length
command can be used to ensure all timestep numbers are the same length
(e.g. 00010), which can make it easier to read a series of dump files
in order with some post-processing tools.
@ -169,7 +169,7 @@ The *vtk* dump style is part of the VTK package. It is only
enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
To use this dump style, you also must link to the VTK library. See
the info in lib/vtk/README and insure the Makefile.lammps file in that
the info in lib/vtk/README and ensure the Makefile.lammps file in that
directory is appropriate for your machine.
The *vtk* dump style supports neither buffering or custom format

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@ -106,7 +106,7 @@ for :math:`f_x`, :math:`f_y`, :math:`f_z`, the energy variable is specified as
v_name, where name is the variable name.
Note that when the *energy* keyword is used during an energy
minimization, you must insure that the formula defined for the
minimization, you must ensure that the formula defined for the
atom-style :doc:`variable <variable>` is consistent with the force
variable formulas (i.e., that :math:`-\vec\nabla E = \vec F`).
For example, if the force were a spring-like, :math:`\vec F = -k\vec x`, then

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@ -100,7 +100,7 @@ be met:
1. All 4 monomers must be in the fix group.
2. All 4 monomers must be owned by the processor (not ghost atoms).
This insures that another processor does not attempt to swap bonds
This ensures that another processor does not attempt to swap bonds
involving the same atoms on the same timestep. Note that this also
means that bond pairs which straddle processor boundaries are not
eligible for swapping on this step.

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@ -96,7 +96,7 @@ default group "all" and the group specified in the fix deposit command
If you are computing temperature values which include inserted
particles, you will want to use the
:doc:`compute_modify <compute_modify>` dynamic option, which insures the
:doc:`compute_modify <compute_modify>` dynamic option, which ensures the
current number of atoms is used as a normalizing factor each time the
temperature is computed.
@ -128,7 +128,7 @@ side = *in*\ .
tests against the larger orthonormal box that bounds the tilted
simulation box. If the specified region includes volume outside the
tilted box, then an insertion will likely fail, leading to a "lost
atoms" error. Thus for triclinic boxes you should insure the
atoms" error. Thus for triclinic boxes you should ensure the
specified region is wholly inside the simulation box.
The locations of inserted particles are taken from uniform distributed

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@ -105,7 +105,7 @@ atom as function of its position. Like variables used for *ex*,
is the variable name.
Note that when the *energy* keyword is used during an energy
minimization, you must insure that the formula defined for the
minimization, you must ensure that the formula defined for the
atom-style :doc:`variable <variable>` is consistent with the force
variable formulas, i.e. that -Grad(E) = F. For example, if the force
due to the electric field were a spring-like F = kx, then the energy

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@ -27,7 +27,7 @@ Description
"""""""""""
Zero out the z-dimension velocity and force on each atom in the group.
This is useful when running a 2d simulation to insure that atoms do
This is useful when running a 2d simulation to ensure that atoms do
not move from their initial z coordinate.
----------

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@ -42,7 +42,7 @@ chosen at random and deleted. If there are less than M eligible
particles, then all of them are deleted.
If the setting for the *molecule* keyword is *no*, then only single
atoms are deleted. In this case, you should insure you do not delete
atoms are deleted. In this case, you should ensure you do not delete
only a portion of a molecule (only some of its atoms), or LAMMPS will
soon generate an error when it tries to find those atoms. LAMMPS will
warn you if any of the atoms eligible for deletion have a non-zero

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@ -127,7 +127,7 @@ stress tensor components. Eng is an extensive quantity,
meaning it should be the sum over per-atom energies of all affected
atoms. It should also be provided in :doc:`energy units <units>`
consistent with the simulation. See the details below for how to
insure this energy setting is used appropriately in a minimization.
ensure this energy setting is used appropriately in a minimization.
Additional public methods that the caller can use to update system
properties are:

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@ -353,7 +353,7 @@ about simulating non-neutral systems with kspace on.
Use of this fix typically will cause the number of atoms to fluctuate,
therefore, you will want to use the
:doc:`compute_modify dynamic/dof <compute_modify>` command to insure that the
:doc:`compute_modify dynamic/dof <compute_modify>` command to ensure that the
current number of atoms is used as a normalizing factor each time
temperature is computed. A simple example of this is:

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@ -83,7 +83,7 @@ specified as an equal-style :doc:`variable <variable>`. If the value is
a variable, it should be specified as v_name, where name is the
variable name. In this case, the variable will be evaluated each
timestep, and its value used to determine the quantity. You should
insure that the variable calculates a result in the appropriate units,
ensure that the variable calculates a result in the appropriate units,
e.g. force/mass or degrees.
Equal-style variables can specify formulas with various mathematical

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@ -240,7 +240,7 @@ well for many solid-state systems.
.. note::
You should insure that ghost atom communication is performed for
You should ensure that ghost atom communication is performed for
a distance of at least *Dcut* + *cutevent* = the distance one or more
atoms move (between quenched states) to be considered an "event". It
is an argument to the "compute event/displace" command used to detect

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@ -194,7 +194,7 @@ For the *omega* keyword there is also a scale factor of
:math:`F_f` (damping) term in the equation above and of
:math:`\sqrt{\frac{10.0}{3.0}}` as a multiplier on the :math:`F_r` term.
This does not affect the thermostatting behavior of the Langevin
formalism but insures that the randomized rotational diffusivity of
formalism but ensures that the randomized rotational diffusivity of
spherical particles is correct.
For the *angmom* keyword a similar scale factor is needed which is

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@ -130,7 +130,7 @@ typically specified via the create_box command or in the data file
read by the read_data command.
If this keyword is specified, then this fix will send the MDI
">ELEMENTS" command to the engine, to insure the two codes are
">ELEMENTS" command to the engine, to ensure the two codes are
consistent in their definition of atomic species. If this keyword is
not specified, then this fix will send the MDI >TYPES command to the
engine. This is fine if both the LAMMPS driver and the MDI engine are

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@ -140,14 +140,14 @@ molecules to the system (see the :doc:`fix pour <fix_pour>`, :doc:`fix
deposit <fix_deposit>`, and :doc:`fix gcmc <fix_gcmc>` commands) or
expect atoms or molecules to be lost (e.g. due to exiting the
simulation box or via :doc:`fix evaporate <fix_evaporate>`), then this
option should be used to insure the temperature is correctly
option should be used to ensure the temperature is correctly
normalized.
.. note::
Other thermostatting fixes, such as :doc:`fix nvt <fix_nh>`, do
not use the *dynamic/dof* keyword because they use a temperature
compute to calculate temperature. See the :doc:`compute_modify dynamic/dof <compute_modify>` command for a similar way to insure
compute to calculate temperature. See the :doc:`compute_modify dynamic/dof <compute_modify>` command for a similar way to ensure
correct temperature normalization for those thermostats.
The *bodyforces* keyword determines whether the forces and torques

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@ -69,7 +69,7 @@ the corresponding flag to 0.
If the *angular* keyword is used, the angular momentum is zeroed by
subtracting a rotational component from each atom.
This command can be used to insure the entire collection of atoms (or
This command can be used to ensure the entire collection of atoms (or
a subset of them) does not drift or rotate during the simulation due
to random perturbations (e.g. :doc:`fix langevin <fix_langevin>`
thermostatting).

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@ -41,7 +41,7 @@ be used for diagnostic purposes or as a debugging tool to monitor some
quantity during a run. The text string must be a single argument, so
it should be enclosed in single or double quotes if it is more than
one word. If it contains variables it must be enclosed in double
quotes to insure they are not evaluated when the input script line is
quotes to ensure they are not evaluated when the input script line is
read, but will instead be evaluated each time the string is printed.
.. note::

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@ -112,7 +112,7 @@ The new atom properties encode values that migrate with atoms to new
processors and are written to restart files. If you want the new
properties to also be defined for ghost atoms, then use the *ghost*
keyword with a value of *yes*\ . This will invoke extra communication
when ghost atoms are created (at every re-neighboring) to insure the
when ghost atoms are created (at every re-neighboring) to ensure the
new properties are also defined for the ghost atoms.
.. admonition:: Properties on ghost atoms

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@ -38,7 +38,7 @@ Constrain the center-of-mass position of a group of atoms by adjusting
the coordinates of the atoms every timestep. This is simply a small
shift that does not alter the dynamics of the system or change the
relative coordinates of any pair of atoms in the group. This can be
used to insure the entire collection of atoms (or a portion of them)
used to ensure the entire collection of atoms (or a portion of them)
do not drift during the simulation due to random perturbations
(e.g. :doc:`fix langevin <fix_langevin>` thermostatting).

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@ -316,7 +316,7 @@ to be part of rigid bodies.
To compute the initial center-of-mass position and other
properties of each rigid body, the image flags for each atom in the
body are used to "unwrap" the atom coordinates. Thus you must insure
body are used to "unwrap" the atom coordinates. Thus you must ensure
that these image flags are consistent so that the unwrapping creates a
valid rigid body (one where the atoms are close together),
particularly if the atoms in a single rigid body straddle a periodic
@ -337,7 +337,7 @@ This may be useful if you wish a body to rotate but not translate, or
vice versa, or if you wish it to rotate or translate continuously
unaffected by interactions with other particles. Note that if you
expect a rigid body not to move or rotate by using these keywords, you
must insure its initial center-of-mass translational or angular
must ensure its initial center-of-mass translational or angular
velocity is 0.0. Otherwise the initial translational or angular
momentum the body has will persist.
@ -702,9 +702,10 @@ also accounted for by this fix.
----------
If your simulation is a hybrid model with a mixture of rigid bodies
and non-rigid particles (e.g. solvent) there are several ways these
rigid fixes can be used in tandem with :doc:`fix nve <fix_nve>`, :doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, and :doc:`fix nph <fix_nh>`.
If your simulation is a hybrid model with a mixture of rigid bodies and
non-rigid particles (e.g. solvent) there are several ways these rigid
fixes can be used in tandem with :doc:`fix nve <fix_nve>`, :doc:`fix nvt
<fix_nh>`, :doc:`fix npt <fix_nh>`, and :doc:`fix nph <fix_nh>`.
If you wish to perform NVE dynamics (no thermostatting or
barostatting), use one of 4 NVE rigid styles to integrate the rigid
@ -713,13 +714,17 @@ particles.
If you wish to perform NVT dynamics (thermostatting, but no
barostatting), you can use one of the 2 NVT rigid styles for the rigid
bodies, and any thermostatting fix for the non-rigid particles (:doc:`fix nvt <fix_nh>`, :doc:`fix langevin <fix_langevin>`, :doc:`fix temp/berendsen <fix_temp_berendsen>`). You can also use one of the
4 NVE rigid styles for the rigid bodies and thermostat them using :doc:`fix langevin <fix_langevin>` on the group that contains all the
particles in the rigid bodies. The net force added by :doc:`fix langevin <fix_langevin>` to each rigid body effectively thermostats
its translational center-of-mass motion. Not sure how well it does at
bodies, and any thermostatting fix for the non-rigid particles
(:doc:`fix nvt <fix_nh>`, :doc:`fix langevin <fix_langevin>`, :doc:`fix
temp/berendsen <fix_temp_berendsen>`). You can also use one of the 4
NVE rigid styles for the rigid bodies and thermostat them using
:doc:`fix langevin <fix_langevin>` on the group that contains all the
particles in the rigid bodies. The net force added by :doc:`fix
langevin <fix_langevin>` to each rigid body effectively thermostats its
translational center-of-mass motion. Not sure how well it does at
thermostatting its rotational motion.
If you with to perform NPT or NPH dynamics (barostatting), you cannot
If you wish to perform NPT or NPH dynamics (barostatting), you cannot
use both :doc:`fix npt <fix_nh>` and the NPT or NPH rigid styles. This
is because there can only be one fix which monitors the global
pressure and changes the simulation box dimensions. So you have 3
@ -727,27 +732,28 @@ choices:
* Use one of the 4 NPT or NPH styles for the rigid bodies. Use the
*dilate* all option so that it will dilate the positions of the
non-rigid particles as well. Use :doc:`fix nvt <fix_nh>` (or any other
thermostat) for the non-rigid particles.
*non-rigid particles as well. Use :doc:`fix nvt <fix_nh>` (or any
*other thermostat) for the non-rigid particles.
* Use :doc:`fix npt <fix_nh>` for the group of non-rigid particles. Use
the *dilate* all option so that it will dilate the center-of-mass
positions of the rigid bodies as well. Use one of the 4 NVE or 2 NVT
rigid styles for the rigid bodies.
* Use :doc:`fix press/berendsen <fix_press_berendsen>` to compute the
pressure and change the box dimensions. Use one of the 4 NVE or 2 NVT
rigid styles for the rigid bodies. Use :doc:`fix nvt <fix_nh>` (or any
other thermostat) for the non-rigid particles.
rigid styles for the rigid bodies. Use :doc:`fix nvt <fix_nh>` (or
any other thermostat) for the non-rigid particles.
In all case, the rigid bodies and non-rigid particles both contribute
to the global pressure and the box is scaled the same by any of the
barostatting fixes.
You could even use the second and third options for a non-hybrid simulation
consisting of only rigid bodies, assuming you give :doc:`fix npt <fix_nh>` an empty group, though it's an odd thing to do. The
barostatting fixes (:doc:`fix npt <fix_nh>` and :doc:`fix press/berensen <fix_press_berendsen>`) will monitor the pressure
and change the box dimensions, but not time integrate any particles.
The integration of the rigid bodies will be performed by fix
rigid/nvt.
You could even use the second and third options for a non-hybrid
simulation consisting of only rigid bodies, assuming you give :doc:`fix
npt <fix_nh>` an empty group, though it's an odd thing to do. The
barostatting fixes (:doc:`fix npt <fix_nh>` and :doc:`fix press/berensen
<fix_press_berendsen>`) will monitor the pressure and change the box
dimensions, but not time integrate any particles. The integration of
the rigid bodies will be performed by fix rigid/nvt.
----------
@ -868,7 +874,7 @@ possible to compute the target temperature correctly. Second, the
assigned velocities may be partially canceled when constraints are
first enforced, leading to a different temperature than desired. A
workaround for this is to perform a :doc:`run 0 <run>` command, which
insures all DOFs are accounted for properly, and then rescale the
ensures all DOFs are accounted for properly, and then rescale the
temperature to the desired value before performing a simulation. For
example:

View File

@ -156,7 +156,7 @@ included in each rigid body.
To compute the initial center-of-mass position and other
properties of each rigid body, the image flags for each particle in the
body are used to "unwrap" the particle coordinates. Thus you must
insure that these image flags are consistent so that the unwrapping
ensure that these image flags are consistent so that the unwrapping
creates a valid rigid body (one where the particles are close together)
, particularly if the particles in a single rigid body straddle a
periodic boundary. This means the input data file or restart file must
@ -173,7 +173,7 @@ This may be useful if you wish a body to rotate but not translate, or
vice versa, or if you wish it to rotate or translate continuously
unaffected by interactions with other particles. Note that if you
expect a rigid body not to move or rotate by using these keywords, you
must insure its initial center-of-mass translational or angular
must ensure its initial center-of-mass translational or angular
velocity is 0.0. Otherwise the initial translational or angular
momentum, the body has, will persist.

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@ -335,7 +335,7 @@ should be used to turn off big/SRD interactions, e.g. by setting their
epsilon or cutoff length to 0.0.
The "delete_atoms overlap" command may be useful in setting up an SRD
simulation to insure there are no initial overlaps between big and SRD
simulation to ensure there are no initial overlaps between big and SRD
particles.
----------

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@ -237,7 +237,7 @@ time. Thus it is easy to specify a time-dependent wall interaction.
.. note::
For all of the styles, you must insure that r is always > 0 for
For all of the styles, you must ensure that r is always > 0 for
all particles in the group, or LAMMPS will generate an error. This
means you cannot start your simulation with particles at the wall
position *coord* (r = 0) or with particles on the wrong side of the
@ -277,7 +277,7 @@ boundaries. The default for *pbc* is *no*, which means the system
must be non-periodic when using a wall. But you may wish to use a
periodic box. E.g. to allow some particles to interact with the wall
via the fix group-ID, and others to pass through it and wrap around a
periodic box. In this case you should insure that the wall if
periodic box. In this case you should ensure that the wall if
sufficiently far enough away from the box boundary. If you do not,
then particles may interact with both the wall and with periodic
images on the other side of the box, which is probably not what you

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@ -104,7 +104,7 @@ respectively, in units of 1/volume.
.. note::
You must insure that r is always bigger than :math:`\sigma_n` for
You must ensure that r is always bigger than :math:`\sigma_n` for
all particles in the group, or LAMMPS will generate an error. This
means you cannot start your simulation with particles touching the wall
position *coord* (:math:`r = \sigma_n`) or with particles penetrating

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@ -77,7 +77,7 @@ region surface will move over time in the corresponding manner.
As discussed on the :doc:`region <region>` command doc page,
regions in LAMMPS do not get wrapped across periodic boundaries. It
is up to you to insure that periodic or non-periodic boundaries are
is up to you to ensure that periodic or non-periodic boundaries are
specified appropriately via the :doc:`boundary <boundary>` command when
using a region as a wall that bounds particle motion. This also means
that if you embed a region in your simulation box and want it to

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@ -96,7 +96,7 @@ specify a time-dependent wall position.
.. note::
Because the trajectory of the SRD particle is tracked as it
collides with the wall, you must insure that r = distance of the
collides with the wall, you must ensure that r = distance of the
particle from the wall, is always > 0 for SRD particles, or LAMMPS
will generate an error. This means you cannot start your simulation
with SRD particles at the wall position *coord* (r = 0) or with
@ -117,7 +117,7 @@ specify a time-dependent wall position.
a mixture containing other kinds of particles, then you should
typically use :doc:`another wall command <fix_wall>` to act on the other
particles. Since SRD particles will be colliding both with the walls
and the other particles, it is important to insure that the other
and the other particles, it is important to ensure that the other
particle's finite extent does not overlap an SRD wall. If you do not
do this, you may generate errors when SRD particles end up "inside"
another particle or a wall at the beginning of a collision step.

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@ -173,15 +173,15 @@ Note that these lines
thermo_style custom step temp pe c_2
run 0
are necessary to insure that the "eatom" variable is current when the
are necessary to ensure that the "eatom" variable is current when the
group command invokes it. Because the eatom variable computes the
per-atom energy via the pe/atom compute, it will only be current if a
run has been performed which evaluated pairwise energies, and the
pe/atom compute was actually invoked during the run. Printing the
thermodynamic info for compute 2 insures that this is the case, since
thermodynamic info for compute 2 ensures that this is the case, since
it sums the pe/atom compute values (in the reduce compute) to output
them to the screen. See the "Variable Accuracy" section of the
:doc:`variable <variable>` page for more details on insuring that
:doc:`variable <variable>` page for more details on ensuring that
variables are current when they are evaluated between runs.
The *include* style with its arg *molecule* adds atoms to a group that

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@ -97,7 +97,7 @@ system temperature has reached a certain value, and if so, breaks out
of the loop to finish the run. Note that any variable could be
checked, so long as it is current on the timestep when the run
completes. As explained on the :doc:`variable <variable>` doc page,
this can be insured by including the variable in thermodynamic output.
this can be ensured by including the variable in thermodynamic output.
.. code-block:: LAMMPS

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@ -99,7 +99,7 @@ system temperature has reached a certain value, and if so, breaks out
of the loop to finish the run. Note that any variable could be
checked, so long as it is current on the timestep when the run
completes. As explained on the :doc:`variable <variable>` doc page,
this can be insured by including the variable in thermodynamic output.
this can be ensured by including the variable in thermodynamic output.
.. code-block:: LAMMPS

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@ -118,7 +118,7 @@ molecule (header keyword = inertia).
so you do not overflow those pre-allocated data structures when adding
molecules later. Both the :doc:`create_box <create_box>` command and
the :doc:`read_data <read_data>` command have "extra" options which
insure space is allocated for storing topology info for molecules that
ensure space is allocated for storing topology info for molecules that
are added later.
The format of an individual molecule file is similar but

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@ -127,7 +127,7 @@ The *cluster* option does a sanity test every time neighbor lists are
built for bond, angle, dihedral, and improper interactions, to check
that each set of 2, 3, or 4 atoms is a cluster of nearby atoms. It
does this by computing the distance between pairs of atoms in the
interaction and insuring they are not further apart than half the
interaction and ensuring they are not further apart than half the
periodic box length. If they are, an error is generated, since the
interaction would be computed between far-away atoms instead of their
nearby periodic images. The only way this should happen is if the
@ -264,7 +264,7 @@ The *molecule/intra* and *molecule/inter* exclusion options can only
be used with atom styles that define molecule IDs.
The value of the *page* setting must be at least 10x larger than the
*one* setting. This insures neighbor pages are not mostly empty
*one* setting. This ensures neighbor pages are not mostly empty
space.
Related commands

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@ -629,7 +629,7 @@ too.
packages, be aware these packages all allow setting of the *Nthreads*
value via their package commands, but there is only a single global
*Nthreads* value used by OpenMP. Thus if multiple package commands are
invoked, you should insure the values are consistent. If they are
invoked, you should ensure the values are consistent. If they are
not, the last one invoked will take precedence, for all packages.
Also note that if the :doc:`-sf hybrid intel omp command-line switch <Run_options>` is used, it invokes a "package intel" command, followed by a
"package omp" command, both with a setting of *Nthreads* = 0. Likewise

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@ -136,7 +136,7 @@ larger, then the pair interacts via the colloid-solvent formula.
Note that the diameter of a particular particle type may appear in
multiple pair_coeff commands, as it interacts with other particle
types. You should insure the particle diameter is specified
types. You should ensure the particle diameter is specified
consistently each time it appears.
The last coefficient is optional. If not specified, the global cutoff
@ -201,7 +201,7 @@ Normally, this pair style should be used with finite-size particles
which have a diameter, e.g. see the :doc:`atom_style sphere <atom_style>` command. However, this is not a requirement,
since the only definition of particle size is via the pair_coeff
parameters for each type. In other words, the physical radius of the
particle is ignored. Thus you should insure that the d1,d2 parameters
particle is ignored. Thus you should ensure that the d1,d2 parameters
you specify are consistent with the physical size of the particles of
that type.

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@ -308,7 +308,7 @@ one of these options:
* :doc:`fix nvt/sphere update dipole <fix_nvt_sphere>`
* :doc:`fix npt/sphere update dipole <fix_npt_sphere>`
In all cases the "update dipole" setting insures the dipole moments
In all cases the "update dipole" setting ensures the dipole moments
are also rotated when the finite-size spheres rotate. The 2nd and 3rd
bullets perform thermostatting; in the case of a Langevin thermostat
the "omega yes" option also thermostats the rotational degrees of

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@ -118,7 +118,7 @@ atom type J. If all three epsilon_j values are zero, they are ignored.
Thus the typical way to define the :math:`\epsilon_i` and
:math:`\epsilon_j` coefficients is to list their values in "pair_coeff
I J" commands when I = J, but set them to 0.0 when I != J. If you do
list them when I != J, you should insure they are consistent with their
list them when I != J, you should ensure they are consistent with their
values in other pair_coeff commands, since only the last setting will
be in effect.
@ -126,7 +126,7 @@ Note that if this potential is being used as a sub-style of
:doc:`pair_style hybrid <pair_hybrid>`, and there is no "pair_coeff I I"
setting made for Gay-Berne for a particular type I (because I-I
interactions are computed by another hybrid pair potential), then you
still need to insure the :math:`\epsilon` a,b,c coefficients are assigned to
still need to ensure the :math:`\epsilon` a,b,c coefficients are assigned to
that type. e.g. in a "pair_coeff I J" command.
.. note::

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@ -468,7 +468,7 @@ Restrictions
When using a long-range Coulombic solver (via the
:doc:`kspace_style <kspace_style>` command) with a hybrid pair_style,
one or more sub-styles will be of the "long" variety,
e.g. *lj/cut/coul/long* or *buck/coul/long*\ . You must insure that the
e.g. *lj/cut/coul/long* or *buck/coul/long*\ . You must ensure that the
short-range Coulombic cutoff used by each of these long pair styles is
the same or else LAMMPS will generate an error.

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@ -123,7 +123,7 @@ that will be used with other potentials.
filenames can appear in any order, e.g. "Si C" or "C Si" in the
example above. However, if the second filename is **not** NULL (as in the
example above), it contains settings that are indexed **by numbers**
for the elements that precede it. Thus you need to insure that you list
for the elements that precede it. Thus you need to ensure that you list
the elements between the filenames in an order consistent with how the
values in the second filename are indexed. See details below on the
syntax for settings in the second file.

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@ -129,14 +129,14 @@ atom type J. If all three :math:`\epsilon_i` values are zero, they are
ignored. Thus the typical way to define the :math:`\epsilon_i` and
:math:`\epsilon_j` coefficients is to list their values in "pair_coeff
I J" commands when I = J, but set them to 0.0 when I != J. If you do
list them when I != J, you should insure they are consistent with their
list them when I != J, you should ensure they are consistent with their
values in other pair_coeff commands.
Note that if this potential is being used as a sub-style of
:doc:`pair_style hybrid <pair_hybrid>`, and there is no "pair_coeff I I"
setting made for RE-squared for a particular type I (because I-I
interactions are computed by another hybrid pair potential), then you
still need to insure the epsilon a,b,c coefficients are assigned to
still need to ensure the epsilon a,b,c coefficients are assigned to
that type in a "pair_coeff I J" command.
For large uniform molecules it has been shown that the :math:`\epsilon_{*,*}`

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@ -92,9 +92,9 @@ short-range part of one of the long-range solvers specified by the
:doc:`kspace_style <kspace_style>` command, then you must use one or
more of the optional keywords listed above for the pair_style command.
These are *ewald* or *pppm* or *msm* or *dispersion* or *tip4p*\ . This
is so LAMMPS can insure the short-range potential and long-range
is so LAMMPS can ensure the short-range potential and long-range
solver are compatible with each other, as it does for other
short-range pair styles, such as :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`. Note that it is up to you to insure
short-range pair styles, such as :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`. Note that it is up to you to ensure
the tabulated values for each pair of atom types has the correct
functional form to be compatible with the matching long-range solver.

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@ -38,7 +38,7 @@ pairwise forces are not otherwise needed. Examples are the :doc:`fix bond/creat
:doc:`compute voronoi/atom <compute_voronoi_atom>` commands.
Note that the :doc:`comm_modify cutoff <comm_modify>` command can be
used to insure communication of ghost atoms even when a pair style is
used to ensure communication of ghost atoms even when a pair style is
not defined, but it will not trigger neighbor list generation.
The optional *nocoeff* flag allows to read data files with a PairCoeff

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@ -133,7 +133,7 @@ each processor's subdomain, as described above. The mapping of
processors to the grid is determined by the *map* keyword setting.
The *twolevel* style can be used on machines with multicore nodes to
minimize off-node communication. It insures that contiguous
minimize off-node communication. It ensures that contiguous
subsections of the 3d grid are assigned to all the cores of a node.
For example if *Nc* is 4, then 2x2x1 or 2x1x2 or 1x2x2 subsections of
the 3d grid will correspond to the cores of each node. This affects
@ -289,7 +289,7 @@ processors, it could create a 4x2x10 grid, but it will not create a
If you use the :doc:`partition <partition>` command to invoke
different "processors" commands on different partitions, and you also
use the *part* keyword, then you must insure that both the sending and
use the *part* keyword, then you must ensure that both the sending and
receiving partitions invoke the "processors" command that connects the
2 partitions via the *part* keyword. LAMMPS cannot easily check for
this, but your simulation will likely hang in its setup phase if this
@ -306,7 +306,7 @@ machine or when the processor ranks were reordered by use of the
:doc:`-reorder command-line switch <Run_options>` or due to use of
MPI-specific launch options such as a config file.
If you have multiple partitions you should insure that each one writes
If you have multiple partitions you should ensure that each one writes
to a different file, e.g. using a :doc:`world-style variable <variable>`
for the filename. The file has a self-explanatory header, followed by
one-line per processor in this format:

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@ -359,7 +359,7 @@ library.
Third, if your Python code calls back to LAMMPS (discussed in the
next section) and causes LAMMPS to perform an MPI operation requires
global communication (e.g. via MPI_Allreduce), such as computing the
global temperature of the system, then you must insure all your Python
global temperature of the system, then you must ensure all your Python
functions (running independently on different processors) call back to
LAMMPS. Otherwise the code may hang.

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@ -149,9 +149,9 @@ is required representing the equivalent offset for molecule IDs.
If *merge* is specified, the data file atoms
are added to the current system without changing their IDs. They are
assumed to merge (without duplication) with the currently defined
atoms. It is up to you to insure there are no multiply defined atom
atoms. It is up to you to ensure there are no multiply defined atom
IDs, as LAMMPS only performs an incomplete check that this is the case
by insuring the resulting max atom-ID >= the number of atoms. For
by ensuring the resulting max atom-ID >= the number of atoms. For
molecule IDs, there is no check done at all.
The *offset* and *shift* keywords can only be used if the *add*
@ -180,7 +180,7 @@ The *shift* keyword can be used to specify an (Sx, Sy, Sz)
displacement applied to the coordinates of each atom. Sz must be 0.0
for a 2d simulation. This is a mechanism for adding structured
collections of atoms at different locations within the simulation box,
to build up a complex geometry. It is up to you to insure atoms do
to build up a complex geometry. It is up to you to ensure atoms do
not end up overlapping unphysically which would lead to bad dynamics.
Note that the :doc:`displace_atoms <displace_atoms>` command can be used
to move a subset of atoms after they have been read from a data file.

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@ -233,7 +233,7 @@ labels for fields *id* and *type*\ .
For dump files in *xyz* format, only the *x*, *y*, and *z* fields are
supported. The dump file does not store atom IDs, so these are
assigned consecutively to the atoms as they appear in the dump file,
starting from 1. Thus you should insure that order of atoms is
starting from 1. Thus you should ensure that order of atoms is
consistent from snapshot to snapshot in the XYZ dump file. See
the :doc:`dump_modify sort <dump_modify>` command if the XYZ dump file
was written by LAMMPS.
@ -243,7 +243,7 @@ For dump files in *molfile* format, the *x*, *y*, *z*, *vx*, *vy*, and
velocities, or their respective plugins may not support reading of
velocities. The molfile dump files do not store atom IDs, so these
are assigned consecutively to the atoms as they appear in the dump
file, starting from 1. Thus you should insure that order of atoms are
file, starting from 1. Thus you should ensure that order of atoms are
consistent from snapshot to snapshot in the molfile dump file.
See the :doc:`dump_modify sort <dump_modify>` command if the dump file
was written by LAMMPS.

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@ -188,7 +188,7 @@ involve pair interactions, such as use compute msd to calculated
displacements over time, you do not need to define a :doc:`pair style
<pair_style>`, which may also mean neighbor lists will not need to be
calculated which saves time. The :doc:`comm_modify cutoff
<comm_modify>` command can also be used to insure ghost atoms are
<comm_modify>` command can also be used to ensure ghost atoms are
acquired from far enough away for operations like bond and angle
evaluations, if no pair style is being used.
@ -203,7 +203,7 @@ If time-averaging fixes like :doc:`fix ave/time <fix_ave_time>` are
used, they are invoked on timesteps that are a function of their
*Nevery*, *Nrepeat*, and *Nfreq* settings. As an example, see the
:doc:`fix ave/time <fix_ave_time>` page for details. You must
insure those settings are consistent with the snapshot timestamps that
ensure those settings are consistent with the snapshot timestamps that
are read from the dump file(s). If an averaging fix is not invoked on
a timestep it expects to be, LAMMPS will flag an error.

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@ -104,7 +104,7 @@ must be done.
.. note::
If your input script changes the system between 2 runs, then the
initial setup must be performed to insure the change is recognized by
initial setup must be performed to ensure the change is recognized by
all parts of the code that are affected. Examples are adding a
:doc:`fix <fix>` or :doc:`dump <dump>` or :doc:`compute <compute>`, changing
a :doc:`neighbor <neigh_modify>` list parameter, or writing restart file

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@ -203,7 +203,7 @@ operates on pair style computations, it is mutually exclusive with
either the *pair* or the *inner*\ /\ *middle*\ /\ *outer* keywords.
When using rRESPA (or for any MD simulation) care must be taken to
choose a timestep size(s) that insures the Hamiltonian for the chosen
choose a timestep size(s) that ensures the Hamiltonian for the chosen
ensemble is conserved. For the constant NVE ensemble, total energy
must be conserved. Unfortunately, it is difficult to know *a priori*
how well energy will be conserved, and a fairly long test simulation

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@ -254,7 +254,7 @@ fraction of the selected atoms. The actual number of atoms changed
will be exactly the requested number. For *type/ratio* the specified
fraction (0 <= *fraction* <= 1) determines the number. For
*type/subset*, the specified *Nsubset* is the number. An iterative
algorithm is used which insures the correct number of atoms are
algorithm is used which ensures the correct number of atoms are
selected, in a perfectly random fashion. Which atoms are selected
will change with the number of processors used. These keywords do not
allow use of an atom-style variable.

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@ -141,7 +141,7 @@ You can always include a divide by the number of atoms in the variable
formula if this is not the case.
The *flush* keyword invokes a flush operation after thermodynamic info
is written to the screen and log file. This insures the output is
is written to the screen and log file. This ensures the output is
updated and not buffered (by the application) even if LAMMPS halts
before the simulation completes. Please note that this does not affect
buffering by the OS or devices, so you may still lose data in case the

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@ -334,7 +334,7 @@ the number of re-builds that LAMMPS considered potentially
the :doc:`neigh_modify <neigh_modify>` command), then dangerous
reneighborings are those that were triggered on the first timestep
atom movement was checked for. If this count is non-zero you may wish
to reduce the delay factor to insure no force interactions are missed
to reduce the delay factor to ensure no force interactions are missed
by atoms moving beyond the neighbor skin distance before a rebuild
takes place.

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@ -1420,7 +1420,7 @@ follows. Also note that the 0-timestep run must actually use and
invoke the compute in question (e.g. via :doc:`thermo <thermo_style>` or
:doc:`dump <dump>` output) in order for it to enable the compute to be
used in a variable after the run. Thus if you are trying to print a
variable that uses a compute you have defined, you can insure it is
variable that uses a compute you have defined, you can ensure it is
invoked on the last timestep of the preceding run by including it in
thermodynamic output.
@ -1460,7 +1460,7 @@ alter the state of the system between runs, causing a variable to
evaluate incorrectly.
The solution to this issue is the same as for case (2) above, namely
perform a 0-timestep run before the variable is evaluated to insure
perform a 0-timestep run before the variable is evaluated to ensure
the system is up-to-date. For example, this sequence of commands
would print a potential energy that reflected the changed pairwise
coefficient:

View File

@ -246,7 +246,7 @@ freedom (DOFs) is known. Thus it is not possible to compute the
target temperature correctly. Second, the assigned velocities may be
partially canceled when constraints are first enforced, leading to a
different temperature than desired. A workaround for this is to
perform a :doc:`run 0 <run>` command, which insures all DOFs are
perform a :doc:`run 0 <run>` command, which ensures all DOFs are
accounted for properly, and then rescale the temperature to the
desired value before performing a simulation. For example:

View File

@ -119,7 +119,7 @@ void Irregular::pattern(int n, int *proclist)
for (int i = 0; i < nrecv; i++)
MPI_Irecv(&recvcount[i],1,MPI_INT,MPI_ANY_SOURCE,0,comm,&request[i]);
// barrier to insure receives are posted
// barrier to ensure receives are posted
MPI_Barrier(comm);
@ -128,7 +128,7 @@ void Irregular::pattern(int n, int *proclist)
for (int i = 0; i < nsend; i++)
MPI_Send(&sendcount[i],1,MPI_INT,sendproc[i],0,comm);
// insure all MPI_ANY_SOURCE messages are received
// ensure all MPI_ANY_SOURCE messages are received
// set recvproc
if (nrecv) MPI_Waitall(nrecv,request,status);
@ -270,7 +270,7 @@ void Irregular::exchange_same(char *sendbuf, char *recvbuf)
char *buf = (char *) memory->smalloc(nsendmax,"buf");
// barrier to insure receives are posted
// barrier to ensure receives are posted
MPI_Barrier(comm);
@ -325,7 +325,7 @@ void Irregular::exchange_varying(char *sendbuf, char *recvbuf)
char *buf = (char *) memory->smalloc(nsendmax,"buf");
// barrier to insure receives are posted
// barrier to ensure receives are posted
MPI_Barrier(comm);

View File

@ -169,7 +169,7 @@ struct _liblammpsplugin {
void (*scatter_subset)(void *, const char *, int, int, int, int *, void *);
/* lammps_create_atoms() takes tagint and imageint as args
* the ifdef insures they are compatible with rest of LAMMPS
* the ifdef ensures they are compatible with rest of LAMMPS
* caller must match to how LAMMPS library is built */
#ifndef LAMMPS_BIGBIG

View File

@ -79,7 +79,7 @@ Copy the LAMMPS executable (lmp_mpi or lmp) into this dir as lmp_mpi.
Copy the LATTE executable LATTE_DOUBLE into this dir.
The run commands below assume you have done this.
(5) Insure LD_LIBRARY_PATH includes the dir where MDI was built in (1)
(5) Ensure LD_LIBRARY_PATH includes the dir where MDI was built in (1)
with its libmdi.so file, e.g. mdi/build/MDI_Library. This is needed
so when LATTE_DOUBLE runs as an executable it will able to find
libmdi.so.

View File

@ -34,7 +34,7 @@ fix ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 &
molecule object molecule.vshape
fix 3 all rigid/small molecule mol object
# insure region size + molecule size does not overlap wall
# ensure region size + molecule size does not overlap wall
region slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
fix ins all pour 500 0 4767548 vol 0.8 10 &

View File

@ -44,7 +44,7 @@ fix 3 all rigid/small molecule mol object
0 rigid bodies with 0 atoms
2.23607 = max distance from body owner to body atom
# insure region size + molecule size does not overlap wall
# ensure region size + molecule size does not overlap wall
region slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
fix ins all pour 500 0 4767548 vol 0.8 10 region slab mol object rigid 3

View File

@ -44,7 +44,7 @@ fix 3 all rigid/small molecule mol object
0 rigid bodies with 0 atoms
2.23607 = max distance from body owner to body atom
# insure region size + molecule size does not overlap wall
# ensure region size + molecule size does not overlap wall
region slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
fix ins all pour 500 0 4767548 vol 0.8 10 region slab mol object rigid 3

View File

@ -40,7 +40,7 @@ Makefile.lammps is created by the make command, by copying one of the
Makefile.lammps.* files. See the EXTRAMAKE setting at the top of the
Makefile.* files.
IMPORTANT: You must examine the final Makefile.lammps to insure it is
IMPORTANT: You must examine the final Makefile.lammps to ensure it is
correct for your system, else the LAMMPS build will likely fail.
Makefile.lammps has settings for 3 variables:

View File

@ -43,7 +43,7 @@ Makefile.lammps is created by the make command, by copying one of the
Makefile.lammps.* files. See the EXTRAMAKE setting at the top of the
Makefile.* files.
IMPORTANT: You must examine the final Makefile.lammps to insure it is
IMPORTANT: You must examine the final Makefile.lammps to ensure it is
correct for your system, else the LAMMPS build will likely fail.
Makefile.lammps has settings for 3 variables:

View File

@ -128,12 +128,12 @@ Makefile.lammps is created by the make command, by copying one of the
Makefile.lammps.* files. See the EXTRAMAKE setting at the top of the
Makefile.* files.
IMPORTANT: You should examine the final Makefile.lammps to insure it is
IMPORTANT: You should examine the final Makefile.lammps to ensure it is
correct for your system, else the LAMMPS build can fail.
IMPORTANT: If you re-build the library, e.g. for a different precision
(see below), you should do a "make clean" first, e.g. make -f
Makefile.linux clean, to insure all previous derived files are removed
Makefile.linux clean, to ensure all previous derived files are removed
before the new build is done.
NOTE: The system-specific setting LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG,

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@ -1204,7 +1204,7 @@ class lammps(object):
# dtype = 0 for integer values, 1 for double values
# count = number of per-atom valus, 1 for type or charge, 3 for x or f
# returned data is a 1d vector - doc how it is ordered?
# NOTE: need to insure are converting to/from correct Python type
# NOTE: need to ensure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes
def gather_atoms(self,name,dtype,count):
@ -1258,7 +1258,7 @@ class lammps(object):
# type = 0 for integer values, 1 for double values
# count = number of per-atom valus, 1 for type or charge, 3 for x or f
# assume data is of correct type and length, as created by gather_atoms()
# NOTE: need to insure are converting to/from correct Python type
# NOTE: need to ensure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes
def scatter_atoms(self,name,dtype,count,data):
@ -1305,7 +1305,7 @@ class lammps(object):
# type = 0 for integer values, 1 for double values
# count = number of per-atom valus, 1 for type or charge, 3 for x or f
# returned data is a 1d vector - doc how it is ordered?
# NOTE: need to insure are converting to/from correct Python type
# NOTE: need to ensure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes
def gather(self,name,dtype,count):
if name: name = name.encode()
@ -1354,7 +1354,7 @@ class lammps(object):
# type = 0 for integer values, 1 for double values
# count = number of per-atom valus, 1 for type or charge, 3 for x or f
# assume data is of correct type and length, as created by gather_atoms()
# NOTE: need to insure are converting to/from correct Python type
# NOTE: need to ensure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes
def scatter(self,name,dtype,count,data):
@ -1414,7 +1414,7 @@ class lammps(object):
# type = type of each atom (1 to Ntypes) (required)
# x = coords of each atom as (N,3) array (required)
# v = velocity of each atom as (N,3) array (optional, can be None)
# NOTE: how could we insure are passing correct type to LAMMPS
# NOTE: how could we ensure are passing correct type to LAMMPS
# e.g. for Python list or NumPy, etc
# ditto for gather_atoms() above

View File

@ -153,7 +153,7 @@ void DumpAtomADIOS::write()
internal->varAtoms.SetShape({nAtomsGlobal, nColumns});
internal->varAtoms.SetSelection({{startRow, 0}, {nAtomsLocal, nColumns}});
// insure buf is sized for packing
// ensure buf is sized for packing
// adios does not limit per-process data size so nme*size_one is not
// constrained to int
// if sorting on IDs also request ID list from pack()

View File

@ -165,7 +165,7 @@ void DumpCustomADIOS::write()
internal->varAtoms.SetShape({nAtomsGlobal, nColumns});
internal->varAtoms.SetSelection({{startRow, 0}, {nAtomsLocal, nColumns}});
// insure filewriter proc can receive everyone's info
// ensure filewriter proc can receive everyone's info
// limit nmax*size_one to int since used as arg in MPI_Rsend() below
// pack my data into buf
// if sorting on IDs also request ID list from pack()

View File

@ -101,7 +101,7 @@ void AtomVecAmoeba::grow_pointers()
void AtomVecAmoeba::pack_restart_pre(int ilocal)
{
// insure negative vectors are needed length
// ensure negative vectors are needed length
if (bond_per_atom < atom->bond_per_atom) {
delete[] bond_negative;

View File

@ -56,7 +56,7 @@ ComputePressureBocs::ComputePressureBocs(LAMMPS *lmp, int narg, char **arg) :
phi_coeff = nullptr;
// store temperature ID used by pressure computation
// insure it is valid for temperature computation
// ensure it is valid for temperature computation
if (strcmp(arg[3],"NULL") == 0) id_temp = nullptr;
else {

View File

@ -85,7 +85,7 @@ ComputeBodyLocal::~ComputeBodyLocal()
void ComputeBodyLocal::init()
{
// if non-body particles in group insure only indices 1,2,3 are used
// if non-body particles in group ensure only indices 1,2,3 are used
int nonbody = 0;
int *mask = atom->mask;

View File

@ -148,7 +148,7 @@ void AtomVecBPMSphere::create_atom_post(int ilocal)
void AtomVecBPMSphere::pack_restart_pre(int ilocal)
{
// insure bond_negative vector is needed length
// ensure bond_negative vector is needed length
if (bond_per_atom < atom->bond_per_atom) {
delete[] bond_negative;

View File

@ -368,7 +368,7 @@ void PairLJSPICACoulLong::init_style()
cut_coulsq = cut_coul * cut_coul;
// insure use of KSpace long-range solver, set g_ewald
// ensure use of KSpace long-range solver, set g_ewald
if (force->kspace == nullptr) error->all(FLERR, "Pair style requires a KSpace style");
g_ewald = force->kspace->g_ewald;

View File

@ -688,7 +688,7 @@ void PairLJClass2CoulLong::init_style()
else
cut_respa = nullptr;
// insure use of KSpace long-range solver, set g_ewald
// ensure use of KSpace long-range solver, set g_ewald
if (force->kspace == nullptr) error->all(FLERR, "Pair style requires a KSpace style");
g_ewald = force->kspace->g_ewald;

View File

@ -38,7 +38,7 @@ void FixWallColloid::init()
if (!atom->sphere_flag)
error->all(FLERR,"Fix wall/colloid requires atom style sphere");
// insure all particles in group are extended particles
// ensure all particles in group are extended particles
double *radius = atom->radius;
int *mask = atom->mask;

View File

@ -449,7 +449,7 @@ void PairBrownian::init_style()
neighbor->add_request(this);
// insure all particles are finite-size
// ensure all particles are finite-size
// for pair hybrid, should limit test to types using the pair style
double *radius = atom->radius;

View File

@ -325,7 +325,7 @@ void PairBrownianPoly::init_style()
if (!atom->sphere_flag)
error->all(FLERR,"Pair brownian/poly requires atom style sphere");
// insure all particles are finite-size
// ensure all particles are finite-size
// for pair hybrid, should limit test to types using the pair style
double *radius = atom->radius;

View File

@ -1133,7 +1133,7 @@ void PairLubricateUPoly::init_style()
if (!atom->sphere_flag)
error->all(FLERR,"Pair lubricate/poly requires atom style sphere");
// insure all particles are finite-size
// ensure all particles are finite-size
// for pair hybrid, should limit test to types using the pair style
double *radius = atom->radius;

View File

@ -123,7 +123,7 @@ void ComputeTempCS::setup()
if (firstflag) {
firstflag = 0;
// insure # of core atoms = # of shell atoms
// ensure # of core atoms = # of shell atoms
int ncores = group->count(cgroup);
nshells = group->count(sgroup);
@ -133,7 +133,7 @@ void ComputeTempCS::setup()
// for each C/S pair:
// set partner IDs of both atoms if this atom stores bond between them
// will set partner IDs for ghost atoms if needed by another proc
// nall loop insures all ghost atom partner IDs are set before reverse comm
// nall loop ensures all ghost atom partner IDs are set before reverse comm
int *num_bond = atom->num_bond;
tagint **bond_atom = atom->bond_atom;

View File

@ -200,7 +200,7 @@ void PairCoulLongDielectric::init_style()
cut_coulsq = cut_coul * cut_coul;
// insure use of KSpace long-range solver, set g_ewald
// ensure use of KSpace long-range solver, set g_ewald
if (force->kspace == nullptr) error->all(FLERR, "Pair style requires a KSpace style");
g_ewald = force->kspace->g_ewald;

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