Merge pull request #3607 from akohlmey/no-inn-sewer-ants
Getting out of the insurance business :-)
This commit is contained in:
@ -63,7 +63,7 @@ In the src directory, there is one top-level Makefile and several
|
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low-level machine-specific files named Makefile.xxx where xxx = the
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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
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||||
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 "
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an exception to this is if a short cutoff is used initially,
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but a longer cutoff will be used for a subsequent run (in the same
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||||
input script), in this case the "maximum cutoff" command should be
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used to insure enough memory is allocated for the later run
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used to ensure enough memory is allocated for the later run
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note that a restart file contains nonbond cutoffs (so it is not necessary
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to use a "nonbond style" command before "read restart"), but LAMMPS
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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
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processors.
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This can be checked by callers who have the option to change the
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global grid size to insure more efficient nearest-neighbor-only
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global grid size to ensure more efficient nearest-neighbor-only
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communication if they wish. In this case, they instantiate a grid of
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a given size (resolution), then invoke *setup_comm()* followed by
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*ghost_adjacent()*. If the ghost cells are not adjacent, they destroy
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@ -753,7 +753,7 @@ their input script syntax, as described on the :doc:`Howto_grid
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* f_ID:gname:dname
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* f_ID:gname:dname[I]
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Each grid a command instantiates has a unique *gname*, defined by the
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Each grid command instantiates has a unique *gname*, defined by the
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command. Likewise each grid cell data structure (scalar or vector)
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associated with a grid has a unique *dname*, also defined by the
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command.
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@ -784,8 +784,7 @@ The *get_grid_by_index()* method is called after the
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*get_grid_by_name()* method, using the grid index it returned as its
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argument. This method will return a pointer to the Grid2d or Grid3d
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class. The caller can use this to query grid attributes, such as the
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global size of the grid. The :doc:`dump grid <dump>` to insure each
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its grid reference arguments are for grids of the same size.
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global size of the grid, to ensure it is of the expected size.
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The *get_griddata_by_name()* method takes a grid index *igrid* and a
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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
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suspect this is happening, it is a good idea to print out
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thermodynamic info frequently (e.g. every timestep) via the
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:doc:`thermo <thermo>` so you can monitor what is happening.
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Visualizing the atom movement is also a good idea to insure your model
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Visualizing the atom movement is also a good idea to ensure your model
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is behaving as you expect.
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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
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after a read_data, read_restart, or create_box command.
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*Next command must list all universe and uloop variables*
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This is to insure they stay in sync.
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This is to ensure they stay in sync.
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*No Kspace style defined for compute group/group*
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Self-explanatory.
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@ -7231,7 +7231,7 @@ keyword to allow for additional bonds to be formed
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*Replacing a fix, but new style != old style*
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A fix ID can be used a second time, but only if the style matches the
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previous fix. In this case it is assumed you with to reset a fix's
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previous fix. In this case it is assumed you want to reset a fix's
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parameters. This error may mean you are mistakenly re-using a fix ID
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when you do not intend to.
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@ -7337,7 +7337,7 @@ keyword to allow for additional bonds to be formed
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*Rigid body atoms %d %d missing on proc %d at step %ld*
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This means that an atom cannot find the atom that owns the rigid body
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it is part of, or vice versa. The solution is to use the communicate
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cutoff command to insure ghost atoms are acquired from far enough away
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cutoff command to ensure ghost atoms are acquired from far enough away
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to encompass the max distance printed when the fix rigid/small command
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was invoked.
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@ -351,7 +351,7 @@ This will most likely cause errors in kinetic fluctuations.
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Self-explanatory.
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*Kspace_modify slab param < 2.0 may cause unphysical behavior*
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The kspace_modify slab parameter should be larger to insure periodic
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The kspace_modify slab parameter should be larger to ensure periodic
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grids padded with empty space do not overlap.
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*Less insertions than requested*
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@ -491,7 +491,7 @@ This will most likely cause errors in kinetic fluctuations.
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*Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies*
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This is because excluding specific pair interactions also excludes
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them from long-range interactions which may not be the desired effect.
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The special_bonds command handles this consistently by insuring
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The special_bonds command handles this consistently by ensuring
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excluded (or weighted) 1-2, 1-3, 1-4 interactions are treated
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consistently by both the short-range pair style and the long-range
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solver. This is not done for exclusions of charged atom pairs via the
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@ -545,7 +545,7 @@ This will most likely cause errors in kinetic fluctuations.
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If there are other fixes that act immediately after the initial stage
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of time integration within a timestep (i.e. after atoms move), then
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the command that sets up the dynamic group should appear after those
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fixes. This will insure that dynamic group assignments are made
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fixes. This will ensure that dynamic group assignments are made
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after all atoms have moved.
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*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
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z-boundaries of the box - e.g. 0.0.
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Use the :doc:`fix enforce2d <fix_enforce2d>` command as the last
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defined fix to insure that the z-components of velocities and forces
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defined fix to ensure that the z-components of velocities and forces
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are zeroed out every timestep. The reason to make it the last fix is
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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
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the core/shell pair, which is an imaginary degree of freedom, from the
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real physical system. To do that, the :doc:`compute temp/cs <compute_temp_cs>` command can be used, in conjunction with
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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
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of the core/shell pairs to calculate a temperature, and insures that
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of the core/shell pairs to calculate a temperature, and ensures that
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velocity is what is rescaled for thermostatting purposes. This
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compute also works for a system with both core/shell pairs and
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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
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finite-size particles also compute the correct interaction with point
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particles as well, e.g. the interaction between a point particle and a
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finite-size particle or between two point particles. If necessary,
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:doc:`pair_style hybrid <pair_hybrid>` can be used to insure the correct
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:doc:`pair_style hybrid <pair_hybrid>` can be used to ensure the correct
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interactions are computed for the appropriate style of interactions.
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Likewise, using groups to partition particles (ellipsoids versus
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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.
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Also note that once you import the mpi4py module, mpi4py initializes MPI
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for you, and you can use MPI calls directly in your Python script, as
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described in the mpi4py documentation. The last line of your Python
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script should be ``MPI.finalize()``, to insure MPI is shut down
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script should be ``MPI.finalize()``, to ensure MPI is shut down
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correctly.
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@ -362,10 +362,10 @@ Reorder the processors in the MPI communicator used to instantiate
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LAMMPS, in one of several ways. The original MPI communicator ranks
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all P processors from 0 to P-1. The mapping of these ranks to
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physical processors is done by MPI before LAMMPS begins. It may be
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useful in some cases to alter the rank order. E.g. to insure that
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useful in some cases to alter the rank order. E.g. to ensure that
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cores within each node are ranked in a desired order. Or when using
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the :doc:`run_style verlet/split <run_style>` command with 2 partitions
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to insure that a specific Kspace processor (in the second partition) is
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to ensure that a specific Kspace processor (in the second partition) is
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matched up with a specific set of processors in the first partition.
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See the :doc:`General tips <Speed_tips>` page for more details.
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@ -398,7 +398,7 @@ so that the processors in each partition will be
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0 1 2 4 5 6 8 9 10
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3 7 11
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See the "processors" command for how to insure processors from each
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See the "processors" command for how to ensure processors from each
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partition could then be grouped optimally for quad-core nodes.
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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
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list rebuilding (see the :doc:`neigh_modify <neigh_modify>` command),
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then dangerous reneighborings are those that were triggered on the
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first timestep atom movement was checked for. If this count is
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non-zero you may wish to reduce the delay factor to insure no force
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non-zero you may wish to reduce the delay factor to ensure no force
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interactions are missed by atoms moving beyond the neighbor skin
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distance before a rebuild takes place.
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@ -282,7 +282,7 @@ showing the use of the *template* atom style versus *molecular*.
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.. note::
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When using the *template* style with a :doc:`molecule template
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<molecule>` that contains multiple molecules, you should insure the
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<molecule>` that contains multiple molecules, you should ensure the
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atom types, bond types, angle_types, etc in all the molecules are
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consistent. E.g. if one molecule represents H2O and another CO2,
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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
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:doc:`pairwise potential <pair_style>` needs to calculate with ghost
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atoms beyond the normal pairwise cutoff for some computation it
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performs (e.g. locate neighbors of ghost atoms in a manybody pair
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potential). Setting the ghost cutoff appropriately can insure it will
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potential). Setting the ghost cutoff appropriately can ensure it will
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find the needed atoms.
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.. note::
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@ -75,7 +75,7 @@ neighbor atom in each requested ADF.
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If you request any outer cutoff *Router* > force cutoff, or if no
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pair style is defined, e.g. the :doc:`rerun <rerun>` command is being used to
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post-process a dump file of snapshots you must insure ghost atom information
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post-process a dump file of snapshots you must ensure ghost atom information
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out to the largest value of *Router* + *skin* is communicated, via the
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:doc:`comm_modify cutoff <comm_modify>` command, else the ADF computation
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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
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performed on mono-component systems.
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The CNA calculation can be sensitive to the specified cutoff value.
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You should insure the appropriate nearest neighbors of an atom are
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You should ensure the appropriate nearest neighbors of an atom are
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found within the cutoff distance for the presumed crystal structure
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(e.g., 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest
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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
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<fix_pour>`, :doc:`fix deposit <fix_deposit>`, and :doc:`fix gcmc
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<fix_gcmc>` commands) or expect atoms or molecules to be lost
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(e.g. due to exiting the simulation box or via :doc:`fix evaporate
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<fix_evaporate>`), then this option should be used to insure the
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<fix_evaporate>`), then this option should be used to ensure the
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temperature is correctly normalized.
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.. note::
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@ -74,7 +74,7 @@ compute command was first invoked.
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This compute stores the original position (of the
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center-of-mass) of each chunk. When a displacement is calculated on a
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later timestep, it is assumed that the same atoms are assigned to the
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||||
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
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||||
:doc:`compute chunk/atom <compute_chunk_atom>` command. Note that if
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this is not the case, the MSD calculation does not have a sensible
|
||||
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@ -82,7 +82,7 @@ distance specified.
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||||
every timestep this command is invoked (or every reneighboring
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||||
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*
|
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cutoff, you must ensure ghost atom information out to *Rcut* + *skin*
|
||||
is communicated, via the :doc:`comm_modify cutoff <comm_modify>`
|
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command, else the RDF computation cannot be performed, and LAMMPS will
|
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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
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|
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For the *box* style, the create_atoms command fills the entire
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||||
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.
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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.
|
||||
|
||||
@ -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.
|
||||
|
||||
|
||||
@ -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*\ .
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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.
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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.
|
||||
|
||||
----------
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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:
|
||||
|
||||
@ -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:
|
||||
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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).
|
||||
|
||||
@ -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::
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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).
|
||||
|
||||
|
||||
@ -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:
|
||||
|
||||
|
||||
@ -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.
|
||||
|
||||
|
||||
@ -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.
|
||||
|
||||
----------
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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.
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
|
||||
@ -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
|
||||
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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.
|
||||
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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::
|
||||
|
||||
@ -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.
|
||||
|
||||
|
||||
@ -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.
|
||||
|
||||
@ -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_{*,*}`
|
||||
|
||||
@ -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.
|
||||
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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:
|
||||
|
||||
@ -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.
|
||||
|
||||
|
||||
@ -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.
|
||||
|
||||
@ -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.
|
||||
|
||||
@ -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.
|
||||
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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.
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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.
|
||||
|
||||
|
||||
@ -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:
|
||||
|
||||
@ -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:
|
||||
|
||||
|
||||
@ -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);
|
||||
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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.
|
||||
|
||||
@ -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 &
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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:
|
||||
|
||||
@ -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:
|
||||
|
||||
@ -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,
|
||||
|
||||
@ -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
|
||||
|
||||
|
||||
@ -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()
|
||||
|
||||
@ -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()
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -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 {
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -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;
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user