Merge pull request #857 from lammps/resetids

"region"_region.html,

"replicate"_replicate.html,

"rerun"_rerun.html,

"reset_ids"_reset_ids.html,

"reset_timestep"_reset_timestep.html,

"restart"_restart.html,

"run"_run.html,

   region

   replicate

   rerun

   reset_ids

   reset_timestep

   restart

   run

ID, group-ID are documented in "compute"_compute.html command :ulb,l

displace/atom = style name of this compute command :l

zero or more keyword/arg pairs may be appended :l

keyword = {refresh} :l

  {refresh} arg = per-atom variable ID :pre

keyword = {refresh} :

  {replace} arg = name of per-atom variable :pre

:ule

[Examples:]

have hopped since the last snapshot.  This can be accomplished with

something like the following commands:

write_dump      all custom tmp.dump id type x y z    # see comment below :pre

variable        Dhop equal 0.6

variable        check atom "c_dsp[4] > v_Dhop"

compute         dsp all displace/atom refresh check

dump            1 all custom 20 tmp.dump id type x y z

dump_modify     1 append yes thresh c_dsp[4] > ${Dhop} refresh c_dsp :pre

The "dump_modify thresh"_dump_modify.html command will cause only

atoms that have displaced more than 0.6 Angstroms to be output on a

given snapshot (assuming metal units).  The dump_modify {refresh}

option triggers a call to this compute at the end of every dump.

The argument for compute displace/atom refresh is the ID of an

"atom-style variable"_variable.html which calculates a Boolean value

(0 or 1) based on the same criterion used by dump_modify thresh.  What

this compute will then do is evaluate the atom-style variable and for

each atom that returns 1 (true), it will update the original

(reference) coordinates of the atom, which are stored by this compute.

dump            1 all custom 100 tmp.dump id type x y z

dump_modify     1 append yes thresh c_dsp[4] > ${Dhop} &

                refresh c_dsp delay 100 :pre

The "dump_modify thresh"_dump_modify.html command will only ouptut

atoms that have displaced more than 0.6 Angstroms on each snapshot

(assuming metal units).  The dump_modify {refresh} option triggers a

call to this compute at the end of every dump.

The {refresh} argument for this compute is the ID of an "atom-style

variable"_variable.html which calculates a Boolean value (0 or 1)

based on the same criterion used by dump_modify thresh.  This compute

evaluates the atom-style variable.  For each atom that returns 1

(true), the original (reference) coordinates of the atom (stored by

this compute) are updated.

The effect of these commands is that a particular atom will only be

output in the dump file on shapshots following a diffusive hop.  It

will not be output again until it performs another hop.

Note that the first snapshot (geneated by the first run after the dump

and this compute are defined), no atoms will be typically be output.

That is because the initial displacement for all atoms is 0.0.  If an

initial dump snapshot is desired, containing the initial reference

position of all atoms, a command like this can be used before the

first simulation is performed

write_dump      all custom tmp.dump.initial id type x y z :pre

output in the dump file on the snapshot after it makes a diffusive

hop.  It will not be output again until it makes another hop.

Note that in the first snapshot of a subsequent run, no atoms will be

typically be output.  That is because the initial displacement for all

atoms is 0.0.  If an initial dump snapshot is desired, containing the

initial reference positions of all atoms, one way to do this is

illustrated above.  An initial write_dump command can be used before

the first run.  It will contain the positions of all the atoms,

Options in the "dump_modify"_dump_modify.html command above will

append new output to that same file and delay the output until a later

timestep.  The {delay} setting avoids a second time = 0 snapshot which

would be empty.

:line

Atom IDs are assigned to created atoms in the following way.  The

collection of created atoms are assigned consecutive IDs that start

immediately following the largest atom ID existing before the

create_atoms command was invoked.  When a simulation is performed on

different numbers of processors, there is no guarantee a particular

created atom will be assigned the same ID.  If molecules are being

created, molecule IDs are assigned to created molecules in a similar

fashion.

create_atoms command was invoked.  This is done by the processor's

communicating the number of atoms they each own, the first processor

numbering its atoms from 1 to N1, the second processor from N1+1 to

N2, etc.  Where N1 = number of atoms owned by the first processor, N2

= number owned by the second processor, etc.  Thus when the same

simulation is performed on different numbers of processors, there is

no guarantee a particular created atom will be assigned the same ID in

both simulations.  If molecules are being created, molecule IDs are

assigned to created molecules in a similar fashion.

Aside from their ID, atom type, and xyz position, other properties of

created atoms are set to default values, depending on which quantities

number of atoms in the system.  Note that this is not done for

molecular systems (see the "atom_style"_atom_style.html command),

regardless of the {compress} setting, since it would foul up the bond

connectivity that has already been assigned.

connectivity that has already been assigned.  However, the

"reset_ids"_reset_ids.html command can be used after this command to

accomplish the same thing.

Note that the re-assignement of IDs is not really a compression, where

gaps in atom IDs are removed by decrementing atom IDs that are larger.

Instead the IDs for all atoms are erased, and new IDs are assigned so

that the atoms owned by individual processors have consecutive IDs, as

the "create_atoms"_create_atoms.html command explains.

A molecular system with fixed bonds, angles, dihedrals, or improper

interactions, is one where the topology of the interactions is

[Related commands:]

"create_atoms"_create_atoms.html

"create_atoms"_create_atoms.html, "reset_ids"_reset_ids.html

[Default:]