Syntax
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one or more keyword/value pairs may be appended
keyword = id or map or first or sort
Examples
Description
Modify certain attributes of atoms defined and stored within LAMMPS,in addition to what is specified by the atom_stylecommand. The id and map keywords must be specified before asimulation box is defined; other keywords can be specified any time.
The id keyword determines whether non-zero atom IDs can be assignedto each atom. If the value is yes, which is the default, IDs areassigned, whether you use the create atoms orread_data or read_restartcommands to initialize atoms. If the value is no the IDs for allatoms are assumed to be 0.
If atom IDs are used, they must all be positive integers. They shouldalso be unique, though LAMMPS does not check for this. Typically theyshould also be consecutively numbered (from 1 to Natoms), though thisis not required. Molecular atom styles are thosethat store bond topology information (styles bond, angle, molecular,full). These styles require atom IDs since the IDs are used to encodethe topology. Some other LAMMPS commands also require the use of atomIDs. E.g. some many-body pair styles use them to avoid doublecomputation of the I-J interaction between two atoms.
The only reason not to use atom IDs is if you are running an atomicsimulation so large that IDs cannot be uniquely assigned. For adefault LAMMPS build this limit is 2^31 or about 2 billion atoms.However, even in this case, you can use 64-bit atom IDs, allowing 2^63or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIGswitch. This is described on the Build_settingsdoc page. If atom IDs are not used, they must be specified as 0 forall atoms, e.g. in a data or restart file.
The map keyword determines how atoms with specific IDs are foundwhen required. An example are the bond (angle, etc) methods whichneed to find the local index of an atom with a specific global IDwhich is a bond (angle, etc) partner. LAMMPS performs this operationefficiently by creating a “map”, which is either an array or hashtable, as described below.
When the map keyword is not specified in your input script, LAMMPSonly creates a map for atom_styles for molecularsystems which have permanent bonds (angles, etc). No map is createdfor atomic systems, since it is normally not needed. However someLAMMPS commands require a map, even for atomic systems, and willgenerate an error if one does not exist. The map keyword thusallows you to force the creation of a map. The yes value willcreate either an array or hash style map, as explained in the nextparagraph. The array and hash values create an atom-style orhash-style map respectively.
For an array-style map, each processor stores a lookup table oflength N, where N is the largest atom ID in the system. This is afast, simple method for many simulations, but requires too much memoryfor large simulations. For a hash-style map, a hash table iscreated on each processor, which finds an atom ID in constant time(independent of the global number of atom IDs). It can be slightlyslower than the array map, but its memory cost is proportional tothe number of atoms owned by a processor, i.e. N/P when N is the totalnumber of atoms in the system and P is the number of processors.
The first keyword allows a group to be specified whoseatoms will be maintained as the first atoms in each processor’s listof owned atoms. This in only useful when the specified group is asmall fraction of all the atoms, and there are other operations LAMMPSis performing that will be sped-up significantly by being able to loopover the smaller set of atoms. Otherwise the reordering required bythis option will be a net slow-down. The neigh_modify include and comm_modify groupcommands are two examples of commands that require this setting towork efficiently. Several fixes, most notably timeintegration fixes like fix nve, also take advantage ofthis setting if the group they operate on is the group specified bythis command. Note that specifying “all” as the group-ID effectivelyturns off the first option.
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It is OK to use the first keyword with a group that has not yet beendefined, e.g. to use the atom_modify first command at the beginning ofyour input script. LAMMPS does not use the group until a simulationis run.
The sort keyword turns on a spatial sorting or reordering of atomswithin each processor’s sub-domain every Nfreq timesteps. IfNfreq is set to 0, then sorting is turned off. Sorting can improvecache performance and thus speed-up a LAMMPS simulation, as discussedin a paper by (Meloni). Its efficacy depends on the problemsize (atoms/processor), how quickly the system becomes disordered, andvarious other factors. As a general rule, sorting is typically moreeffective at speeding up simulations of liquids as opposed to solids.In tests we have done, the speed-up can range from zero to 3-4x.
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Reordering is performed every Nfreq timesteps during a dynamics runor iterations during a minimization. More precisely, reorderingoccurs at the first reneighboring that occurs after the targettimestep. The reordering is performed locally by each processor,using bins of the specified binsize. If binsize is set to 0.0,then a binsize equal to half the neighbor cutoffdistance (force cutoff plus skin distance) is used, which is areasonable value. After the atoms have been binned, they arereordered so that atoms in the same bin are adjacent to each other inthe processor’s 1d list of atoms.
The goal of this procedure is for atoms to put atoms close to eachother in the processor’s one-dimensional list of atoms that are alsonear to each other spatially. This can improve cache performance whenpairwise interactions and neighbor lists are computed. Note that ifbins are too small, there will be few atoms/bin. Likewise if bins aretoo large, there will be many atoms/bin. In both cases, the goal ofcache locality will be undermined.
Note
Running a simulation with sorting on versus off should notchange the simulation results in a statistical sense. However, adifferent ordering will induce round-off differences, which will leadto diverging trajectories over time when comparing two simulations.Various commands, particularly those which use random numbers(e.g. velocity create, and fix langevin), may generate (statistically identical)results which depend on the order in which atoms are processed. Theorder of atoms in a dump file will also typically changeif sorting is enabled.
Restrictions
The first and sort options cannot be used together. Since sortingis on by default, it will be turned off if the first keyword isused with a group-ID that is not “all”.
Default
By default, id is yes. By default, atomic systems (no bond topologyinfo) do not use a map. For molecular systems (with bond topologyinfo), a map is used. The default map style is array if no atom ID islarger than 1 million, otherwise the default is hash. By default, a“first” group is not defined. By default, sorting is enabled with afrequency of 1000 and a binsize of 0.0, which means the neighborcutoff will be used to set the bin size. If no neighbor cutoff isdefined, sorting will be turned off.
(Meloni) Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).