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fix property/atom command

Accelerator Variants: property/atom/kk

Syntax

fix ID group-ID property/atom name1 name2 ... keyword value ...

  • ID, group-ID are documented in fix command

  • property/atom = style name of this fix command

  • name1,name2,… = mol or q or rmass or i_name or d_name or i2_name or d2_name

    mol = molecule IDs
q = charge
rmass = per-atom mass
temperature = internal temperature of atom
heatflow = internal heat flow of atom
i_name = new integer vector referenced by name
d_name = new floating-point vector referenced by name
i2_name = new integer array referenced by name
   i2_name arg = N = number of columns in the array
d2_name = new floating-point array referenced by name
   d2_name arg = N = number of columns in the array

  • zero of more keyword/value pairs may be appended

  • keyword = ghost

    ghost value = no or yes for whether ghost atom info in communicated

Examples

fix 1 all property/atom mol
fix 1 all property/atom i_myflag1 i_myflag2
fix 1 all property/atom d2_sxyz 3 ghost yes

Description

Create one or more additional per-atom vectors or arrays to store information about atoms and to use during a simulation. The specified group-ID is ignored by this fix.

The atom style used for a simulation defines a set of per-atom properties, as explained on the atom_style and read_data doc pages. The latter command defines these properties for each atom in the system when a data file is read. This fix augments the set of per-atom properties with new custom ones. This can be useful in several scenarios.

If the atom style does not define molecule IDs, per-atom charge, per-atom mass, internal temperature, or internal heat flow, they can be added using the mol, q, rmass, temperature, or heatflow keywords. This could be useful to define “molecules” to use as rigid bodies with the fix rigid command, or to carry around an extra flag with atoms (stored as a molecule ID) that can be used by various commands like compute chunk/atom to group atoms without having to use the group command (which is limited to a total of 32 groups including all). For finite-size particles, an internal temperature and heat flow can be used to model heat conduction as in the GRANULAR package.

Another application is to use the rmass flag in order to have per-atom masses instead of per-type masses. This could be used to study isotope effects with partial isotope substitution. See below for an example of simulating a mixture of light and heavy water with the TIP4P water potential.

An alternative to using fix property/atom for these examples is to use an atom style that does define molecule IDs or charge or per-atom mass (indirectly via diameter and density) or to use a hybrid atom style that combines two or more atom styles to provide the union of all their atom properties. However, this has two practical drawbacks: first, it typically necessitates changing the format of the Atoms section in the data file and second, it may define additional properties that are not needed such as bond lists, which incurs some overhead when there are no bonds.

In the future, we may add additional existing per-atom properties to fix property/atom, similar to mol, q, rmass, temperature, or heatflow which “turn-on” specific properties defined by some atom styles, so they can be easily used by atom styles that do not define them.

More generally, the i_name and d_name options allow one or more new custom per-atom vectors to be defined. Likewise the i2_name and d2_name options allow one or more custom per-atom arrays to be defined. The i2_name and d2_name options take an argument N which specifies the number of columns in the per-atom array, i.e. the number of attributes associated with each atom. N >= 1 is required.

Each name must be unique and can use alphanumeric or underscore characters. These vectors and arrays can store whatever values you decide are useful in your simulation. As explained below there are several ways to initialize, access, and output these values, via input script commands, data files, and in new code you add to LAMMPS.

This is effectively a simple way to add per-atom properties to a model without needing to write code for a new atom style that defines the properties. Note however that implementing a new atom style allows new atom properties to be more tightly and seamlessly integrated with the rest of the code.

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 ensure the new properties are also defined for the ghost atoms.

Properties on ghost atoms

If you use the mol, q or rmass names, you most likely want to set ghost yes, since these properties are stored with ghost atoms if you use an atom_style that defines them. Many LAMMPS operations that use molecule IDs or charge, such as neighbor lists and pair styles, will expect ghost atoms to have these values. LAMMPS will issue a warning it you define those vectors but do not set ghost yes.

Limitations on ghost atom properties

The specified properties for ghost atoms are not updated every timestep, but only once every few steps when neighbor lists are re-built. Thus the ghost keyword is suitable for static properties, like molecule IDs, but not for dynamic properties that change every step. For the latter, the code you add to LAMMPS to change the properties will also need to communicate their new values to/from ghost atoms, an operation that can be invoked from within a pair style or fix or compute that you write.

This fix is one of a small number that can be defined in an input script before the simulation box is created or atoms are defined. This is so it can be used with the read_data command as described next.

Per-atom properties that are defined by the atom style are initialized when atoms are created, e.g. by the read_data or create_atoms commands. The per-atom properties defined by this fix are not. So you need to initialize them explicitly. One way to do this is read_data command, using its fix keyword and passing it the fix-ID of this fix.

Thus these commands:

fix prop all property/atom mol d_flag
read_data data.txt fix prop NULL Molecules

would allow a data file to have a section like this:

Molecules

1 4 1.5
2 4 3.0
3 10 1.0
4 10 1.0
5 10 1.0
...
N 763 4.5

where N is the number of atoms, the first field on each line is the atom-ID, the next two are a molecule-ID and a floating point value that will be stored in a new property called “flag”. If a per-atom array was specified in the fix property/atom command then the N values for that array must be specified consecutively for that property on each line. Note that the order of values on each line corresponds to the order of custom names in the fix property/atom command.

Note that the the lines of per-atom properties can be listed in any order. Also note that all the per-atom properties specified by the fix ID (prop in this case) must be included on each line in the specified data file section (Molecules in this case).

Another way of initializing the new properties is via the set command. For example, if you wanted molecules defined for every set of 10 atoms, based on their atom-IDs, these commands could be used:

fix prop all property/atom mol
variable cluster atom ((id-1)/10)+1
set atom * mol v_cluster

The atom-style variable will create values for atoms with IDs 31,32,33,…40 that are 4.0,4.1,4.2,…,4.9. When the set commands assigns them to the molecule ID for each atom, they will be truncated to an integer value, so atoms 31-40 will all be assigned a molecule ID of 4.

Note that atomfile-style variables can also be used in place of atom-style variables, which means in this case that the molecule IDs could be read-in from a separate file and assigned by the set command. This allows you to initialize new per-atom properties in a completely general fashion.

For new atom properties specified as i_name, d_name, i2_name, or d2_name, the dump custom and compute property/atom commands can access their values. This means that the values can be used accessed by fixes like fix ave/atom, accessed by other computes like compute reduce, or used in atom-style variables.

For example, these commands will output both the instantaneous and time-averaged values of two new properties to a custom dump file:

fix myprops all property/atom i_flag1 d_flag2
compute 1 all property/atom i_flag1 d_flag2
fix 1 all ave/atom 10 10 100 c_1[1] c_1[2]
dump 1 all custom 100 tmp.dump id x y z i_flag1 d_flag2 f_1[1] f_1[2]

If you wish to add new pair styles, fixes, or computes that use the per-atom properties defined by this fix, see the Modify atom doc page which has details on how the custom properties of this fix can be accessed from added classes.

Here is an example of using per-atom masses with TIP4P water to study isotope effects. When setting up simulations with the TIP4P pair styles for water, you have to provide exactly one atom type each to identify the water oxygen and hydrogen atoms. Since the atom mass is normally tied to the atom type, this makes it impossible to study multiple isotopes in the same simulation. With fix property/atom rmass however, the per-type masses are replaced by per-atom masses. Asumming you have a working input deck for regular TIP4P water, where water oxygen is atom type 1 and water hydrogen is atom type 2, the following lines of input script convert this to using per-atom masses:

fix Isotopes all property/atom rmass ghost yes
set type 1 mass 15.9994
set type 2 mass 1.008

When writing out the system data with the write_data command, there will be a new section named with the fix-ID (i.e. Isotopes in this case). Alternatively, you can take an existing data file and just add this Isotopes section with one line per atom containing atom-ID and mass. Either way, the extended data file can be read back with:

fix Isotopes all property/atom rmass ghost yes
read_data tip4p-isotopes.data fix Isotopes NULL Isotopes

Please note that the first Isotopes refers to the fix-ID and the second to the name of the section. The following input script code will now change the first 100 water molecules in this example to heavy water:

group hwat id 2:300:3
group hwat id 3:300:3
set group hwat mass 2.0141018

Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the Accelerator packages page. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

These accelerated styles are part of the GPU, INTEL, KOKKOS, OPENMP, and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the Build package page for more info.

You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

See the Accelerator packages page for more instructions on how to use the accelerated styles effectively.

Restart, fix_modify, output, run start/stop, minimize info

This fix writes the per-atom values it stores to binary restart files, so that the values can be restored when a simulation is restarted. See the read_restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion.

Warning

When reading data from a restart file, this fix command has to be specified after the read_restart command and exactly the same was in the input script that created the restart file. LAMMPS will only check whether a fix is of the same style and has the same fix ID and in case of a match will then try to initialize the fix with the data stored in the binary restart file. If the names and associated date types in the new fix property/atom command do not match the old one exactly, data can be corrupted or LAMMPS may crash. If the fix is specified before the read_restart command its data will not be restored.

None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.

Restrictions

none

Default

The default keyword value is ghost = no.