.. index:: fix property/atom fix property/atom command ========================= Syntax """""" .. parsed-literal:: fix ID group-ID property/atom vec1 vec2 ... keyword value ... * ID, group-ID are documented in :doc:`fix ` command * property/atom = style name of this fix command * vec1,vec2,... = *mol* or *q* or *rmass* or *i_name* or *d_name* .. parsed-literal:: *mol* = molecule IDs *q* = charge *rmass* = per-atom mass *i_name* = new integer vector referenced by name *d_name* = new floating-point vector referenced by name * zero of more keyword/value pairs may be appended * keyword = *ghost* .. parsed-literal:: *ghost* value = *no* or *yes* for whether ghost atom info in communicated Examples """""""" .. parsed-literal:: fix 1 all property/atom mol fix 1 all property/atom i_myflag1 i_myflag2 fix 1 all property/atom d_sx d_sy d_sz Description """"""""""" Create one or more additional per-atom vectors 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 :doc:`atom_style ` and :doc:`read_data ` doc pages. The latter command allows these properties to be defined for each atom in the system when a data file is read. This fix will augment the set of properties with new custom ones. This can be useful in several scenarios. If the atom style does not define molecule IDs, per-atom charge, or per-atom mass, they can be added using the *mol*\ , *q* or *rmass* keywords. This can be useful, e.g, to define "molecules" to use as rigid bodies with the :doc:`fix rigid ` command, or just to carry around an extra flag with the atoms (stored as a molecule ID) that can be used to group atoms without having to use the group command (which is limited to a total of 32 groups including *all*\ ). Another application would be to use the *rmass* flag in order to have per-atom masses instead of per-type masses, for example this can be useful to study isotope effects with partial isotope substitution. Please :ref:`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* in these ways 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 atom properties. However, this has two practical drawbacks: first, it typically necessitates changing the format of the data file, which can be tedious for large systems; and second, it may define additional properties that are not needed such as bond lists, which has some overhead when there are no bonds. In the future, we may add additional per-atom properties similar to *mol*\ , *q* or *rmass*\ , which "turn-on" specific properties defined by some atom styles, so they can be used by atom styles that do not define them. More generally, the *i_name* and *d_name* vectors allow one or more new custom per-atom properties to be defined. Each name must be unique and can use alphanumeric or underscore characters. These vectors can store whatever values you decide are useful in your simulation. As explained below there are several ways to initialize and access and output these values, both via input script commands and in new code that 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 :doc:`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 insure the new properties are also defined for the ghost atoms. .. note:: If you use this command with the *mol*\ , *q* or *rmass* vectors, then you most likely want to set *ghost* yes, since these properties are stored with ghost atoms if you use an :doc:`atom_style ` that defines them, and many LAMMPS operations that use molecule IDs or charge, such as neighbor lists and pair styles, will expect ghost atoms to have these valuse. LAMMPS will issue a warning it you define those vectors but do not set *ghost* yes. .. note:: The 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 :doc:`pair style ` or :doc:`fix ` or :doc:`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 :doc:`read_data ` command as described below. Per-atom properties that are defined by the :doc:`atom style ` are initialized when atoms are created, e.g. by the :doc:`read_data ` or :doc:`create_atoms ` commands. The per-atom properaties defined by this fix are not. So you need to initialize them explicitly. This can be done by the :doc:`read_data ` command, using its *fix* keyword and passing it the fix-ID of this fix. Thus these commands: .. parsed-literal:: 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: .. parsed-literal:: Molecules .. parsed-literal:: 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, and the first field on each line is the atom-ID, followed by a molecule-ID and a floating point value that will be stored in a new property called "flag". Note that the list of per-atom properties can be in any order. Another way of initializing the new properties is via the :doc:`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: .. parsed-literal:: fix prop all property/atom mol variable cluster atom ((id-1)/10)+1 set id * mol v_cluster The :doc:`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 :doc:`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 :doc:`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 assinged by the :doc:`set ` command. This allows you to initialize new per-atom properties in a completely general fashion. ---------- For new atom properties specified as *i_name* or *d_name*\ , the :doc:`compute property/atom ` command can access their values. This means that the values can be output via the :doc:`dump custom ` command, accessed by fixes like :doc:`fix ave/atom `, accessed by other computes like :doc:`compute reduce `, or used in `atom-style variables `_. For example, these commands will output two new properties to a custom dump file: .. parsed-literal:: fix prop all property/atom i_flag1 d_flag2 compute 1 all property/atom i_flag1 d_flag2 dump 1 all custom 100 tmp.dump id x y z c_1[1] c_1[2] ---------- If you wish to add new :doc:`pair styles `, :doc:`fixes `, or :doc:`computes ` that use the per-atom properties defined by this fix, see :ref:`Section modify ` of the manual which has some details on how the properties can be accessed from added classes. ---------- .. _isotopes: Example for using per-atom masses with TIP4P water to study isotope effects. When setting up simulations with the :ref:`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: .. parsed-literal:: 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 :doc:`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: .. parsed-literal:: 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: .. parsed-literal:: group hwat id 2:300:3 group hwat id 3:300:3 set group hwat mass 2.0141018 ---------- Restart, fix_modify, output, run start/stop, minimize info """""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the per-atom values it stores to :doc:`binary restart files `, so that the values can be restored when a simulation is restarted. See the :doc:`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. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :ref:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" none Related commands """""""""""""""" :doc:`read_data `, :doc:`set `, :doc:`compute property/atom ` Default """"""" The default keyword values are ghost = no. .. _lws: http://lammps.sandia.gov .. _ld: Manual.html .. _lc: Section_commands.html#comm