As noted above, NWChem consists of independent modules that perform the various functions of the code. Examples include the input parser, self-consistent field (SCF) energy, SCF analytic gradient, and density functional theory (DFT) energy modules. The independent NWChem modules can share data only through a disk-resident database, which is similar to the GAMESS-UK dumpfile or the Gaussian checkpoint file. This allows the modules to share data, or to share access to files containing data.
It is not necessary for the user to be intimately familiar with the contents of the database in order to run NWChem. However, a nodding acquaintance with the design of the code will help in clarifying the logic behind the input requirements, especially when restarting jobs or performing multiple tasks within one job.
As described above (Input File Structure), all start-up directives are processed at the beginning of the job by the main program, and then the input module is invoked. Each input directive usually results in one or more entries being made in the database. When a TASK directive is encountered, control is passed to the appropriate module, which extracts relevant data from the database and any associated files. Upon completion of the task, the module will store significant results in the database, and may also modify other database entries in order to affect the behavior of subsequent computations.
Data is shared between modules of NWChem by means of the database. Three main types of information are stored in the data base: (1) arrays of data, (2) names of files that contain data, and (3) objects. Arrays are stored directly in the database, and contain the following information:
- the name of the array, which is a string of ASCII characters (e.g., "reference energies")
- the type of the data in the array (i.e., real, integer, logical, or character)
- the number (N) of data items in the array (Note: A scalar is stored as an array of unit length.)
- the N items of data of the specified type
It is possible to enter data directly into the database using the SET directive. For example, to store a (64-bit precision) three-element real array with the name "reference energies" in the database, the directive is as follows:
set "reference energies" 0.0 1.0 -76.2
NWChem determines the data to be real (based on the type of the first element, 0.0), counts the number of elements in the array, and enters the array into the database.
Much of the data stored in the database is internally managed by NWChem and should not be modified by the user. However, other data, including some NWChem input options, can be freely modified.
Objects are built in the database by storing associated data as multiple entries, using an internally consistent naming convention. This data is managed exclusively by the subroutines (or methods) that are associated with the object. Currently, the code has two main objects: basis sets and geometries. GEOMETRY and BASIS present a complete discussion of the input to describe these objects.
As an illustration of what comprises a geometry object, the following table contains a partial listing of the database contents for a water molecule geometry named "test geom". Each entry contains the field test geom, which is the unique name of the object.
Contents of RTDB h2o.db ----------------------- Entry Type[nelem] --------------------------- ---------------------- geometry:test geom:efield double geometry:test geom:coords double geometry:test geom:ncenter int geometry:test geom:charges double geometry:test geom:tags char ...
Using this convention, multiple instances of objects may be stored with different names in the same database. For example, if a user needed to do calculations considering alternative geometries for the water molecule, an input file could be constructed containing all the geometries of interest by storing them in the database under different names.
The runtime database contents for the file h2o.db listed above were generated from the user-specified input directive,
geometry "test geom" O 0.00000000 0.00000000 0.00000000 H 0.00000000 1.43042809 -1.10715266 H 0.00000000 -1.43042809 -1.10715266 end
The GEOMETRY directive allows the user to specify the coordinates of the atoms (or centers), and identify the geometry with a unique name.
Unless a specific name is defined for the geometry, (such as the name "test geom" shown in the example), the default name of geometry is assigned. This is the geometry name that computational modules will look for when executing a calculation. The SET directive can be used in the input to force NWChem to look for a geometry with a name other than geometry. For example, to specify use of the geometry with the name "test geom" in the example above, the SET directive is as follows:
set geometry "test geom"
NWChem will automatically check for such indirections when loading geometries. Storage of data associated with basis sets, the other database resident object, functions in a similar fashion, using the default name "ao basis".
Persistence of data and restart
The database is persistent, meaning that all input data and output data (calculation results) that are not destroyed in the course of execution are permanently stored. These data are therefore available to subsequent tasks or jobs. This makes the input for restart jobs very simple, since only new or changed data must be provided. It also makes the behavior of successive restart jobs identical to that of multiple tasks within one job.
Sometimes, however, this persistence is undesirable, and it is necessary to return an NWChem module to its default behavior by restoring the database to its input-free state. In such a case, the UNSET directive can be used to delete all database entries associated with a given module (including both inputs and outputs).