DIRAC is an ab initio quantum chemistry program for all electron relativistic calculation. It features a variety of methods including HF, MP2, DFT, CI and CC. More information about DIRAC can be found on its official website.
PLAMS offers a simple DIRAC interface and is capable of running DIRAC calculations.
The relevant classes are
126.96.36.199. Preparing a calculation¶
Preparing an instance of
DiracJob follows general principles for
Information adjusting input file is stored in
myjob.settings.input branch, whereas a runscript is created based on contents of
The geometry of your system can be supplied in two ways.
Unlike ADF or BAND, DIRAC uses two separate files, one for input settings and the other for atomic coordinates.
Geometry file needs to be in
.xyz format and it can be either generated automatically based on
myjob.molecule or given directly by the user (see below for details).
Input files for DIRAC are organized using blocks and subblocks with three level hierarchy.
On the top level there are blocks (indicated by keywords starting with
**) which can contain keys (starting with
.) or subblocks (starting with
*), which in turn can contain more keys.
This structure can be easily reflected with tree-like
In general, the preparation process is quite similar to
SCMJob, however, there are a few nuances.
The details are explained below.
Each key present on the top level of
myjob.settings.inputis translated to a block. Values of those keys should be
Settingsinstances. The block
DIRACis always printed as the first one, all other are ordered lexicographically (this behavior can be changed with
In each block various keys and subblocks can be present. Subblocks are indicated by nested
Settingsinstances, all other values are interpreted as keys.
An empty value of a key can be obtained by setting its value to
An empty block or subblock can be obtained with an empty
If the value of a key is a list, each element of this list will be printed in a separate line.
All keywords are written to the input file with upper case, values remain unchanged.
Many DIRAC keywords contain spaces (for example
LINEAR RESPONSE) and thus cannot be used with convenient dot notation. Usual bracket notation has to be used in those cases (see Dot notation).
Some subblocks follow the special requirement - they need to be “enabled” by presence of the corresponding keyword in the parent block. For example, in
**HAMILTONIANblock a subblock
*FDEcan be used to specify frozen density embedding parameters, but this subblock is taken into account only if a key
.FDEis present in
**HAMILTONIAN. This introduces a problem, since you cannot store two entries with the same name in
#sets the .FDE key on the top level of HAMILOTNIAN block myjob.setting.input.hamiltonian.fde = True #sets the *FDE subblock in the HAMILTONIAN block, but overwrites the key .FDE defined above myjob.setting.input.hamiltonian.fde.frdens = 'value2'
To solve this problem a special “enabler” key
_encan be used inside the subblock. If such a key is present, the parent block of this subblock will be enriched with corresponding key and value:
#sets the .FDE key on the top level of HAMILOTNIAN block, its value can be set just like any other key myjob.setting.input.hamiltonian.fde._en = True #sets the "proper" contents of *FDE subblock. myjob.setting.input.hamiltonian.fde.frdens = 'value2'
Calculations with DIRAC are executed using a start script called
This script accepts a range of option flags adjusting various technical aspects of calculation, including input and geometry files.
You can type
pam -h in you command line for details.
A runscript calling
pam is automatically generated by PLAMS.
Its contents are based on
myjob.settings.runscript branch and follow general rules described in Contents of job settings.
Besides that, the subbranch
myjob.settings.runscript.pam is used to store option flags.
Every key-value pair present there is transformed to
--key=value flag appended to
pam execution command.
Following the usual convention,
True represents an “empty value” (to get flags like
--key) and list can be used for keys with multiple values (
--key="val1 val2 val3").
Initially, when an instance of
DiracJob is created, the following
pam options are set by default:
self.settings.runscript.pam.noarch = True self.settings.runscript.pam.get = ['DFCOEF', 'GRIDOUT', 'dirac.xml']
Their role is to obtain from DIRAC scratch space all the files produced by your calculation (they can be later discarded with Cleaning job folder if not needed) and prevent creating a
.tgz archive out of them (to allow PLAMS to process them).
These two default flags can be changed or removed if needed, but this can hinder some
Results functionalities, so make sure to know what you are doing.
You don’t need to manually set mandatory
mol flags, they are added automatically just before the runscript is generated.
If, for some reason, you don’t want to use automatic molecule handling and wish to provide a geometry file by yourself, all you need to do is to set
mol entry in
myjob.settings.runscript.pam with the path of your geometry file.
PLAMS will then ignore geometry stored in
myjob.molecule and use the supplied path.
188.8.131.52. Results extraction¶
DIRAC produces two output files that can contain meaningful information.
One is a “real” output of the calculation and the other is more technical output of
For the sake of consistency PLAMS concatenates those two files into a single output file.
pam output is appended at the end of the “real” output, separated by a visual delimeter.
Besides the regular text output some other files are produced by DIRAC.
dirac.xml are fetched from the scratch space and renamed to, respectively,
General text processing methods from
Results can be used to obtain data from results files.
At the moment, no special tools are present for binary files.
.xml files can be easily accessed with standard Python libraries present in
DiracJob(molecule=None, name='plamsjob', settings=None, depend=None)¶
A class representing a single computational job with DIRAC.
Initialize self. See help(type(self)) for accurate signature.
Before generating runscript and input with parent method
self.settings.runscript.pam. If already present there,
molwill not be added.
Transform all contents of
settingsinto string with blocks, subblocks, keys and values.
On the highest level alphabetic order of iteration is modified: keys occuring in class attribute
_topare printed first. See Input for details.
Generate a runscript. Returned string is a
pamcall followed by option flags generated based on
self.settings.runscript.pamcontents. See Runscript for details.
Check if the calculation was successful by examining the last line of