qmworks.plams.interfaces.adfsuite.SCMResults Class Reference

Inheritance diagram for qmworks.plams.interfaces.adfsuite.SCMResults:

Collaboration diagram for qmworks.plams.interfaces.adfsuite.SCMResults:

Public Member Functions
def	collect (self)
def	refresh (self)
def	readkf (self, section, variable)
def	newkf (self, filename)
def	get_molecule (self, section, variable, unit='bohr', internal=False, n=1)
Public Member Functions inherited from qmworks.plams.core.results.Results
def	__init__ (self, job)
def	refresh (self)
def	collect (self)
def	wait (self)
def	grep_file (self, filename, pattern='', options='')
def	awk_file (self, filename, script='', progfile=None, kwargs)
def	grep_output (self, pattern='', options='')
def	awk_output (self, script='', progfile=None, kwargs)
def	rename (self, old, new)
def	__getitem__ (self, name)

Additional Inherited Members
Public Attributes inherited from qmworks.plams.core.results.Results
	job
	files
	finished
	done

Detailed Description

Abstract class gathering common mechanisms for results of all ADF Suite binaries.

Member Function Documentation

collect()

def qmworks.plams.interfaces.adfsuite.SCMResults.collect

(

self

)

Collect files present in the job folder. Use parent method from |Results|, then create an instance of |KFFile| for the main KF file and store it as ``_kf`` attribute.

get_molecule()

def qmworks.plams.interfaces.adfsuite.SCMResults.get_molecule	(		self,
			section,
			variable,
			unit = 'bohr',
			internal = False,
			n = 1
	)

get_molecule(section, variable, unit='bohr', internal=False, n=1)
Read molecule coordinates from *section*/*variable* of the main KF file.

Returned |Molecule| instance is created by copying a molecule from associated |SCMJob| instance and updating atomic coordinates with values read from *section*/*variable*. The format in which coordinates are stored is not consistent for all programs or even for different sections of the same KF file. Sometimes coordinates are stored in bohr, sometimes in angstrom. The order of atoms can be either input order or internal order. These settings can be adjusted with *unit* and *internal* parameters. Some variables store more than one geometry, in those cases *n* can be used to choose the preferred one.

Here is the call graph for this function:

newkf()

def qmworks.plams.interfaces.adfsuite.SCMResults.newkf	(		self,
			filename
	)

newkf(filename)
Create new |KFFile| instance using file *filename* in the job folder.

Example usage::

    >>> res = someadfjob.run()
    >>> tape13 = res.newkf('$JN.t13')
    >>> print(tape13.read('Geometry', 'xyz'))

Here is the call graph for this function:

readkf()

def qmworks.plams.interfaces.adfsuite.SCMResults.readkf	(		self,
			section,
			variable
	)

readkf(section, variable)
Read data from *section*/*variable* of the main KF file.

The type of the returned value depends on the type of *variable* defined inside KF file. It can be: single int, list of ints, single float, list of floats, single boolean, list of booleans or string. 

Here is the caller graph for this function:

refresh()

def qmworks.plams.interfaces.adfsuite.SCMResults.refresh

(

self

)

Refresh the contents of ``files`` list. Use parent method from |Results|, then look at all attributes that are instances of |KFFile| and check if they point to existing files. If not, try to reinstantiate them with current job path (that can happen while loading a pickled job after the entire job folder was moved).

---

The documentation for this class was generated from the following file:

• /home/docs/checkouts/readthedocs.org/user_builds/pyfragdocument/checkouts/latest/qmworks/plams/interfaces/adfsuite.py