augmentDb.py

nrelmat.augmentDb.main()

This program adds additional information to the model database table. The following functions in this file fill the indicated columns in the model table. The columns must have been created previously by the fillDbVasp.py function createTable.

Function	Column	Notes
addChemform	formula	Standard chemical formula: "H2 O".
addChemform	sortedformula	Chemical formula: "H2 O", with atoms sorted in alphabetic order.
addChemForm	chemtext	Structured formula, easier for parsing. Every token is surrounded by spaces, and single occurance atoms have the explicit “1” count: " H 2 O 1 ".
addMinenergy	minenergyid	== mident having min energyperatom for this formula and finalspacegroupnum.

Command line parameters:

Parameter	Type	Description
-bugLev	integer	Debug level. Normally 0.
-useCommit	boolean	false/true: do we commit changes to the DB.
-inSpec	string	JSON file containing DB parameters. See below.

inSpec File Parameters:

Parameter	Description
dbhost	Database hostname.
dbport	Database port number.
dbuser	Database user name.
dbpswd	Database password.
dbname	Database database name.
dbschema	Database schema name.
dbtablemodel	Database name of the “model” table.

inSpec file example::

{
  "dbhost"         : "scctest",
  "dbport"         : "6432",
  "dbuser"         : "x",
  "dbpswd"         : "x",
  "dbname"         : "cidlada",
  "dbschema"       : "satom",
  "dbtablemodel"   : "model"
}

nrelmat.augmentDb.augmentDb(bugLev, useCommit, inSpec)

Adds additional information to the model database table.

See documentation for the main() function.

Parameters:

• bugLev (int): Debug level. Normally 0.

• useCommit (bool): do we commit changes to the DB.

• inSpec (str): Name of JSON file containing DB parameters.

  See description at main().

Returns

• None

nrelmat.augmentDb.addMinenergy(bugLev, objPairs)

Calculates the min energyperatom for each formula.

minenergyid == the mident of the row having the min energyperatom for this formula.

Parameters:

• bugLev (int): Debug level; normally 0.
• curObjs: current objects, one per DB row
• newObjs: objects with new fields only, one per DB row

nrelmat.augmentDb.addEnthalpy(bugLev, objPairs)

Calculates the enthalpy of formation per atom, for all structures.

Parameters:

• bugLev (int): Debug level; normally 0.
• curObjs: current objects, one per DB row
• newObjs: objects with new fields only, one per DB row

nrelmat.augmentDb.calcEnthalpy(bugLev, mident, typenames, typenums, typepseudos, energy)

Calculates the enthalpy of formation per atom, for a single structure.

Parameters (using example magnetitie, Fe3 O4):

• mident (int): The unique DB identifier.

• typenames (str[]): List of unique type names, ex. [‘Fe’, ‘O’]

• typenums (int[]): Number of each unique type, ex. [3, 4]

• typepseudos (str[]): Pseudopotential for each type,

  [‘PAW_PBE Fe 06Sep2000’, ‘PAW_PBE O_s 07Sep2000’]

• energy (float): final total energy without entropy, per atom in cell

Returns

• enthalpy (float): enthalpy of formation per atom

See: DOI: 10.1103/PhysRevB.85.115104

http://prb.aps.org/pdf/PRB/v85/i11/e115104 Correcting density functional theory for accurate predictions of compound enthalpies of formation: Fitted elemental-phase reference energies Vladan Stevanovic, Stephan Lany, Xiuwen Zhang, Alex Zunger

page 11, Table V: mu^{FERE}

Email from Stevanovic, Monday, August 12, 2013 5:45 PM For the enthalpy of formation calculations I will use the following example. So, if we have a ternary compound with the chemical formula A_mB_nX_l, where A, B and X represent the symbols of the elements forming the compound and if N=m+n+l the total number of atoms in the compound the enthalpy of formation can be calculated as:

dHf (eV/atom) = [Etot(eV/atom) * N - (m*musMap[‘A’] + n*musMap[‘B’] + l*musMap[‘X’] ) ] / N

where Etot(eV/atom) is the VASP total energy per atom which is currently listed in the database and musMap[‘A’], musMap[‘B’], and musMap[‘X’] you read from the attached dictionary.

This is the same as:

enthalpy = - sum_i( n_i * mus_i) / sum( n_i)

where n_i = number of element i, and mus_i = mus value for element i. We use this calculation for ALL structures, not just ternaries.

nrelmat.augmentDb.throwerr(msg)

Prints an error message and raises Exception.

Parameters:

• msg (str): Error message.

Returns

• (Never returns)

Raises

• Exception