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CRYSTALpytools.base.propd3 module

The Properties_inputBASE object is strictly structured by ‘blocks’, which, in general, is defined as keywords that are closed by ‘END’. It is inherited from the BlockBASE object and is inherited by the Properties_input object. All the blocks are organized in layers and each corresponds to a list of keywords that can be called and set. The current structure of Properties_inputBASE is listed below:

Layer 1: Optional, repeated block (same calculation, another time) append1 to append5

Layer 2: Data grid and DFT/MP2 correlation energy ECHG, POTM, CLAS, EDFT/ENECOR, ADFT/ACOR

For the usages of BlockBASE and Properties_input objects, please refer to the corresponding documentations.

Examples

Note that methods listed below are for Properties_input objects, which is typically consistent with Properties_inputBASE, except file read and write functions.

To set a band structure and a projected doss calculation:

>>> obj = Properties_input()
>>> obj.band('Band calc title', 3, 6, 188, 203, 224, 1, 0,
             [[[0, 0, 0], [3, 0, 0]], # A 3*2*3 list, for 3 line segments, 2 ending points of each segment, xyz for each point
              [[3, 0, 0], [2, 2, 0]],
              [[2, 2, 0], [0, 0, 0]]])
>>> obj.newk(8, 16, 1, 0)
>>> obj.doss(1, 600, 203, 224, 1, 12, 0, [[-1, 57], [-1, 64]]) # Project to atom 54 and atom 64

By calling the ‘block-like’ attribute, a sub-block object will be automatically generated if no such object is saved in the upper block object. It also be initialized and deleted in a similar way as keyword commands.

>>> obj = Properties_input()
>>> obj.echg() # Initialize ECHG
>>> obj.echg(None) # Remove ECHG
>>> obj.echg(0, 95) # Charge density map, Npoint of MAPNET is 95 (default value 100)

To set the values of keywords, their names are called as methods:

>>> obj.echg.coordina([-2.498, 0., 1.696], [-2.498, 0., -1.696], [-1.249, -2.164, -1.696])
>>> obj.echg.rectangu() # Print RECTANGU keyword, without value
>>> obj.echg.margins(3, 3, 3, 3)

Though one can set CRYSTAL input object by manually setting up all the attributes, it is also possible to read a template d3 file and do modifications.

>>> obj = Properties_input('charge2d.d3')
>>> obj.echg(None) # Remove ECHG block
>>> obj.ech3(100) # Define ECH3 block
>>> obj.ech3.range(-10, 10) # Range of Non-periodic direction
>>> obj.to_file('charge3d.d3') # Print it into file

It is also possible to set individual blocks by a string. This is achieved by simply assigning the string variable as input when calling the corresponding method.

>>> obj.ech3('ECH3\n100\nRANGE\n-10\n10\n')

As stressed in the doc of base.inputbase, repeated keywords not protected by sub-blocks are not permitted. That leads to problems when, for example, plotting the charge difference map to analyze bonds, where ‘ECHG’ is repeated twice in the main block. To address this, the following sub-block is called when the second ‘ECHG’ is used:

>>> obj = Properties_input()
>>> obj.echg(0) # Set the first ECHG. MAPNET density = 100, default value is used.
>>> obj.echg.coordina([-2.498, 0., 1.696], [-2.498, 0., -1.696], [-1.249, -2.164, -1.696])
>>> obj.echg.rectangu()
>>> obj.echg.margins(3, 3, 3, 3)
>>> obj.append1() # Initialize the first appended calculation
>>> obj.append1.pato(1, 0)
>>> obj.append1.echg(0) # Set the second ECHG. MAPNET density = 100, default value is used.
>>> obj.append1.echg.coordina([-2.498, 0., 1.696], [-2.498, 0., -1.696], [-1.249, -2.164, -1.696])
>>> obj.append1.echg.rectangu()
>>> obj.append1.echg.margins(3, 3, 3, 3)

5 appended calculations (append1 to append5) at most can be added and the Properties_input object is the initial calculation, so the same keyword, which is not protected by subblocks, can repeat 6 times at most. Error is reported if it appears more than 6 times.

To examine the data in a block object, including the Properties_input obj itself, call the data attribute.

>>> print(obj.data)

Classes and methods of keywords used in ‘properties’ input file (d3).

class PInputBlock

Bases: BlockBASE

The base class of a ‘property input block’, i.e., a properties calculation, with non-repeated keywords.

rdfmwf(rdfmwf='')

band(TITLE='', NLINE='', ISS='', NSUB='', INZB='', IFNB='', IPLO='', LPR66='', path=[]): path can either be a NLINE*2 list of string (labels), or a NLINE*2*3 list of int (fractional coordinates).

anbd(NK='', NB='', TOL='', *args)

bwidth(INZB='', IFNB='')

commens(ICASO='')

pato(IBN='', NPR='')

nosymada(nosymada='')

newk(*args): Inputs are separated by comma.

pban(NB='', nbands=[])

pgeomw(pgeomw='')

pdide(EMI='', EMX='')

property adft: Subblock object ADFT.

property acor: Alias of block ADFT.

property edft: Subblock object EDFT.

property enecor: Alias of block EDFT.

property clas

Subblock object CLAS. Call self.clas() to set parameters. Call self.clas.coordina() (for example) to set mapnet keywords.

Parameters:

IDER (int) – Order of the derivative
IFOR (int) – Number of point multipoles
charge (list) – Formal net charge
NPY (int) – Number of points (MAPNET). Default 100.

property echg

Subblock object ECHG. Call self.echg() to set parameters. Call self.echg.coordina() (for example) to set mapnet keywords.

Parameters:

IDER (int) – Order of the derivative
NPY (int) – Number of points (MAPNET). Default 100.

property ech3

Subblock object ECH3. Call self.ech3() to set parameters. Call self.ech3.range() (for example) to set 3D grid keywords.

Parameters:: NP (int) – Number of points along the first direction

property potm

Subblock object POTM. Call self.potm() to set parameters. Call self.potm.coordina() (for example) to set mapnet keywords.

Parameters:

IDER (int) – Order of the derivative
ITOL (int) – Penetration tolerance
NPY (int) – Number of points (MAPNET). Default 100.

property pot3

Subblock object POT3. Call self.pot3() to set parameters. Call self.pot3.range() (for example) to set 3D grid keywords.

Parameters:

NP (int) – Number of points along the first direction
ITOL (int) – Penetration tolerance

potc(ICA='', NPU='', IPA='', datagrid=[]): datagrid corresponds to X, Y, Z, ZP, ZM and ZD parameters, which can be NPU*3 (ICA=0), 2*1 (ICA=1) or 3*1 (ICA=2) lists.

hirshchg(hchg='')

ppan(pchg='')

emdldm(N='', PMAX='', STEP='', IPLO='', hkl=[], ICASO='', NSA1='', NSA2=''): hkl is a N*3 list of int.

kinetemd(PMAX='', PINT='', STEP='', STEPDIST='', ICASO='')

poli(IDIPO='', ITENS='', LPR68='')

polspin(IDIPO='', ITENS='', LPR68='')

anisotro(keyword='', N='', IA=''): Available keywords: ‘ALL’, ‘UNIQUE’, ‘SELECT’

isotropic(keyword='', N='', IA=''): Available keywords: ‘ALL’, ‘UNIQUE’, ‘SELECT’

doss(NPRO='', NPT='', INZB='', IFNB='', IPLO='', NPOL='', NPR='', *args): Energy range (BMI, BMA, 2*1 list) and projections (N, NDM, Nproj*(NDM+1) list) are defined by extendable list variables. If both are defined, projections should be the last entry.

coop(NINT='', NPT='', INZB='', IFNB='', IPLO='', NPOL='', NPR='', *args): Energy range (BMI, BMA, 2*1 list) and projections (N, NDM, Nproj*(NDM+1) list) are defined by extendable list variables. If both are defined, projections should be the last entry.

cohp(NINT='', NPT='', INZB='', IFNB='', IPLO='', NPOL='', NPR='', *args): Energy range (BMI, BMA, 2*1 list) and projections (N, NDM, Nproj*(NDM+1) list) are defined by extendable list variables. If both are defined, projections should be the last entry.

pscf(pscf='')

static _doss_like(NPRO, NPT, INZB, IFNB, IPLO, NPOL, NPR, arg): Get formatted input text for ‘DOSS’-like keywords, including ‘DOSS’, ‘COHP’ and ‘COOP’.

class Properties_inputBASE

Bases: PInputBlock

The base class of Properties_input class. At maximum 5 same ‘properties’ calculations can be appended

property append1

property append2

property append3

property append4

property append5

analyze_text(data)

Analyze formatted d3 file.

Parameters:: data (str) – Formatted string.

class EDFT

Bases: BlockBASE

EDFT sub-block

becke(becke='')

savin(savin='')

radial(NR='', RL=[], IL=[])

angular(NI='', AL=[], IA=[])

print(prt='')

printout(prt='')

tolldens(ID='')

tollgrid(IG='')

class ADFT

Bases: EDFT

ADFT sub-block

property newbasis: Subblock object NEWBASIS

class Grid2D(header='')

Bases: BlockBASE

A base class for 2D data grid (ECHG, POTM, CLAS).

Parameters:: header (str) – Formatted headers

coordina(crda='', crdb='', crdc='')

atoms(IA='', IB='', IC=''): IA IB IC are 4*1 lists

rectangu(rec='')

margins(ABM='', CDM='', ADM='', BCM='')

print(prt='')

angstrom(ang='')

bohr(br='')

fraction(frac='')

class ECHG(header='')

Bases: Grid2D

Class for ECHG. Initialization can be done by formatted string only. Otherwise call this object from upper block.

Parameters:

IDER (int) – Order of the derivative
NPY (int) – Number of points (MAPNET)

class POTM(header='')

Bases: Grid2D

Class for POTM. Initialization can be done by formatted string only. Otherwise call this object from upper block.

Parameters:

IDER (int) – Order of the derivative
ITOL (int) – Penetration tolerance
NPY (int) – Number of points (MAPNET)

class CLAS(header='')

Bases: Grid2D

Class for CLAS. Initialization can be done by formatted string only. Otherwise call this object from upper block.

Parameters:

IDER (int) – Order of the derivative
IFOR (int) – Number of point multipoles
charge (list) – Formal net charge
NPY (int) – Number of points (MAPNET)

class Grid3DBASE(header='')

Bases: BlockBASE

A base class for 3D data grid (ECH3, POT3). Not for ‘GRID3D’ keyword

Parameters:: header (str) – Formatted headers

scale(scale1='', scale2='', scale3='')

range(rg1='', rg2='', rg3=''): Inputs are 2*1 lists. [minvalue, maxvalue]. The sequence of rg123 is consistent with CRYSTAL (2D: z; 1D: y, z; 0D: x, y, z)

class ECH3(header='')

Bases: Grid3DBASE

Class for ECH3. Initialization can be done by formatted string only. Otherwise call this object from upper block.

Parameters:: NP (int) – Number of points along the first direction

class POT3(header='')

Bases: Grid3DBASE

Class for POT3. Initialization can be done by formatted string only. Otherwise call this object from upper block.

Parameters:

NP (int) – Number of points along the first direction
ITOL (int) – Penetration tolerance