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CRYSTALpytools.base.crysd12 module

The Crystal_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 Crystal_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 Crystal_inputBASE is listed below:

Layer 1: geom, basisset, scf

Layer 2: optgeom, freqcalc, hf3c, hfsol3c, dft, dftd3, gcp, geom, base, geba

Layer 3: preoptgeom

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

Examples

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

To set force convergence threshold of a optimization run:

>>> obj = Crystal_input()
>>> obj.geom.optgeom.toldeg(0.0001)

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 = Crystal_input()
>>> obj.geom.optgeom() # Initialize OPTGEOM
>>> obj.geom.optgeom(None) # Remove OPTGEOM

To set the values of keywords, their names are called as methods with a really rare exception (1 so far):

>>> obj.geom.freqcalc.preoptgeom() # Initialize PREOPTGEOM
>>> obj.geom.freqcalc.preoptgeom.toldeg(0.0003)
>>> obj.scf.toldee(9) # Set SCF TOLDEE = 9
>>> obj.scf.toldee(None) # Clean the TOLDEE keyword and value
>>> obj.scf.ppan() # Print PPAN keyword, without value

The only exception is given below. However, when doing text analysis and printing formatted string to files, the correct keyword is recognized and printed.

>>> obj.geom.molecule2() # MOLECULE keyword to extract molecule from lattice. Renamed to address the conflict with modelling keyword MOLECULE

Though one can set CRYSTAL input object by manually setting up all the attributes, it is also possible to read a template d12 file and do modifications.

>>> obj = Crystal_input('opt.d12')
>>> obj.geom.optgeom(None) # Remove OPTGEOM block
>>> obj.to_file('scf.d12') # 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.scf.dft('SPIN\nEXCHANGE\nPBE\nCORRELAT\nP86\n')

For basis set, it is not a typical BlockBASE object (though it inherits BlockBASE). When ‘BASISSET’ keyword is used, it is called in the same way as other blocks. When explicit definitions of basis set are used, it can be defined via formatted string, file, Basis Set Exchange (BSE) and BasisSetBASE object. The ending line ‘99 0’ is required.

>>> obj.basisset.basisset('def2-SVP')
>>> obj.basisset.from_file('mybasis.txt')
>>> obj.basisset.from_bse('6-311G*', [6, 1, 8]) # conventional atomic numbers are supported.

Wrapper methods (bs_user() and bs_keyword()) are added in Crystal_input. For details please checkt the manual there.

>>> obj.bs_keyword('def2-SVP')
>>> obj.bs_user('mybasis.txt')
>>> obj.bs_user('6-311G*', [6, 1, 8]) # bs_user accepts file, string and BSE variables

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

>>> print(obj.data)

Classes and methods of keywords used in ‘crystal’ input file (d12).

class Crystal_inputBASE(geba=False)

Bases: BlockBASE

The base class of Crystal_input class

Parameters:: geba (bool) – Whether it is a normal d12 object or a GEBA subblock

property geom: Geometry subblock

property basisset: Basis set subblock

property scf: SCF subblock

property data: Settings in all the attributes are summarized here.

analyze_text(data)

Analyze formatted d12 file. A ‘complete’ d12 file with geometry, basis set and SCF blocks is suggested.

Parameters:: data (str) – Formatted string.

class Geom

Bases: BlockBASE

Geometry block object

property data: Settings in all the attributes are summarized here. Covers the data property in BlockBASE, to address the ambiguity of ‘MOLECULE’ keywords.

analyze_text(text): Overrides the same method from parent class for title line.

title(title='Generated by CRYSTALpytools')

crystal(IGR='', latt=[], atom=[], IFLAG=0, IFHR=0, IFSO=0, origin=[])

Define ‘CRYSTAL’ structure

Parameters:

sg (int) – Space group number. Parameter IGR in the manual
latt (list) – Minimal set of crystallographic cell parameters
atom (list) – Natom * 4 list of conventional atomic number and 3D fractional coordinates.
IFLAG (int) – See the manual
IFHR (int) – See the manual
IFSO (int) – See the manual
origin (list) – IFSO > 1 See the manual

slab(IGR='', latt=[], atom=[]): Define ‘SLAB’ structure

polymer(IGR='', latt=[], atom=[]): Define ‘POLYMER’ structure

helix(N1='', N2=0, latt=[], atom=[])

Define ‘HELIX’ structure

Parameters:

N1 (int) – See the manual
N2 (int) – See the manual

molecule(IGR='', atom=[]): Define ‘MOLECULE’ structure

external(external=''): Define ‘EXTERNAL’ structure

dlvinput(dlvinput=''): Define ‘DLVINPUT’ structure

supercel(mx='')

Supercell by ‘SUPERCEL’ keyword

Parameters:: mx (array | list | str) – ndimen * ndimen matrix, None or ''

supercon(mx=''): Supercell by ‘SUPERCON’ keyword

scelconf(mx=''): Supercell by ‘SCELCONF’ keyword

scelphono(mx=''): Supercell by ‘SCELPHONO’ keyword

elastic(IDEF='', mx='')

atombsse(IAT='', NSTAR=None, RMAX=None)

atomdisp(NDISP='', atom=[])

ATOMDISP keyword

Parameters:

NDISP (int) – See manual
atom (list) – NDISP*4 list. Including LB, DX, DY, DZ

atominse(NINS='', atom=[])

ATOMINSE keyword

Parameters:

NINS (int) – See manual
atom (list) – NINS*4 list. Including NA, X, Y, Z

atomorde(atomorde='')

atomremo(NL='', atom=[])

ATOMREMO keyword

Parameters:

NL (int) – See manual
atom (list) – NL*1 list. Including LB

atomsubs(NSOST='', atom=[])

ATOMSUBS keyword

Parameters:

NSOST (int) – See manual
atom (list) – NSOST*2 list. Conventional atomic number of atoms to be substituted and to substituted

molecule2(NMOL='', atom=[])

Note

Corresponds to the option MOLECULE to isolate molecules from lattice. Only the method’s name is changed to avoid ambiguity with the one to set 0D geometry.

Parameters:

NMOL (int)
atom (list[list[int]]) – NMOL*4 list. See CRYSTAL manual.

extprt(extprt='')

cifprt(cifprt='')

cifprtsym(cifprtsym='')

coorprt(coorprt='')

testgeom(testgeom='')

property optgeom: Subblock object OPTGEOM

property freqcalc: Subblock object FREQCALC

class Optgeom

Bases: BlockBASE

OPTGEOM block object

fulloptg(fulloptg='')

cellonly(cellonly='')

intredun(intredun='')

itatocel(itatocel='')

cvolopt(cvolopt='')

hessiden(hessiden='')

hessmod1(hessmod1='')

hessmod2(hessmod2='')

hessnum(hessnum='')

toldeg(TG=0.0003)

toldex(TX=0.0012)

toldee(IG=7)

maxcycle(MAX=50)

fragment(NL='', LB=[])

Parameters:

NL (int | str) – Number of atoms. See manual
LB (list[int]) – Label of atoms. See manual

restart(restart='')

finalrun(ICODE=4)

extpress(pres='')

allowtrustr(allowtrustr='')

notrustr(notrustr='')

maxtradius(TRMAX=4.0)

trustradius(TRADIUS=0.5)

onelog(onelog='')

noxyz(noxyz='')

nosymmops(nosymmops='')

printforces(printforces='')

printhess(printhess='')

printopt(printopt='')

print(prt='')

tsopt(tsopt='')

modefollow(MODEFOL='')

pathfollow(NPATHFOL='')

fittopath(NPATHFOL2='', NPATHWEIGHT='')

chngtsfol(chngtsfol='')

scanatom(NATSCAN='', TARGET='', MSCAN='')

scanredu(IREDSCA='', ENDSCA='', MAXSCA='')

class Freqcalc

Bases: BlockBASE

FREQCALC block object

nooptgeom(nooptgeom='')

property preoptgeom: Subblock object PREOPTGEOM

dispersion(dispersion='')

bands(ISS='', NSUB=None, NLINE=None, points=[])

modes(modes='')

nomodes(nomodes='')

numderiv(N=1)

pressure(NP='', P1=None, P2=None)

restart(restart='')

stepsize(STEP=0.003)

temperat(NT='', T1=None, T2=None)

class BasisSet

Bases: BlockBASE

Basis Set block object

property data: Settings in all the attributes are summarized here. Covers the data property in BlockBASE, to deal with user’s definition of basis sets.

analyze_text(text): Analyze the input and return to corresponding attributes. Add support to basis set strings

basisset(NAME='')

ghosts(NA='', LA=[])

from_bse(name, z, append=False)

Download basis set definitions from Basis Set Exchange (BSE).

Parameters:

name (str) – Basis set’s name.
z (list[int]) – List of elements, specified by conventional atomic numbers.
append (bool) – Whether to cover old entries. If the old entry contains ‘BASISSET’, it will be removed anyway. Useful when different series of basis sets are defined

from_string(string, fmt='crystal', append=False)

Basis set from a string

Parameters:

string (str) – Basis set definition.
fmt (str) – Format string. Consistent with BSE python API. For non-CRYSTAL formats, only all-electron basis sets are supported. Charge of each shell will be automatically assigned to get charge neutral atoms.
append (bool) – Whether to cover old entries. If the old entry contains ‘BASISSET’, it will be removed anyway. Useful when different series of basis sets are defined

from_file(file, fmt='crystal', append=False)

Basis set from a file

Parameters:

file (file) – Basis set definition.
fmt (str) –
Format string. Consistent with BSE python API. For non-CRYSTAL formats, only all-electron basis sets are supported. Charge of each shell will be automatically assigned to get charge neutral atoms.
append (bool) – Whether to cover old entries. If the old entry contains ‘BASISSET’, it will be removed anyway. Useful when different series of basis sets are defined

from_obj(bs_obj, append=False)

Define basis set from a base.basisset.BasisSetBASE object.

Parameters:

bs_obj (BasisSetBASE)
append (bool) – Whether to cover old entries. If the old entry contains ‘BASISSET’, it will be removed anyway. Useful when different series of basis sets are defined

class SCF

Bases: BlockBASE

SCF block object

property data: Print formatted input. Redefined to address the END keywords of FIXINDEX blocks

rhf(rhf='')

uhf(uhf='')

rohf(NSPIN='')

property dft: Subblock object DFT

property hf3c: Subblock object HF3C

property hfsol3c: Subblock object HFSOL3C

property dftd3: Subblock object DFTD3

property gcp: Subblock object GCP

gcpauto(gcpauto='')

atomspin(NA='', LA=[])

toldee(ITOL=6)

guessp(guessp='')

maxcycle(MAX=50)

ldremo(value='')

smear(WIDTH='')

levshift(ISHIFT='', ILOCK='')

shrink(IS='', ISP='', IS1='', IS2='', IS3=''): Shrink parameters.

tolinteg(ITOL1=7, ITOL2=7, ITOL3=7, ITOL4=7, ITOL5=14)

biposize(ISIZE=4000000)

exchsize(ISIZE=4000000)

bipolar(ITCOUL=18, ITEXCH=14)

nobipola(nobipola='')

nobipcou(nobipcou='')

nobipexc(nobipexc='')

fmixing(IPMIX=30)

diis(diis='')

nodiis(nodiis='')

diisallk(diisallk='')

sloshing(sloshing='')

histdiis(NCYC='')

thrediis(DEDIIS='')

thrkdiis(DIISTHR='')

sloshfac(FKERK=1.2)

prtdiis(prtdiis='')

anderson(anderson='')

broyden(W0=0.0001, IMIX=50, ISTART=2)

ppan(ppan='')

gradcal(gradcal='')

exchange(exchange='')

postscf(postscf='')

cmplxfac(WEIGHT=2.0)

repldata(repldata='')

stdiag(stdiag='')

fixindex(fixindex=''): Fixindex keywords.

Note

‘GEOM’ is a Geom object. To modify keywords (‘CRYSTAL’ as example), use input.scf.geom.crystal().

‘BASE’ is a BasisSet object. To define basis set from bse, use input.scf.base.from_bse().

‘GEBA’ is a Crystal_inputBASE object. To modify keywords (‘CRYSTAL’ as example), use input.scf.geba.geom.crystal().

property geom: Subblock object GEOM

property base: Subblock object BASE

property geba: Subblock object GEBA

class HF3C

Bases: BlockBASE

HF3C block object

rescales8(s8='')

scalegcp(gcp='')

class HFSOL3C

Bases: HF3C

HFSOL3C block object

class DFT

Bases: BlockBASE

DFT block object

spin(spin='')

exchange(ex='')

correlat(cor='')

xcfunc(xc='')

sr_omega(sr_omega='')

mr_omega(mr_omega='')

lr_omega(lr_omega='')

sr_hyb_wb97x(sr_c='')

lsrsh_pbe(omega='', sr_c=0.0, lr_c=0.0)

lgrid(lgrid='')

oldgrid(oldgrid='')

xlgrid(xlgrid='')

xxlgrid(xxlgrid='')

xxxlgrid(xxxlgrid='')

hugegrid(hugegrid='')

radial(NR='', RL=[], IL=[])

angular(NI='', AL=[], LEV=[])

class DFTD3

Bases: BlockBASE

DFTD3 block object

version(NAT=4)

func(CHAR='')

abc(abc='')

s6(s6='')

s8(s8='')

a1(a1='')

a2(a2='')

rs6(rs6='')

rs8(rs8='')

radius(radius='')

cnradius(cnradius='')

abcradius(abcradius='')

printc6(printc6='')

class GCP

Bases: BlockBASE

GCP block object

method(method='')

sigma(sigma='')

alpha(alpha='')

beta(beta='')

eta(eta='')

radius(radius='')

printemiss(printemiss='')