CONFLEX Manual

Crystal Structure Optimization keywords

Keyword	Options	Description
CRYSTAL		Crystal calculation will be performed.
SPACE_GROUP=	P1 P21 P212121 etc...	Specify space group by the Hermann-Mauguin symbol. For details, see the tutorials.
SPGP_SUBINFO=		Monoclinic space group settings; Default is ‘B’.
	B	Monoclinic cell with the B unique axis (α, γ= 90.0°)
	C	Monoclinic cell with the C unique axis (α, β= 90.0°).
		Origin setting; Default is ‘1’.
	1	origin choice 1
	2	origin choice 2
		Trigonal space group settings: Default is ‘H’
	R	Trigonal system using rhombohedral axes (a=b=c, α=β=γ≠90°,<120°)
	H	Trigonal system using hexagonal axes (a=b≠c, α=β=90°,γ=120°)
LATTICE_CONSTANT=	(a,b,c,α,β,γ)	Definition of lattice constants.
CRYSTAL_OPTIMIZATION= Default: ALL		Crystal optimization setting.
	MOL	The geometry, orientation, and translation of molecules in the crystal are optimized. The lattice constants do not change.
	RIGID	The orientation and translation of molecules in the crystal and the lattice constants are optimized. The molecular geometry does not change.
	ALL	The geometry, orientation and translation of molecules in the crystal and the lattice constants are optimized.
	NONE	Crystal structure optimization will not be performed.
REMOVE_NEV=	YES NO	If the optimized structure has imaginary frequency, the structure is deformed and is subjected to the geometry optimization again to obtain the equilibrium structure. (This is available when the full diagonal Newton-Raphson method is selected as the optimization method.) Default: NO (NO re-optimization)
CRYSTAL_RADIUS= Default: 20.0 (Å)	f.ff	Specify range of intermolecular interaction calculation. The setting value is reflected both on “VDW_CUTOFF=” and on “COULOMBIC_CUTOFF=”.
VDW_CUTOFF= Default: 20.0 (Å)	f.ff	Specify cutoff value for van der Waals interaction calculation.
COULOMBIC_CUTOFF= Default: 20.0 (Å)	f.ff	Specify cutoff value for coulombic interaction calculation.
COULOMBIC_TYPE=	EWALD CUTOFF	Specify method of Coulomb interaction calculation. EWALD: Ewald method CUTOFF: Cutoff method Default: EWALD
EWALD_RECIP_CUTOFF=	f.ff	Specify cutoff value for reciprocal lattice space in Ewald calculation. By default, the program automatically decides based on the cutoff value in real space.
EWALD_PARAM=	f.ff	Specify convergence parameter in Ewald calculation. By default, the program automatically decides based on the cutoff value in real space.
EWALD_PRECISION=	f.ff	The convergence parameter and the cutoff value for reciprocal lattice space in Ewald calculation are automatically determined so that energy value is smaller than the value specified by this keyword, based on the cutoff value in real space. Default: 1.0E-8
EWALD_SURFACE_TERM=	ON OFF	Specify whether or not to include Surface term into Ewald calculation. Default: OFF (omit the term)
INTER_ENERGY= Default: HALF	HALF FULL	Set coefficient for the term of intermolecular interaction energies between original molecule(s) and replica unit as to be either 1/2 (HALF) or 1.0 (FULL).
CRYSTAL_RESETUP_CONVERGE= Default: 1.0E-10	ff.ff	This keyword controls reconstruction of crystal structure in optimization. In each optimization step, if RMS average of energy gradients is less than the specified threshold (ff.ff kcal/mol/Å), the reconstruction of crystal structure is skipped.
SUPERCELL=	(l,m,n)	Create supercell. The supercell is defined by basis lattice vectors, A, B, C, which are respectively represented by integral multiples of basis lattice vectors, a, b, c, of original unit cell, i.e. A=la, B=mb, C=nc. The supercell has P1 symmetry. For example, “(2,2,1)” makes 2x2x1 supercell by replicating the original unit cell along the a and b axes.
MAKEP1CELL		Create a unit cell which has P1 symmetry. This keyword is corresponding to “SUPERCELL=(1,1,1)”. See above.
CIF_BOND= Example: CIF_BOND=(1,2,2)	(I,J,K)	Bond between I and J atoms with K-bond type in using CIF file. K=1: Single K=2: Double K=3: Triple
CIF_FCHARGE= Example: CIF_FCHARGE=(1,-1)	(I,K)	Put a formal charge K on I atom in using CIF file.
BOND_LENGTH=	(m,I,J,ff.ff)	Modification of bond length. When m=0, I and J indicate serial number in model. Atom J position is adjusted along vector from atom I to atom J, and bond length between I and J atoms is converted to ff.ff. When m=1, I and J are atomic number. Atomic number J positions are adjusted along vector from atomic number I to atomic number J, and all bond lengths between defended atomic elements are converted to ff.ff. For example, in the case of “(1,8,1,0.983)”, all bond length between hydrogen atom and oxygen atom are converted to 0.983 by adjusting hydrogen atom positions.
HYGEN_LENGTH		All lengths of bond which have covalently attached hydrogen atom are converted to equivalent bond lengths in using force field by adjusting hydrogen atom positions.
RADIATION= Default: CU	CU MO etc...	Specify element of X-ray source. CU: Copper Kα1 (wave length: 1.54059290 Å) MO: Molybden Kα1 (wave length: 0.70931715 Å)
RADIATION_WAVELENGTH=	ff.ff	Definition of a wave length of radiation. Example: If you want to use Copper Kα1 radiation for calculating diffractogram, set up as follows. RADIATION_WAVELENGTH=1.54059290 (Same with copper Kα1)
TWOTHETA= Default: TWOTHETA=(0.0,50.0,0.02)	(f1,f2,f3)	Range of 2θ and incremental step width settings. f1: Starting point in degree f2: Terminal point in degree f3: Incremental step width in degree
INTENSITY_SCALING= Default: 10000.0	ff.ff	Definition of a value of the highest intensity in the diffraction peaks.
PVOIGT_ETA= Default: 0.5	f.ff	Definition of a value of Lorentz-polarization factor in the pseudo-voigt function.
PVOIGT_HK= Default: 0.1	f.ff	Definition of a value of full width at half maximum in the pseudo-voigt function.
PRESSURE_EFFECT		A crystal calculation is performed under a finite pressure. This option is available for crystals in the triclinic, monoclinic, and orthorhombic systems. The energy is estimated by an enthalpy. (H = E_crystal + PV, or H = E_lattice + PV)
PRESSURE= Default: 0.0001 GPa.	f.ff	Specify value of pressure in unit of GPa. If you use this option, you don't need to additionally write “PRESSURE_EFFECT” keyword in the ini file.
USE_CHARGE_GROUP= Default: OFF (not use)	ON OFF	Definition of whether use molecular cutoff method based on charge groups.
CRYSTAL_CHARGE_GROUP=	(dd,dd)	Definition of charge groups. For example, if user want to treat all molecules in the asymmetric unit as one group when the number of molecules in the asymmetric unit is 3, CRYSTAL_CHARGE_GROUP=(1,1) CRYSTAL_CHARGE_GROUP=(2,1) CRYSTAL_CHARGE_GROUP=(3,1) Default: Neutral molecules are defined as different charge group each other. Ionic molecules belong to one charge group.
CRYSTAL_FIXED_MOL=	n EXCLUDE_HYDROGEN	Structure and position of a molecule with molecular ID n in asymmetric unit are frozen during crystal structure optimization of “CRYSTAL_ OPTIMIZATION=MOL”. Example 1: Freezing of structure and position of molecule with molecular ID 1. CRYSTAL_FIXED_MOL=1 Example 2: Freezing of structure and position of molecule with molecular ID 1, but hydrogen atom positions in the molecule to be optimized. CRYSTAL_FIXED_MOL=1 CRYSTAL_FIXED_MOL=EXCLUDE_HYDROGEN

Crystal Structure Prediction related keywords

Keyword	Options	Description
CRYSTAL_SEARCH		Crystal structure search will be performed.
CSP_MODE= Default: MOLECULE	CRYSTAL	When a crystal structure is used as input for crystal structure search, CSP_MODE should be set to CRYSTAL. Trial crystal structures will be generated by rotating molecule(s) in asymmetric unit. Space group, lattice constants, molecular spatial position in asymmetric unit of the trial crystal structures will be set to them of the input crystal structure.
CSP_MODE= Default: MOLECULE	MOLECULE	When isolated molecule or molecular complex (not crystal) is used as input for crystal structure search, CSP_MODE should be set to MOLECULE.
CSP_SEARCH= Default: ENERGY	ENERGY	Found crystal structures will be ranked according to their crystal energies. The crystal structure with the lowest crystal energy is 1st rank.
CSP_SEARCH= Default: ENERGY	POWDER_PATTERN	Found crystal structures will be ranked according to their similarities between their calculated powder patterns and reference powder pattern. The crystal structure with the highest similarity is 1st rank.
CSP_OPT= Default: NEWTON		Specify method of crystal structure optimization in the search (you can also set that by “OPT=” keyword).
	NEWTON	Full diagonal Newton-Raphson method
	CONGRD	Conjugate gradient method
	CONGRD-NEWTON	The conjugate gradient and full-diagonal Newton-Raphson methods are used. The threshold for switching from the conjugate gradient method to the full-diagonal Newton-Raphson method is set by “CSP_CNOPT=” keyword.
CSP_CNOPT= Default: (1.0E-1,1.0E-2)	(Gconverg,Xconverg)	In the crystal structure optimization with “CSP_OPT=CONGRD-NEWTON”, the optimization method will switch from the conjugate gradient method to the full-diagonal Newton-Raphson method when the gradient (Gconverg) and displacement (Xconverg) become less than the thresholds specified by this keyword.
CSP_LATTICE=	(a,b,c,α,β,γ)	Lattice constants of trial crystal structures generated in crystal structure search are set to these values. When this keyword is used, the lattice constants do not change in the structure optimization in the search. Therefore, the atomic positions in unit cell will be searched.
CSP_LATTICE_RESTRAIN		Lattice constants are not optimized in crystal structure search.
CSP_LATTICE_NORESTRAIN		Lattice constants are optimized in crystal structure search.
CSP_SPGP= Default: CSP_SPGP=(P21/C,P212121)	P1 P21 P212121 etc...	Definition of search space within space group symmetry. If you want to run a structure search in P21/c, P212121, and P21 space group symmetries, “CSP_SPGP=(P21/C,P212121,P21)” should be wrote in ini file.
CSP_MAX_CRYSTAL= Default: 200	n	Definition of the number of trial crystal structures generated in crystal structure search with "RANDOM" option.
CSP_LIMIT_MAXCRYSTAL= Default: 30000	n	Definition of limit value for the number of trial crystal structures generated in crystal structure search.
CSP_RSTEP= Default: CSP_RSTEP=30.0	ff.ff	Specify step width in degree for performing molecular rotation.
CSP_RUN_SEED= Default: -1000	-n	Random seed setting. This value must be set to a negative number.
CSP_PREOPT= Default: ON	ON OFF	Definition of optimization for input structure before performing crystal structure search. ON: The input structure will be optimized. OFF: The input structure is not optimized.
CSP_DEBUG=	INITIAL	Trial crystal structures generated in crystal structure search will be outputted as CIF file format.
CSP_DEBUG=	FINAL	Optimized crystal structure will be outputted as CIF file format after the optimization finished.
CSP_ROT_MODE= Default: GRID		Selection of crystal structure search method for performing molecular rotation. The step width of molecular rotation is specified by CSP_RSTEP keyword.
	RANDOM	Molecule(s) in asymmetric unit will be rotated randomly.
	GRID	Molecule(s) in asymmetric unit will be systematically rotated.
CSP_AUS_MODE= Default: FULL		Selection of crystal structure search method for deciding initial molecular spatial position in unit cell.
	RANDOM	Molecular spatial positions will be decided randomly.
	FULL	All available molecular spatial positions within space group symmetry will be considered.
CSP_RESTART		A crystal structure search that was performed previously can be restarted.
CSP_REOPT= Default: OFF	ON OFF	ON: The crystal structures that was optimized in the previous search will be optimized again in the restarted search. OFF: The crystal structures that was optimized in the previous search are not optimized in the restarted search.
CSP_ROT_UNIT=		Definition of treatment of molecule(s) in asymmetric unit. Default: If CSP_MODE=CRYSTAL, CSP_ROT_UNIT=MOLECULE. If CSP_MODE=MOLECULE, CSP_ROT_UNIT=COMPLEX.
	MOLECULE	The molecule(s) in the asymmetric unit will be rotated respectively in the generation of trial crystal structures.
	COMPLEX	The molecule(s) in the asymmetric unit will be treated as one molecular complex. Thus, the molecular rotation will be adapted to the molecular complex.
CSP_NOROT_AXIS=	(n1,n2,n3)	Definition of molecular rotation around the x, y, and z axes. n1: molecular rotation setting around the x axis. (1 or 0) n2: molecular rotation setting around the y axis. (1 or 0) n3: molecular rotation setting around the z axis. (1 or 0) 1: molecular rotation around the axis is not performed. 0: molecular rotation around the axis will be performed. If you want to fix molecular rotation around the x axis, CSP_NOROT_AXIS should be set to (1,0,0).
CSP_NOROT_MOL=	n	A molecule with the molecular ID n in asymmetric unit is not rotated in the generation of trial crystal structures.
CSP_ROT_MOL=	n	A molecule with the molecular ID n in asymmetric unit will be rotated in the generation of trial crystal structures.
CSP_NOROT_ALLMOL		All molecules in asymmetric unit are not rotated in the generation of trial crystal structures.
CSP_ROT_ALLMOL		All molecules in asymmetric unit will be rotated in the generation of trial crystal structures.
CSP_PXRD_COMPARISON= Default: SIMILARITY	SIMILARITY RWP	Select method for comparing between calculated and reference powder X-ray diffraction patterns. RWP: Rwp factor is used. SIMILARITY: Similarity between patterns is used and it is calculated by Gelder's method. (J. Comput. Chem. 22, 3, 273, 2001)
SIMILARITY_L= Default: 2.0	ff.ff	Set parameter 𝓁 of the Gelder's equation.
CSP_GROUPING= Default: NO	YES NO	The structures obtained from the crystal structure search are grouped based on the similarity of the powder X-ray diffraction patterns. The similarity will be calculated by Gelder's method (J. Comput. Chem. 22, 3, 273, 2001).
CSP_GROUPING_GLIMIT= Default: 0.8	ff.ff	Structures related by similarity value greater than the value defined by this keyword will be belonged to same group.
CSP_GROUPING_ELIMIT= Default: 5.0	ff.ff	Set a relative energy value from the lowest energy. Structures with relative energy value lower than the value defined by this keyword are subjected to the grouping process. This keyword is available for “CSP_SEARCH=ENERGY”.
CSP_GROUPING_SLIMIT= Default: 0.7	ff.ff	Structures with similarity value greater than the value defined by this keyword are subjected to the grouping process. This keyword is available for “CSP_SEARCH=POWDER_PATTERN”.
CSP_GROUPING_L= Default: 0.6		Set parameter 𝓁 of the Gelder's equation for the grouping process.
CSP_DCHK= Default: YES	YES NO	Exclude structures with low packing density among structures obtained by a crystal structure search.

Crystal Surface Analysis Keywords

Keyword	Options	Description
CRYSTAL_PLANE=	(h,k,l)	Crystal plane (hkl) can be specified. Example: CRYSTAL_PLANE=(1,0,0)
CRYSTAL_PLANE_STATE= Default: IN	IN ON	State of target molecule for energy calculation can be specified. IN: The molecule “in” the crystal plane ON: the molecule “on” the crystal plane
CRYSTAL_PLANE_TRANS=	ff.ff	Horizontal position of interface can be specified. If not given, this value is automatically set. Example: CRYSTAL_PLANE_TRANS=1.0
CRYSTAL_PLANE_BASE=	n	Target molecule for energy calculation can be specified. If not given, the molecule is automatically set. Example: CRYSTAL_PLANE_BASE=1
CRYSTAL_PLANE_PRINT= Default: OFF	ON OFF	Information of candidates which are available to select as the target molecule be output (ON) or not (OFF).