CHARMM Element doc/crystl.doc 1.1#File: Crystl, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Calculations on Crystals using CHARMM The crystal section within CHARMM allows calculations oncrystals to be performed. It is possible to build a crystal with anyspace group symmetry, to optimise its lattice parameters and molecularcoordinates and to carry out a vibrational analysis using the options.* Menu:* Syntax:: Syntax of the CRYSTAL command* Function:: A brief description of each command* Examples:: Sample testcases* Implementation:: Background and implementation#File: Crystl, Node: Syntax, Up: Top, Next: Function[Syntax CRYStal command]CRYStal [BUILd_crystal] [CUTOff real] [NOPErations int] [DEFIne xtltyp a b c alpha beta gamma] [FREE] [PHONon] [NKPOints int] [KVECtor real real real TO real real real] [VIBRation] [READ] [CARD UNIT int] [PHONons UNIT int] [PRINt] [PRINt] [PHONons] [FACT real] [MODE int THRU int] [KPTS int TO int] [WRITe] [CARD UNIT int] [PHONons UNIT int] [VIBRations] [MODE int THRU int] [UNIT int]xtltyp ::= { CUBIc } { TETRagonal } { ORTHorhombic } { MONOclinic } { TRIClinic } { HEXAgonal } { RHOMohedral } { OCTAhedral/trnc} { RHDO }a b c alpha beta gamma ::= (six real numbers) The crystal module is an extension of the image facilitywithin the CHARMM program. All crystal commands are invoked by thekeyword CRYStal. The next word on the command line can be one of thefollowing :Build - builds a crystal.Define - defines the lattice type and constants of the crystal to bestudied.Free - clear the crystal and image facility.Phonon - calculates the crystal frequencies for a single value or a range of values of the wave vector, KVEC.Print - prints various crystal information.Read - reads the crystal image file.Vibration - calculates the harmonic crystal frequencies when the wave vector is the zero vector.Write - writes out to file various crystal information.#File: Crystl, Node: Function, Previous: Syntax, Up: Top, Next: Examples A brief description of each command follows.1. Crystal Build. A crystal of any desired symmetry can be constructed by repeatedlyapplying a small number of transformations to an asymmetric collection ofatoms (called here the primary atoms). The transformations include theprimitive lattice translations A, B and C which are common to all crystalsand a set of additional transformations, {T}, which determines the spacegroup symmetry. The Build command will generate, given {T}, a data structure of allthose transformations which produce images lying within a user-specifiedcutoff distance of the primary atoms. The data structure can then be usedby CHARMM to represent the complete crystal of the system in subsequentcalculations. The symmetry operations, {T}, are read from the linesfollowing the Crystal Build command. The syntax of the commmand is :Crystal Build Cutoff <real> Noperations <int>... <int> lines defining the symmmetry operations. The Cutoff parameter is used to determine the images which are includedin the transformation list. All those images which are within the cutoffdistance are included in the list. There is no limit to the number oftransformations included in the lists as they are allocated dynamically. The crystal symmetry operations are input in standard crystallographicnotation. The identity is assumed to be present so that (X,Y,Z) need notbe specified (in fact, it is an error to do so). For example, a P1crystal is defined by the identity operation and so the input would beCrystal Build .... Noper 0 whilst a P21 crystal would need the following input lines : Crystal Build .... Noper 1(-X,Y+1/2,-Z)A P212121 crystal is specified by Noper 3(X+1/2,-Y+1/2,-Z)(-X,Y+1/2,-Z+1/2)(-X+1/2,-Y,Z+1/2) It should be noted that in those cases where the atoms in theasymmetric unit have internal symmetry or in which a molecule is sitedupon a symmetry point within the unit cell not all symmetrytransformations for the crystal need to be input. Some will beredundant. It is up to the user to check for these cases and modifythe input accordingly.2. Crystal Define. The define command defines the crystal-type on which calculationsare to be performed. It is usually the first crystal command that isspecified in any job using the crystal facility. It has the format :Define lattice-type a b c alpha beta gamma The input lattice parameters are checked against the lattice-type toensure that they are compatible. Nine lattice types are permitted. Theyare listed below along with any restrictions on the lattice parameters :CUBIc - a = b = c and alpha = beta = gamma = 90.0 degrees. (example: 50.0 50.0 50.0 90.0 90.0 90.0 ) (volume = a**3) (degrees of freedom = 1)TETRagonal - a = b and alpha = beta = gamma = 90.0 degrees. (example: 50.0 50.0 40.0 90.0 90.0 90.0 ) (volume = c*a**2) (degrees of freedom = 2)ORTHorhombic - alpha = beta = gamma = 90.0 degrees. (example: 50.0 40.0 30.0 90.0 90.0 90.0 ) (volume = c*b*a) (degrees of freedom = 3)MONOclinic - alpha = gamma = 90.0 degrees. (example: 50.0 40.0 30.0 90.0 70.0 90.0 ) (volume = c*b*a*sin(beta) ) (degrees of freedom = 4)TRIClinic - no restrictions on a, b, c, alpha, beta or gamma. (example: 50.0 40.0 30.0 60.0 70.0 80.0 ) (volume = c*b*a*sqrt(1.0 - cos(alpha)**2 - cos(beta)**2 - cos(gamma)**2 + 2.0*cos(alpha)*cos(beta)*cos(gamma)) ) (degrees of freedom = 6)HEXAgonal - a = b, alpha = beta = 90.0 degrees and gamma = 120.0 (example: 40.0 40.0 120.0 90.0 90.0 120.0 ) (volume = sqrt(0.75)*c*a**2 ) (degrees of freedom = 2)RHOMbohedral - a = b = c ; alpha=beta=gamma<120 (trigonal) (example: 40.0 40.0 40.0 67.0 67.0 67.0 ) (volume =