********************************************************************************* ********************************************************************************* ********************** *************************** ********************** Documentation for TRACER *************************** ********************** *************************** ********************************************************************************* ********************************************************************************* PROGRAM AUTHOR - S. L. Lawton, Research Dept., Mobil Technology Company, P. O. Box 480, Paulsboro, New Jersey 08066-0480 U.S.A. TRACER - PROGRAM TO CHECK CELL =============================== TRACER: ------- Tracer by S.L. Lawton, A Lattice Transformation - Cell Reduction Program. The reduced cell is defined to be the unit cell with the smallest volume whose axes are the three shortest non-coplanar translations in the lattice. TRACER converts the cell parameters which you put in as input to the reduced cell. Such a reduction to a triclinic lattice with c < a < b and the angles alpha and beta as non-acute allows for the identification of the Bravais lattice of highest symmetry which it represents. This is accomplished by calculation of the scalar products A.A, B.B, C.C, B.C, C.A, A.B and comparison to matrices within the program. This is facilitated by using the reduced cell and considering all possible combinations of axial lengths in the 14 Bravais lattices. There exists only 43 independent cells whose axes correspond to the 3 shortest non-coplanar translations in the lattice. The one input parameter which might require clarification is the value of DEL to be used. Lawton reports that for lattice parameters with errors as low as 1 part in 10,000 Angstrom that a DEL = 0.10 is sufficient, while errors of the order of one part in 1000 Angstrom might require DEL values in the range of 0.50 to 1.00 (for Proteins use at least 1.0). The DEL value imposes the upper limit on the equivalence of special relationships between the scalar products used in the program. It essentially defines the absolute value of the largest allowable difference between any two of the six reduced cell scalar products. In as much as a DEL value to any extreme is undesirable it has been our practice to run TRACER using DEL values of 0.10, 0.50 and 1.00 in the same run and then examine the output as a function of these different DEL values. Usually the higher the standard deviation in the cell parameters the higher the DEL value that should be used. INPUT ------ ----line 1 Run number (terminates if equal to -1) ---- line 2 TITLE card ---- line 3 CONTROL input DEL CONTROL = 1 for direct space = 2 for reciprocal space cell dimensions DEL = Absolute value of the largest permissible difference between any two of the six reduced cell scalar products. ---- line 4 cell dimensions (free format) a, b, c, alpha, beta, gamma (Angstrom /degrees) ---- line 5 INSTRUCTION (format I3 !!!!!!!!!) This card(s) function as the commands to the program in transforming one cell to another. Each card contains an instruction. As many cards as necessary may be used to complete the desired successive transformations for any one compound. Their order specifies to the program the order in which the transformations are to be executed. The last instruction for a particular sequence of transformations must have either 7 or 8!!!! Both may not be present and neither may precede any with 1,,2,3,4,5,6. NQ = 7 triggers cell reduction. NQ = 8 merely identifies the last cell in a sequence to which a transformation is to be made with no cell reduction is performed. INSTRUCTIONS ============= NQ = 1 :Transform this cell to a new cell using a matrix supplied by the user on the corresponding transformation card. NQ = 2 :The initial cell is A-centred, transform to a primitive cell using a matrix held in subroutine CENTER NQ = 3 :..... B-Centred........ NQ = 4 :...... C-Centred ....... NQ = 5 :...... I-Centred ...... NQ = 6 :........ F-Centred ....... NQ = 7 :Get reduced cell and then identify and generate from it the unit cell of highest symmetry and its corresponding lattice parameters NQ=8 : This is a non-executive instruction notifying the program that no transformation is to be applied to this cell. This may be used for; (i) to calculate the inverse cell data of the input parameters, or (ii) to identify the name of the cell to which the previous cell is transformed when the previous cell in a transformation sequence involves any of NQ = 1,2,3,4,5,6) TRANSFORMATION cards each contains a 3 x 3 matrix one per card for each NQ = 1 in the order 1,1 1,2 1,3 2,1 2,2 2,3 3,1 3,2 3,3 INPUT FILE FORMAT ... The input file name is entirely the choice of the user. As an example, consider the file "test.dat" in the current directory. Format : line 1 : run number line 2 : title line 3 : control card TYPE and DEL TYPE=1 direct space input cell TYPE=2 reciprocal space input cell DEL= allowed error for transformation match DEL = 0.10, 0.50, 1.00 ie use three consective runs in one file line 4 : cell parameters line 5 : INSTRUCTION number (FORMAT I3 !!!!!!!) =1 you supply matrix =2 A to P =3 B to P =4 C to P =5 I to P =6 F to P =7 find reduced cell (normal value) if you use 1 then next line has a 3x3 matrix on it next line can be next run number and repeat input last line : -1 in columns 1 and 2 to terminate job all other lines FREE FORMAT. Contents of file "test.dat" ------------ 1 !run number test tracer ! title 1 0.1 ! real cell/ del 10.51 15.15 6.54 90 151.7 90 ! cell 4 ! supplied cell is C-faced 7 ! find reduced cell -1 ! terminate run ---------- OPERATIONAL DETAILS : To invoke the program, simply type "tracer" from a UNIX system or "run tracer" from a VMS system. Then, please insert the name of the input file and the name you wish to give to the output file, when you are prompted. The filename qualifier (".dat", ".out", etc.) should be included when the filename is typed in following the corresponding prompt. ---------------------------------------------------------------