THMA11 - Instructions
Instructions for THMA11 program
INSTRUCTIONS FOR PROGRAM THMA11
FOR THERMAL MOTION ANALYSIS, INCLUDING INTERNAL TORSION
################## SUMMARY OF INPUT ###################
Approx Line in
Line # Parameters Writeup on VAX*
1. Title (First 4 letters = FREE if free format input) 1000
2. 6 cell dimen, IFMX, IFMB, ETA, DIS (up to 10 quantities) 1035
3. CONTROL LINE:
NTOT,NO,ISET,IB,NONRIG,NVIB,NS,ISIG,ISYM,ICORL,IWU,
IFU,ICSVIB (up to 13 quantities) 1600
4A. FIRST OPTION LINE: 3215
TEMP,IRECAL,ISIGX,IRIDE,IMIN,IUNC (up to 6 quantities) 3285
4B. SECOND OPTION LINE:
IFREQ,IATWT,IEIG,IMAT,IOUT,CONSLV (up to 6 quantities) 3495
(IFREQ is new as of 20.I.87)
(4C. infrequently used; only if ISET>5; see CONTROL line 3) 4010
5A,5B. Pairs of lines for atomic parameters: 4275
5A. x, y, z, ATOMNAME, WEIGHT, MULT (order depends 4285
on format used; see lines 1 and 2)
5B. ANISOTROPIC Displacement Parameters (order may vary
with format used; see lines 1 and 2), NUORB 5285
(5C. ISIG lines of SIGMAS of displacement parameters;
if NO SIGMAS input, ISIG = 0; see CONTROL line (3)) 5465
(6A. NAFA,LBAT1,LBAT2,NONSY,AXMOM; and 5605, 5745
(6B. a total of NAFA names; 6A and 6B may be omitted, 6010
depending on NONRIG, see CONTROL line 3)
((6C. LBAT3,LBAT4,LBAT5; may omit depending on NAFA, see
line 6A)) 6050
(6D. Pairs of atom names; may be omitted, depending on 6100
IRIDE; see OPTION line 4A) 6105
(6E. Pairs of atom names; may be omitted, depending on
IMIN; see OPTION line 4A) 6180
(6F. Pairs of atom names and equivalent positions; may be
omitted, depending on IUNC; see OPTION line 4A) 6215
(7. SYML(I), I=1,3 May be omitted, depending on ISYM;
see CONTROL line (3)) 6345
(8A. NVIB pairs of atom names and equivalent positions,
if NVIB is positive; see CONTROL line 3) 6430
(8B. 2xICSVIB lines if ICSVIB is not 0; see CONTROL line 3) 6600
(9, 10 etc. Data for another calculation or for another compound;
whether these lines are called for depends on NS (CONTROL line
3) and IRECAL (OPTION line 4a))
* Approximate line numbers if you sequence lines from 100 by 5.
NOTE that the minimum input is five lines plus NTOT pairs of
atomic parameter lines. Other input may be required depending on
the values of ISET,NONRIG,NVIB,NS,ISIG,ISYM,ICSVIB,IRECAL,ISIGX,
IRIDE,IMIN,IUNC and NAFA.
################ END OF SUMMARY OF INPUT #################
***!!!! CAUTION !!!!*** OLD INPUT WILL NEED MODIFICATION **
MAJOR CHANGES IN INPUT THAT EARLIER USERS SHOULD NOTE IF THEY ARE
TRYING TO RUN JOBS ASSEMBLED PREVIOUSLY:
1. TWO NEW INPUT LINES, THE "OPTION LINES", HAVE BEEN ADDED AFTER
THE "CONTROL LINE". SOME OPTIONS THAT WERE FORMERLY GOVERNED
BY NEGATIVE OR OTHER SPECIAL VALUES ON THE CONTROL LINE ARE
NOW GOVERNED BY INPUT ON THE "OPTION LINE". THESE INCLUDE:
TEMPERATURE OTHER THAN THE DEFAULT TEMP OF 296 K
ESD'S OF X,Y,Z INTERMIXED WITH ESD'S OF U'S
RECALCULATION WITH THE SAME INPUT ATOMIC PARAMETERS
BYPASSING THE GENERATION OF ATOMIC WTS BY THE PROGRAM
FREQUENCY AND RELATED CALCULATIONS ARE NO LONGER DONE
AUTOMATICALLY; THEY CAN BE DONE BY APPROPRIATE SETTING
OF THE NEW VARIABLE IFREQ ON 2nd OPTION LINE. THE
RESULTS OF SUCH CALCULATIONS SHOULD, IN ANY EVENT, BE
VIEWED WITH GREAT SKEPTICISM.
SEVERAL NEW OPTIONS HAVE BEEN ADDED, INCLUDING PROVISION FOR
CALC OF RIDING-MOTION, MINIMUM-MOTION AND INDEPENDENT-
MOTION CORRECTIONS TO SELECTED INTERATOMIC DISTANCES.
RIDING MOTION CORRECTIONS AND CORRECTIONS FOR ANHARMONICITY
OF THE POTENTIAL FUNCTION ARE AUTOMATIC FOR BONDS TO
(ANISOTROPIC) HYDROGEN OR DEUTERIUM ATOMS.
CAUTION: IF THE "ANHARMONIC" CORRECTION IS POSITIVE, THE DATA
ARE SUSPECT; IT WILL BE POSITIVE WHENEVER THE H OR D HAS A
LOWER MSDA THAN THE "HEAVY ATOM" TO WHICH IT IS BONDED (e.g.,
C, N, O) ALONG THE BONDING DIRECTION. NORMALLY THE MSDA IN
THIS DIRECTION FOR H OR D SHOULD BE 40-60 pm**2 LARGER THAN
THAT OF THE C, N OR O TO WHICH IT IS BONDED. WHEN NVIB IS
NEGATIVE, CHECK THE PRINTED MSDA MATRIX CONCERNING THIS POINT.
[Reference for anharm corrn: Jeffrey and Ruble, Trans. ACA,
20, 129-131 (1984) -- Lexington meeting reports]
2. DEFAULT IS TO INCLUDE INTERNAL AND OVERALL CORRELATIONS IF
INTERNAL LIBRATION IS INCLUDED. TO BYPASS THESE CORRELATIONS
NOW, MAKE ICORL (FORMERLY "IFP") NEGATIVE
SEE INSTRUCTIONS FOR LINE 3 ('CONTROL LINE')
3. THE PARAMETER NRBCON(I), FORMERLY INCLUDED IN THE "NON-RIGID
BODY INPUT", HAS BEEN ABANDONED. IT WAS PHYSICALLY MEANING-
LESS, WAS USEFUL ONLY FOR DEBUGGING, AND CAUSED CONFUSION.
4. FREE-FORMAT INPUT IS NOW USED THROUGHOUT EXCEPT THAT, FOR
ATOMIC POSITION AND DISPLACEMENT PARAMETERS AND THEIR ESDS,
IT IS OPTIONAL, SO THAT PARAMETER SETS FROM OTHER PROGRAMS
MAY BE USED WITHOUT THE NEED TO ADD APOSTROPHES TO ATOM
NAMES (CHARACTER STRINGS MUST HAVE ' ' IN FREE FORMAT).
******************************************************************
RESTRICTION ON THIS VERSION:
1. NO MORE THAN 7 "ATTACHED RIGID GROUPS" (ARG'S; CALLED 'NON-RIGID
GROUPS' IN EARLIER VERSIONS) IF THE POINT GROUP FOR THE MOLECULE
IS CENTROSYMMETRIC, OR 6 IF IT IS ACENTRIC.
2 NO ATOM MAY BE AFFECTED BY THE MOTION OF MORE THAN THREE ATTACHED
RIGID GROUPS.
******************************************************************
THIS VERSION USES THE QUADRATIC APPROXIMATION OF
SCHOMAKER AND TRUEBLOOD (1968), ACTA CRYST. B24, 63-76, FOR THE
RIGID-BODY MOTION AND THE APPROXIMATION OF DUNITZ AND WHITE
(1973), ACTA CRYST. A29, 93-94, FOR THE LIBRATION OF ATTACHED
RIGID GROUPS ON THE MOLECULE, INCLUDING CORRELATIONS OF THE
INTERNAL AND OVERALL MOTION (SCHOMAKER and TRUEBLOOD, 1984, 1987)
For discussion of force constants, frequencies and barriers
see also Trueblood and Dunitz (1983) Acta Cryst. B39,
120-133.
**************************************************************
INPUT INSTRUCTIONS
**************************************************************
DATA LINES
###################################################################
# ATOM NAMES ARE INCLUDED IN INPUT WITH ATOM PARAMETERS AND ARE #
# LATER USED TO IDENTIFY ESD LINES AND FOR VARIOUS INSTRUCTIONS. #
# THESE LATER NAMES MUST BE IDENTICAL, INCLUDING SPACES (E.G., #
# LEFT ADJUSTMENT), TO THOSE USED INITIALLY. IF NOT, THERE MAY #
# BE AN ERROR MESSAGE, OR JUST AN UNEXPLAINED FAILURE (E.G., A #
# DIVIDE-BY-ZERO STOP, BECAUSE THE PROGRAM COULD NOT FIND THE #
# ATOM YOU THOUGHT YOU WERE DESIGNATING). #
###################################################################
(1) TITLE LINE FORMAT(10(2A4))
IF COLS 1-4 OF TITLE LINE ARE FREE
FREE-FORMAT INPUT ASSUMED FOR ATOMIC PARAMETERS
AND ESDS, AS WELL AS FOR ALL OTHER INPUT.
(THESE FOUR CHARACTERS WILL NOT BE PRINTED AS PART OF TITLE.)
(2) SIX CELL DIMENSIONS, IFMX, IFMB, ETA, DIS
NOW ALWAYS FREE FORMAT ('LIST DIRECTED INPUT')
WITH LIST-DIRECTED INPUT, NEED ONLY SEPARATE ITEMS BY SPACES, BY
COMMAS, OR BY SPACES AND COMMAS. USE / TO TERMINATE LIST IF ALL
ITEMS ARE NOT INCLUDED (E.G., IF SOME ARE DEFAULT ZEROS).
OPTIONS
CELL DIMENSIONS:
1) REAL CELL WITH EITHER ANGLES OR COSINES OF ANGLES
SEQUENCE A,B,C,ALPHA,BETA,GAMMA OR A,B,C,COS(ALPHA),
COS(BETA),COS(GAMMA)
2) RECIPROCAL CELL WITH EITHER ANGLES OR COSINES OF ANGLES
SEQUENCE ANALOGOUS TO THAT FOR REAL CELL
IFMX, IFMB ARE INPUT FORMAT CONTROLS FOR ATOMIC PARAMETERS
(THEY ARE IRRELEVANT IF FREE-FORMAT INPUT USED)
IFMX = 0 FORMAT FOR X,Y,Z IS A4,23X,3F9.6,2F5.1
FOR NAME, X,Y,Z, ATOMIC WEIGHT, MULTIPLICITY
= 1 SHELX INPUT FOR X,Y,Z AND ANISOTROPIC U'S:
LINE 1: (A4,F5.0,6F10.5,1X,I1) FOR
NAME, AT WT, X,Y,Z, MULT, U11, U22, NUORB
(as indicated below, SHELX parameter lines
can usually be used unmodified, unless
atom is in a special position; see 5A,5B).
LINE 2: (5X, 4F10.5) FOR
U33, U23, U13, U12 (NOTE ORDER!)
(WHEN IFMX = 1, IFMB IS IGNORED)
GT.1 FORMAT FOR X,Y,Z IS 3F8.5,14X,A4,4X,2F5.1
FOR X,Y,Z, NAME, ATOMIC WEIGHT, MULTIPLICITY
LT.0 FORMAT FOR X,Y,Z, IS A4,5X,5F9.6
FOR NAME, ATOMIC WEIGHT, MULTIPLICITY, X,Y,Z
(SEE ALSO LINES (5) BELOW)
IFMB (VALUE IS IRRELEVANT FOR SHELX INPUT, IFMX = 1, OR WHEN
FREE-FORMAT INPUT USED FOR ATOMIC PARAMETERS)
WHEN IFMX.NE.1,
IFMB.EQ.0 FORMAT FOR 'THERMAL' PARAMETERS IS 6F9.6,I1
NE.0 FORMAT FOR 'THERMAL' PARAMETERS IS 6F10.6,I1
(SEE ALSO LINES (5) BELOW)
ETA HIRSHFELD-SHMUELI (ACTA A28, 648) CORRELATION COEFFICIENT
BETWEEN MUTUALLY PERPENDICULAR MEAN-SQUARE AMPLI-
TUDES. THIS VALUE SHOULD BE THAT APPROPRIATE FOR
THE DATA INPUT (SEE PRINTED TABLE, DISCUSSED BELOW).
*******************************************************
* RECOMMENDED: USE THE DEFAULT VALUE IF YOU HAVE *
* ANY DOUBT. THIS WILL GIVE WHAT ARE *
* PRESUMABLY THE MOST MEANINGFUL VALUES *
* FOR THE ESD'S OF THE U(I,J) IN THE *
* ABSENCE OF SPECIFIC INFORMATION ABOUT *
* CORRELATIONS. ALTERNATIVELY, ONE CAN *
* USE UNIT WEIGHTS, BUT WHEN THE ESD'S *
* VARY WIDELY, THIS SEEMS QUESTIONABLE. *
*******************************************************
ETA IS NEEDED (AND IS USED BY THE PROGRAM)
FOR TRANSFORMATION OF ESD'S OF U'S FROM ONE COORDI-
NATE SYSTEM TO ANOTHER, IN THE ABSENCE OF SPECIFIC
INFORMATION ON THE COVARIANCES OF THE U'S. THE
APPROXIMATION USED IS THAT THE COVARIANCES ARE ISO-
TROPIC, AND THAT THE ONLY IMPORTANT TERMS ARE AMONG
THE U(I,I) AND THE U(I,J) OF A GIVEN ATOM. THE ACTUAL
VALUE OF ETA USED SEEMS TO BE IMPORTANT ONLY FOR
NON-ORTHOGONAL AXES.
WHEN NS (CONTROL LINE) IS NON-NEGATIVE,
A TABLE IS PRINTED TO INDICATE HOW APPROPRIATE THE
HIRSHFELD-SHMUELI ASSUMPTIONS AND/OR THE VALUE OF ETA
THAT WAS INPUT ARE. INSPECTION OF THIS TABLE (SEE
THE LEGEND ACCOMPANYING IT) MAY MAKE IT REASONABLE
TO TRY ANOTHER INPUT VALUE. WHATEVER THE VALUE INPUT,
ONCE A REASONABLY CONSTANT OVERALL VARIANCE (S) IS
FOUND, IT IS USED WITH THE STANDARD ETA (-0.25) AND
THE INTERAXIAL ANGLES TO ESTIMATE COVARIANCES.
HIRSHFELD AND SHMUELI RECOMMEND AN ETA OF -0.25,
AND THIS IS THE DEFAULT IF ETA IS INPUT AS BLANK OR
ZERO. TO GET ETA = 0.0, USE ETA = 99.0 FOR INPUT.
EXPERIENCE HAS INDICATED THAT IF THE ESD'S OF THE
U(I,J) (OFF-DIAGONAL ELEMENTS) ARE SIGNIFICANTLY
SMALLER THAN ONE-HALF THOSE OF THE U(I,I), AN ETA
VALUE OF ABOUT 0.75 IS IMPLIED. THIS IS (1 - 0.25),
AND WE HAVE FOUND QUITE SMALL VALUES OF THE ESD'S OF
THE U(I,J) WHEN AN OVERALL ISOTROPIC B HAS BEEN IN-
CLUDED AS A PARAMETER IN THE REFINEMENT. THIS HAS
THE EFFECT OF INTRODUCING A STRONG POSITIVE CORRELATION
AMONG THE U(I,I). THE HIRSHFELD-SHMUELI RECOMMENDATION
OF -1/4 PRESUMED NO SUCH CORRELATION.
IF THE VARIANCE-COVARIANCE MATRIX, OR THE RELATED
MATRIX OF CORRELATION COEFFICIENTS FOR THE L.S. REFINE-
MENT OF THE STRUCTURE WITH U(I,J) (OR B OR BETA) HAS
BEEN PRINTED OUT, IT SHOULD BE INSPECTED TO CHECK ON
THE TYPICAL CORRELATION COEFFICIENTS BETWEEN THE DIFF-
ERENT U(I,I) OF A GIVEN ATOM. THEY ARE OF THE FORM
ETA + (1 - ETA)*(COS SQUARED ANGLE)
WHERE ANGLE IS THE ANGLE BETWEEN THE CORRESPONDING
RECIPROCAL AXES. USUALLY THE SECOND TERM IS VERY
SMALL, SO THIS CORRELATION COEFFICIENT IS ABOUT ETA.
DIS ALL DISTANCES/ANGSTROMS SMALLER THAN 'DIS' FROM
ANY INPUT ATOM TO ANY OTHER INPUT ATOM OR ANY
ATOM GENERATED BY SYMMETRY WILL BE LISTED WHEN
NS (CONTROL LINE) IS NOT -2 OR -4. DEFAULT
OF DIS (I.E., WHEN 'DIS' INPUT ZERO) IS 2.0
DIS also is the upper limit for distances
to be corrected for the effects of internal or
overall motion.
A SEPARATE LIST OF ATOMS WITH NO NEIGHBORS OR ONLY ONE
NEIGHBOR WITHIN THIS DISTANCE, 'DIS', IS ALSO PRINTED.
AS WELL AS A LIST OF THE CONNECTIONS (BY THIS 'DIS'
CRITERION) BETWEEN DIFFERENT ASYMMETRIC UNITS. THIS
OPTION PERMITS CHECKING THAT A SINGLE MOLECULE HAS BEEN
INPUT (NOT SEVERAL DISCONNECTED FRAGMENTS).
(3) CONTROL LINE FREE FORMAT (LIST-DIRECTED)
THIS FORMERLY WAS FORMATTED 13I5; COLUMN NUMBERS ARE GIVEN HERE
BECAUSE THEY ARE CONVENIENT FOR KEEPING TRACK OF WHAT IS
WHERE. HOWEVER, AS LONG AS ITEMS ARE SEPARATED BY SPACE OR
COMMA, THEY MAY BE IN ANY COLUMNS. THE SEQUENCE MATTERS!
(SINCE FREE FORMAT, BE SURE END WITH / IF NOT ALL ITEMS ENTERED)
NTOT,NO,ISET, IB,NONRIG,NVIB, NS,ISIG,ISYM, ICORL,IWU,IFU, ICSVIB
*** NOTE ORDER IS SLIGHTLY DIFFERENT FROM WHAT IT WAS EARLIER ***
*** AND MOST OPTIONS FORMERLY INVOKED BY NEGATIVE VALUES OF ***
*** THESE ARE NOW HANDLED BY THE "OPTIONS LINES" (LINES 4A,4B) ***
NTOT - NUMBER OF ATOMS TO BE INPUT (MAX = 150)
(COLS 1-5) If the molecule (ion) whose motion is to be
analyzed has two-fold or higher site-symmetry
in the crystal, only those atoms comprising
the asymmetric unit need be input. Those
equivalent by symmetry will be generated by
the program.
IF THE TOTAL NUMBER OF ATOMS, INCLUDING ANY
GENERATED BY SYMMETRY EXCEEDS 150, THE JOB
WILL BE TERMINATED WITH AN ERROR MESSAGE.
THE LIMIT FOR THE NUMBER OF ATOMS IS GIVEN BY
NTOT +(NA+NA1)*(NMULT-1) .LE. 150
NA = NUMBER OF ATOMS TO BE INCLUDED IN ANALYSIS
OF THE MOTION + THOSE WITH WEIGHT 800.0
(NA is calculated by the program from the
input data. You need not supply it.)
NA1 = ADDITIONAL ATOMS INCLUDED IN SETTING
UP THE SYSTEM OF INERTIA (WT NEGATIVE AS
DISCUSSED UNDER (5) BELOW).
(NA1 is also calculated by the program)
NMULT = NO. OF SYM OPERATIONS OF THE PT GROUP
(NMULT is also calculated by the program;
it includes the identity operation)
(Note: Many if not most of these terms are
contained in COMMON blocks, and are defined in
the list of COMMON blocks at end of these
instructions.)
NO - A NUMBER CORRESPONDING TO THE SITE SYMMETRY OF THE
(6-10) MOLECULE IN THE CRYSTAL. IT IS THE NUMBER OF THE
CORRESPONDING SPACE GROUP IN VOL I OF THE
INTERNATIONAL TABLES FOR XRAY CRYSTALLOGRAPHY)
********************************************************
* CAUTION: The SITE SYMMETRY of the molecule -- the *
* molecule's point group in the crystal -- is what *
* is wanted here. The space group of the CRYSTAL *
* containing the molecule may be quite irrelevant. *
* See the test examples. If the molecule comprises *
* the asymmetric unit of the crystal (or only part *
* of it because there are several molecules in the *
* asymmetric unit), then the point-group number to *
* use is necessarily 1, since the molecule has no *
* necessary symmetry. *
********************************************************
THE ONLY PERMITTED VALUES OF NO ARE AS FOLLOWS; THEY
ARE GROUPED HERE, FOR CONVENIENCE, IN DIFFERENT SYMMETRY
CLASSES:
Site Symmetry Number Site Symmetry Number
1 (C1) 1 2/m (C2h) 10
1bar (Ci) 2 222 (D2) 16
P2 (C2) 3 mm2 (C2v) 25
m (Cs) 6 mmm (D2h) 47
4 (C4) 75 4mm (C4v) 99
4bar (S4) 81 (4bar)2m (D2d) 111
4/m (C4h) 83 4/mmm (D4h) 123
4222 (D4) 89
The next group of site symmetries is to be used ONLY for
crystals indexed on hexagonal axes. If you have a molecule
or ion with 3-fold symmetry indexed with "rhombohedral axes",
you must first transform the positions (and U's or B's) to
hexagonal axes.
3 (C3) 143 6 (C6) 168
3bar (C3i) 147 6bar (C3h) 174
312 (D3) 149 6/m (C6h) 175
321 (D3) 150 622 (D6) 177
3m1 (C3v) 156 6mm (C6v) 183
31m (C3v) 157 (6bar)m2 (D3h) 187
(3bar)1m (D3d) 162 (6bar)2m (D3h) 189
(3bar)m1 (D3d) 164 6/mmm (D6h) 191
The final group of site symmetries listed here is to be used
ONLY for CUBIC crystals:
3 (C3) 146 3m (C3v) 160
3bar (C3i) 148 (3bar)m (D3d) 166
32 (D3) 155
23 (T) 195 (4bar)3m (Td) 215
m3 (Th) 200 m3m (Oh) 221
432 (O) 207
CAUTION: As indicated, the R space-group numbers (146, 148,
155, 160, 166) are to be used ONLY for molecules
with the indicated point-group symmetry that are
found in CUBIC crystals.
IF A MOLECULE WITH SUCH POINT-GROUP SYMMETRY IS
FOUND IN A TRIGONAL CRYSTAL, USE CORRESPONDING
HEXAGONAL AXES AND THE POINT-GROUP NUMBER
APPROPRIATE TO THOSE AXES. SYMMETRY IS TAKEN
INTO ACCOUNT CHIEFLY IN THE SUBROUTINE SYMET
(WHICH CALLS SYMPOS).
ISET - SETTING OF PRINCIPAL AXIS IN CRYSTAL COORD. SYSTEM
(11-15) - IF ISET = 1 PRINCIPAL AXIS Z
- IF ISET = 2 PRINCIPAL AXIS X
- IF ISET = 3 PRINCIPAL AXIS Y
- IF ISET = 4 PRINCIPAL AXIS XY-DIAGONAL
(THIS MEANS [110], NOT [-1,1,0], ETC)
- IF ISET = 5 PRINCIPAL AXIS XYZ-DIAGONAL
(THIS MEANS [111], NOT [-1,1,1], ETC)
- IF ISET.GT.5, SPECIAL SETTING NEEDED (E.G., FOR
A MOLECULE THAT HAS mmm SYMMETRY WITH THE
AXES ORIENTED AT 45 DEGREES TO X AND Y).
SEE (4C) BELOW FOR INPUT OF MATRICES.
THE 'PRINCIPAL AXIS' IS THE UNIQUE AXIS (IF
ANY) OF THE POINT GROUP. FOR MOLECULES WITH
SYMMETRY ELEMENTS OF ORDER HIGHER THAN 2 IT IS
ASSUMED THAT THE PRINCIPAL AXIS WILL BE ALONG
THE Z-DIRECTION (ISET.EQ.1) EXCEPT FOR GROUPS
WITH 3-FOLD SYMMETRY ELEMENTS IN CUBIC CRYSTALS
FOR WHICH THE R-SPACE GROUP NUMBER (146,148,
155,160, OR 166) CORRESPONDING TO THE APPRO-
PRIATE POINT-GROUP SYMMETRY SHOULD BE USED.
USE ISET = 5 FOR SUCH GROUPS AND ONLY FOR
SUCH GROUPS.
Thus, when (e.g.) you have a 2-fold axis parallel to
the b-axis (i.e., y), make ISET = 3, or the symmetry
operations appropriate to the point-symmetry chosen
will not be correct. See the example in THMTEST3.
USE ISET = 1 FOR C1 AND CI (NO = 1 AND 2).
USE ISET = 3 FOR MONOCLINIC CRYSTALS WITH b
AS THE UNIQUE AXIS
IB INDICATOR OF TYPE OF 'THERMAL' (DISPLACEMENT) PARAMETER
(16-20)
IB IS THE SAME INDEX USED BY ORTEP TO DENOTE THE
KIND OF 'THERMAL' PARAMETER. ONLY INDICES 0, 1, 4,
AND 8 ARE USED HERE. ANY OTHER VALUE WILL CAUSE THE
PROGRAM TO EXIT.
IB = 0 DIMENSIONLESS B(I,J), EXPLICIT 2 WITH CROSS TERMS
IB = 1 DIMENSIONLESS B(I,J), NO FACTOR 2 WITH CROSS TERMS
THUS ANISOTROPIC TEMPERATURE FACTOR FOR IB = 1 IS:
EXP -(B11*h**2+B22*k**2+B33*l*2+B12*h*k+B13*h*l+B23*k*l)
FOR IB = 4 AND 8, 'THERMAL' PARAMETERS ARE ASSUMED TO BE U(I,J)
(DIMENSIONS ANGSTROMS SQUARED), WITH AN EXPLICIT FACTOR OF
2 INCLUDED WITH THE CROSS TERMS. THE FORM IS:
EXP -D*(RA(I)*RA(J)*U(I,J)*H(I)*H(J))
WITH RA MEANING RECIPROCAL AXIS LENGTH AND H MEANING
REFLECTION INDEX. SUMMATION OVER I,J IS ASSUMED.
IB = 8 D = 2.0*(PI SQUARED)
IB = 4 D = 0.25
NONRIG - IF.NE.0, INPUT FOLLOWS FOR ATTACHED RIGID GROUPS
(21-25) (i.e., INPUT CONCERNING INTERNALLY MOVING GROUPS)
- NONRIG DEFINES NUMBER OF ATTACHED RIGID GROUPS
TO BE CONSIDERED MOVING (MAX = 7 IN THMA11)
THESE WERE FORMERLY CALLED 'NON-RIGID GROUPS'.
SIX PARAMETERS TO BE DETERMINED PER GROUP
NVIB - IF NEGATIVE, MEAN SQUARE DISPLACEMENT AMPLITUDES
(26-30) ALONG INTERATOMIC LINES ARE TO BE CALCULATED FOR
ALL UNIQUE PAIRS OF ATOMS, OMITTING ISOTROPIC
ATOMS (defined as ANY atom with U22 or B22 = 0.0).
"UNIQUE PAIRS" MEANS from ALL ATOMS IN ASYMMETRIC
UNIT to ALL OTHERS IN ASYM UNIT AND ALL GENERATED
BY SYMMETRY. These values will be printed in a list
whenever NVIB.LE.(-2); this list can get very long
when there are many atoms input, or many generated
by symmetry.
***** NVIB WAS FORMERLY IN COLS 56-60 *****
WHEN NVIB IS NEGATIVE, ARRANGE ATOMS AT TIME OF INPUT SO
THAT THOSE WITHIN GROUPS EXPECTED TO BE INTERNALLY RIGID
ARE CONSECUTIVE. OUTPUT INCLUDES (REGARDLESS OF THE
VALUE OF NS) A MATRIX OF DIFFERENCES OF MSDA VALUES;
IF ATOMS ARE SO GROUPED, RIGIDITY OF GROUPS AND
LACK OF RIGIDITY BETWEEN GROUPS IS EASIER TO SPOT
(MATRIX will not include atoms with WT 800. or 999.9,
or negative; such atoms are, however, included in the
long MSDA listing obtained when NVIB.LT.-1 and NS.GE.0,
unless U22 (or B22) for the atom was input as 0.0)
- POSITIVE IF MEAN SQUARE DISPLACEMENT AMPLITUDES ARE
TO BE CALCULATED ONLY FOR SELECTED PAIRS OF
ATOMS, ALONG LINES DEFINED BY THESE PAIRS.
THE ATOM PAIRS ARE READ ON LINE (8A). NVIB IS
DEFINED AS A POSITIVE INTEGER, EQUAL TO THE
NUMBER OF PAIRS OF ATOMS FOR WHICH MEAN SQUARE
AMPLITUDES ALONG THE CORRESPONDING INTERATOMIC
LINES ARE WANTED. NVIB CANNOT EXCEED 40 (THERE
IS NO LIMIT ON THE NUMBER OF PAIRS IF NVIB IS
NEGATIVE -- SEE ABOVE).
NS - IF GT.0, ANOTHER SET OF DATA FOLLOWS
(31-35) STARTING WITH TITLE LINE
NS NEGATIVE GIVES SHORTER OUTPUT, SPECIFICALLY:
NS = -1, SOMEWHAT SHORTER, NO COMPOUND FOLLOWS
= -2, MUCH SHORTER OUTPUT, NO COMPOUND FOLLOWS
= -3, SOMEWHAT SHORTER, ANOTHER COMPOUND FOLLOWS
= -4, MUCH SHORTER, ANOTHER COMPOUND FOLLOWS
(Use "much shorter" in second and later runs of the
same data, when trying variations; in initial runs,
use either full output or "shorter". NS = -2, -4
("much shorter") skips output of such things as
principal-axis setting, input ESD's, transformation
matrices, cartesian coordinates, information about
the inertia tensor, intramolecular distances,
correlation coefficients, comparison of observed
and calculated U's, and a few other items. Some of
these are also skipped when NS = 1- or -3. The long
detailed listing of MSDA differences can be obtained
only when NS .LE.0 and NVIB .LE.(-2).
(WHEN NS NEGATIVE, ONLY 5 LINES ARE SKIPPED BETWEEN "PAGES",
RATHER THAN GOING TO AN ACTUAL NEW SHEET; SEE OUTH6)
ISIG - IF = 0, NO SIGMA U's (or B's) TO BE PROVIDED
(36-40) IF SIGMA U's (or B's) ARE TO BE GIVEN, THEY NEED NOT
BE GIVEN FOR MORE THAN THE NUMBER OF ATOMS
WHOSE U's ARE TO BE USED IN THE ANALYSIS OF
THE MOTION.
THE ABSOLUTE VALUE OF ISIG SHOULD BE THE NUMBER OF
ATOMS WHOSE Us ARE TO BE USED; MORE ESDs MAY BE
INPUT (AND ISIG INCREASED ACCORDINGLY), BUT THE
PROGRAM WILL IGNORE THEM. THUS THEY NEED NOT
BE GIVEN FOR ATOMS WITH NEGATIVE WEIGHTS OR
DUMMY ATOMS WITH WEIGHT 800.0 OR 999.9.
(ISIG MAY BE POSITIVE OR NEGATIVE; THE FULL
IMPLICATIONS OF THESE ARE DISCUSSED BELOW).
IF ISIG IS POSITIVE,
INPUT IS SIGMA OF B'S OR U'S AND THE
WORKING WEIGHTS WILL BE:
(1) IF(IWU.NE.1),
WU(I,K)= [AVERAGE SIGU(I,K)]/SIGU(I,K))
(Average not including sigmas of 0.0 or
atoms with weight 800.; sigmas of atoms
with weight 999.9 or > 0 always ignored)
(2) IF(IWU.EQ.1), THEN
WU(I,K) = 1.0 AND THE SIGMA U'S ARE USED
ONLY TO CALCULATE THE MEAN STANDARD
DEVIATION OF THE U OBSERVED VALUES
IF ISIG IS NEGATIVE,
THE INPUT IS TREATED AS WORKING WEIGHTS
WU(I,K) FOR THE OBSERVATIONAL EQUATIONS.
WEIGHTS MUST BE THOSE APPROPRIATE FOR
U'S IN THE CARTESIAN SYSTEM (IN WHICH
CALCULATIONS ARE DONE) , NOT THE INPUT
CRYSTAL SYSTEM. NO TRANSFORMATION DONE.
IF YOU WISH TO PUT IN 'WORKING WEIGHTS'
APPROPRIATE FOR THE CRYSTAL SYSTEM, AND
HAVE THEM TRANSFORMED TO WORKING SYSTEM,
USE SIGU'S PROPORTIONAL TO INVERSE OF
THE WEIGHTS (WITH ISIG POSITIVE).
ISYM - IF ISYM = 0 OR BLANK,
(41-45) ORIGIN OF CRYSTAL SYSTEM LIES ON THE
MOLECULAR SYMMETRY ELEMENTS, i.e., the
molecular symmetry elements pass through
(0,0,0) of the coordinate system used.
IF ISYM.NE.0, THEN THE CRYSTAL ORIGIN DOES NOT
LIE ON THE MOLECULAR SYMMETRY ELEMENTS.
WHEN ISYM.NE.0 AN ADDITIONAL LINE IS
READ WITH THE COORDINATES OF A POINT ON
THE SYMMETRY ELEMENTS. SEE (6) BELOW.
ICORL - LT.0 BYPASS CALCULATION OF CORRELATIONS OF
(46-50) INTERNAL TORSIONS WITH OVERALL MOTION
BYPASS IS AUTOMATIC FOR GROUPS WITH
ONLY ONE ATOM (NAFA(I).EQ.1) SINCE TOO
FEW U(I,J) TO DETERMINE 6 PARAMETERS
IWU - GE.0, IGNORED UNLESS ISIG.GT.0 (SEE 'ISIG' ABOVE)
(51-55)
IFU - IF NE.0, DETAILED INFORMATION WANTED FOR EACH
(56-60) ATOM ('INTERPRETATION'). OUTPUT GIVES
ATOM-BY-ATOM COMPARISON OF OBS AND CALC
U'S IN INERTIAL SYSTEM, THEIR EIGEN-
VALUES AND EIGENVECTORS AND THE ANGLES
BETWEEN THE LATTER, AND THE ANGLES
BETWEEN THE EIGENVECTORS OF UOBS AND
THOSE OF L AND T.
ICSVIB - NON-ZERO IF MEAN SQUARE DISPLACEMENT AMPLITUDES
(61-65) ARE TO BE CALCULATED FOR INDIVIDUAL
SPECIFIED ATOMS ALONG DIRECTIONS THAT
ARE DEFINED BY INPUT DIRECTION COSINES.
ICSVIB MUST BE A POSITIVE INTEGER (NO
LARGER THAN 10) AND IS THE NUMBER OF
DIRECTIONS FOR WHICH THE CALCULATIONS
ARE TO BE MADE. THE DIRECTION COSINES
AND ATOM NAMES ARE READ IN ON LINES
(8B). THE MAXIMUM NUMBER OF ATOMS FOR
ANY DIRECTION IS 12. A GIVEN
DIRECTION MAY BE USED MORE THAN ONCE.
(4) TWO (NEW in 1985) OPTION LINES (FREE FORMAT)
(BE SURE TO END LINE WITH / IF ALL VARIABLES NOT ENTERED)
(4A) TEMP, IRECAL, ISIGX, IRIDE, IMIN, IUNC
(4B) IFREQ, IATWT, IEIG, IMAT, IOUT, CONSLV
THE OPTIONS IN LINE (4A) WILL PROBABLY BE MORE GENERALLY
USED; THOSE IN (4B) ARE FOR LESS COMMON SITUATIONS.
SOME OF THESE OPTIONS ARE NEW; OTHERS WERE EFFECTED IN EARLIER
VERSIONS OF THE PROGRAM IN OTHER WAYS, OFTEN BY MAKING SOME
ITEMS IN THE "CONTROL LINE" [LINE (3)] HAVE SPECIAL VALUES.
(IFREQ, new January 1987, governs calculation of frequencies,
force consts and barriers, which was formerly automatic)
LINE (4A):
TEMP IF ENTERED AS 0.0 (OR IF JUST / IS ENTERED), THE
DEFAULT TEMPERATURE OF 296 K IS ASSUMED. OTHERWISE
TEMP IS ENTERED AS THE TEMPERATURE IN KELVIN (WITH
A DECIMAL POINT, E.G., 115. OR 239.)
IRECAL NE.0 SIGNIFIES THAT A SECOND CALCULATION IS WANTED
WITH THE SAME ATOMIC PARAMETERS. TO START IT,
USE NEW TITLE LINE, OMIT CELL DIMENSIONS, INCLUDE
CONTROL AND OPTION LINES, OMIT ATOMIC PARAMETERS
AND ESD'S, INCLUDE OTHER LINES IF SPECIFIED ON
CONTROL LINE OR OPTION LINE
ISIGX .NE.0, IMPLIES THAT LINES INCLUDING ESD'S OF X,Y,Z
ARE INTERMIXED WITH SIGMAS OF U'S OR B'S
(SEE UNDER LINES (5C) BELOW).
IRIDE .NE.0, MEANS UP TO 20 PAIRS OF ATOMS TO BE INPUT
AT LINE (6D) BELOW FOR RIDING-CORRECTION
CALCULATION. ALL BONDS TO (ANISO) H AND
D ATOMS WILL AUTOMATICALLY HAVE RIDING CORRN
CALCULATED, SO USE IRIDE.NE.0 ONLY IF SUCH
CORRECTIONS ARE TO BE APPLIED TO OTHER ATOMS
IMIN .NE.0, MEANS UP TO 20 PAIRS OF ATOMS TO BE INPUT
AT LINE (6E) BELOW TO DEFINE DISTANCES FOR
THE 'MINIMUM' THERMAL MOTION CORRECTION.
[BUSING AND LEVY, ACTA 17, 142 (1964)]
IUNC .NE.0, MEANS UP TO 20 PAIRS OF ATOMS TO BE INPUT
AT LINE (6F) BELOW FOR CORRECTION FOR
UNCORRELATED (INDEPENDENT) MOTION (SEE
BUSING and LEVY, ACTA CRYST. 17, 142 (1964))
THE FIRST ATOM OF EACH PAIR OF ATOMS IS
ASSUMED TO BE ONE OF THE ATOMS INPUT; THE
2ND MAY BE RELATED TO AN INPUT ATOM BY A
CENTER OF SYM AT ORIGIN AND BY TRANSLATION.
*******END OF INPUT FOR OPTION LINE (4A)*******
LINE (4B):
IFREQ .EQ.0, NO FREQUENCY, FORCE CONSTANT OR BARRIER
ESTIMATIONS WILL BE MADE
.GT.0, EST FREQUENCIES, FORCE CONSTANTS AND
BARRIERS FOR INTERNAL MOTION ONLY, i.e.,
FOR MOTION OF ATTACHED RIGID GROUPS
.LT.0 EST FREQUENCIES FOR OVERALL MOTION ALSO
A MINOR SOURCE OF ERRORS IN FREQUENCIES WILL
ARISE IF H ATOMS ARE NOT INCLUDED IN THE ATTACHED
GROUPS, BECAUSE THE MOMENTS OF INERTIA WILL BE
LOW (BY AS MUCH AS 20 OR 25 PERCENT FOR GROUPS
SUCH AS METHYL OR T-BUTYL). NORMALLY, HOWEVER,
THIS WILL NOT AFFECT CALCULATION OF FORCE
CONSTANTS. SEE START OF SUBROUTINE NRCOR.
IATWT .EQ.0, ATOMIC WTS TO BE ASSIGNED BY PROGRAM
.NE.0, NO ATOMIC WTS TO BE ASSIGNED BY PROGRAM
(FORMERLY DONE BY MAKING NTOT NEGATIVE)
WHEN IATWT = 0, ATOMIC WEIGHTS GENERATED FROM CHEM
SYMBOL (FIRST NON-BLANK CHARACTERS IN COLS 1-4 OF ATOM
NAME) FOR ELEMENTS 1-53 AND ALSO D, W, Re, Os, Ir, Pt
(EXCLUDING, HOWEVER: He, Ne, Ar, Kr, Tc), UNLESS
ATOM ALREADY HAS NEG WT OR WT 800.0 OR 999.9. EITHER
UPPER OR LOWER CASE LETTERS (OR MIXTURE) OK FOR ATOM
NAMES. TO PREASSIGN WT TO A PARTICULAR ATOM (OTHER
THAN ITS AT WT, OR SPECIAL VALUE), CHANGE ITS SYMBOL
TO SOMETHING NON-STANDARD. ISOTROPIC ATOMS ARE
ASSIGNED NEGATIVE WEIGHTS BY THE PROGRAM (UNLESS WT
800., 999.9 OR NEG WT INPUT).
[NOTE THAT IF AN ATOM HAS BEEN IDENTIFIED AS CA (OR
Ca ), IMPLYING CARBON A OR CARBON ALPHA, THE PROGRAM
WILL IDENTIFY IT AS CALCIUM]. FOR ANY ATOMS NOT IN
THE "STANDARD LIST" GIVEN ABOVE, USE THE DESIRED WT
AS INPUT VALUE (PROGRAM WILL RETAIN THE INPUT VALUE
FOR ANY ATOM IT DOES NOT RECOGNIZE). AS MENTIONED
ABOVE, PROGRAM WILL OVERRIDE ANY ASSIGNED WEIGHT FOR
A 'COMMON ATOM' UNLESS IATWT.NE.0 OR WEIGHT INPUT
AS 800., 999.9 OR NEGATIVE.
IEIG .GT.0 WRITE OUT MATRIX OF NORMAL EQUATIONS ON UNIT
1 FOR LATER ANALYSIS BY AN EIGENVALUE/EIGENVECTOR
PROGRAM. (AT PRESENT I DO NOT HAVE AVAILABLE A
VAX SUBROUTINE OF THIS KIND SUFFICIENTLY PRECISE
TO GIVE RELIABLE VALUES WHEN THE MATRIX IS NEARLY
SINGULAR. INSPECTION OF THE EIGENVECTORS UNDER
THIS SITUATION CAN BE HELPFUL IN UNDERSTANDING
THE INTERDEPENDENCE OF DIFFERENT VARIABLES.)
[MATRIX IS WRITTEN UNFORMATTED, ((A(I,J), J = 1,N),
I = 1,N), WHERE N IS ITS DIMENSION]
IMAT THIS VARIABLE IS USED ONLY FOR SPECIAL CHECKING
OF THE MATRIX OF NORMAL EQUATIONS; IT DOES WHAT
WAS DONE IN EARLIER VERSIONS BY ISYM.GE.100
WHEN THE MATRIX OR ITS INVERSE IS PRINTED,
THE ACCOMPANYING VECTOR IS THE LAST ELEMENT
LISTED IN EACH ROW.
WHENEVER THE MATRIX OF NORMAL EQUATIONS IS
PRINTED, THE CORRESPONDING SOLUTION VECTOR IS ALSO
PRINTED (ONE ELEMENT PER LINE) IMMEDIATELY AFTER.
IMAT = 100 OR MORE PROVIDES SPECIAL OPTIONS FOR
CHECKING MATRIX OF NORMAL EQUATIONS AND
EFFECTS OF CONTRACTING IT (SEE SOLVE).
IF IMAT .GE. 250 DO NOT CONTRACT MATRIX OR
DELETE ANY ROWS OR COLUMNS
IF IMAT .GE. 200 PRINT MATRIX, AFTER
CONTRACTION AND DELETION (SEE 'SOLVE')
IF IMAT.EQ.175 OR IMAT.EQ.225, PRINT INVERSE
MATRIX
IF IMAT .GE. 100 PRINT MATRIX FIRST WITH CON-
TRIBUTIONS OF UNIQUE ATOMS ONLY, THEN
WITH ALL. PRINT SOLUTION VECTOR (ONE
ELEMENT PER LINE) AND ESD'S (SIMILARLY)
IOUT NE.0 OUTPUT ON UNIT 7 COORDS CORRECTED FOR
RIGID-BODY (BUT NOT INTERNAL) MOTION.
THESE CORRECTED COORDINATES WILL HAVE
FORMAT (A4,23X,3F9.6), WHICH IS THE
FORMAT APPROPRIATE FOR THE OAK-RIDGE
PROGRAMS. THIS IS FORMAT 24 IN SUB-
ROUTINE OUTR, CALLED BY ENTRY OUTR9.
CONSLV - MAY BE IGNORED EXCEPT ON MACHINES WITH RELATIVELY
SMALL WORD SIZE (E.G., SOME VAX), AND EVEN
THEN MAY BE IGNORED MOST OF THE TIME. IS SET
TO .01 BY PROGRAM UNLESS SOME NON-ZERO VALUE IS
INPUT. NEEDED ONLY WHEN GET OVERFLOW ERROR IN
SUBROUTINE "MATINV", WHICH MAY (RARELY) HAPPEN
WITH HIGH-SYMMETRY SPACE GROUPS (OR POSSIBLY
VERY LARGE STRUCTURES) ON THE VAX.
TRY CONSLV = 0.005 OR 0.001 IF OVERFLOW
OCCURS. IT IS USED TO REDUCE SIZE OF TERMS IN
THE MATRIX AT START OF SUBROUTINE "SOLVE"
(4C) IF ON THE CONTROL LINE ISET IS LARGER THAN 5:
ISET.GT.5 INSERT 1 LINE WITH TITLE OF SPECIAL SETTING
FORMAT(20A4)
INPUT 9 COMPONENTS OF THE TRANSFORMATION MATRIX,
(ROWS VARYING FASTEST; SEE EXAMPLE BELOW), AND 9
COMPONENTS OF THE INVERSE TRANSFORMATION MATRIX.
THERE MAY BE UP TO 9 VALUES PER LINE, OR (FOR
EASIER VISUALIZING) 3 PER LINE AS BELOW.
IN ANY EVENT, ALL VALUES ARE FREE FORMAT.
************************
NOTE THAT THROUGHOUT THIS PROGRAM ALL MATRICES PREMULTIPLY
VECTORS, EVEN WHEN THE LATTER ARE CONTRAVARIANT.
************************
TMAT IS THE TRANSFORMATION MATRIX, AS A PREFACTOR, TO BE
APPLIED TO THE STANDARD SETTING (Z-AXIS AS UNIQUE
AXIS) TO TRANSFORM IT TO THE PARTICULAR SETTING IN THE
CRYSTAL OF INTEREST. SEE ALSO THE COMMENTS UNDER ISET
(LINE (3) ABOVE).
RTMAT MATRIX FOR BACKTRANSFORMATION
EXAMPLE ORIGINAL SETTING Z-AXIS, DESIRED PRINCIPAL AXIS = X
(TMAT(I,J),J=1,3)
TMAT(1,J) 0. 0. 1.
TMAT(2,J) 1. 0. 0.
TMAT(3,J) 0. 1. 0.
(RTMAT(I,J),J=1,3)
RTMAT(1,J) 0. 1. 0.
RTMAT(2,J) 0. 0. 1.
RTMAT(3,J) 1. 0. 0.
THIS CASE IS IMPLEMENTED IN THE PROGRAM, ISET = 2
THIS TMAT, AS A PREFACTOR MULTIPLYING X,Y,Z WILL PRODUCE
NEW X = OLD Z
NEW Y = OLD X
NEW Z = OLD Y
THE PROGRAM (IN SUBROUTINE SYMPOS) GETS THE SYMMETRY
OPERATIONS APPROPRIATE TO THE SPECIFIED SETTING OF THE PRIN-
CIPAL AXIS FROM THOSE THAT ARE STORED (IN SYMET) BY APPLYING
TMAT AS A PREFACTOR AND RTMAT AS A POSTFACTOR IN A TRIPLE
MATRIX MULTIPLICATION. THE STORED SYMMETRY OPERATIONS ARE
THOSE APPROPRIATE FOR THE Z-AXIS AS THE PRINCIPAL AXIS;
THEY ARE INTERNALLY MODIFIED AS NEEDED WHEN ISET IS NOT 1.
(5) ATOMIC PARAMETER LINES
(5A) POSITION PARAMETERS
FORMATTED INPUT: [FORMATS GIVEN ABOVE, UNDER LINE (2)]
ATOMNAME, x, y, z, WEIGHT, MULT (IFMX.EQ.0)
SHELX FORMAT: (IFMX.EQ.1)
ATOMNAME,WT,x,y,z,MULT,U11,U22
x, y, z, ATOMNAME, WEIGHT, MULT (IFMX.GT.1)
ATOMNAME, WEIGHT, MULT, x, y, z (IFMX.LT.0)
FREE-FORMAT INPUT (IF COLUMNS 1-4 OF TITLE LINE WERE "FREE")
ORDER IS THEN:
ATOMNAME, x, y, z, WT, MULT
(MULT WILL BE SET TO 1.0 IF INPUT AS 0.0 (SEE BELOW);
HENCE IT NEED BE GIVEN ONLY WHEN ATOM IS IN A SPECIAL POSN)
(WT NEED BE GIVEN ONLY WHEN PROGRAM IS NOT ASSIGNING AT WTS
-- IATWT.NE.0 ON 2nd OPTION LINE -- OR IF ATOM IS IN SPEC
POSN, SO MULT IS TO BE INPUT. VALUE FOR WT IRRELEVANT IF
AT WTS TO BE SET BY PROGRAM. BE SURE TO TERMINATE LINE
WITH / IF MULT, OR BOTH MULT AND WT, NOT GIVEN.)
x, y, z ARE FRACTIONAL COORDINATES ALONG a, b, c
ATOMNAME IS A FOUR-CHARACTER NAME, WHICH MUST BEGIN WITH
THE CHEMICAL SYMBOL FOR THE ELEMENT IF AT WTS ARE TO BE
ASSIGNED BY THE PROGRAM. THE IDENTICAL NAME MUST BE USED
FOR THE SAME ATOM FOR INPUT OF SIGU AND NON-RIGID GROUP
INFORMATION (SEE BELOW).
CAUTION: BE SURE THE x, y, z VALUES USED CORRESPOND (AFTER
SYMMETRY OPERATIONS, IF ANY) TO A SINGLE MOLECULE, NOT PARTS
OF SEVERAL SEPARATE MOLECULES. IF YOU ARE UNCERTAIN, USE
NS.GE.(-1) THE FIRST TIME, AND CHECK THE PRINTED LIST OF
INPUT DISTANCES AND PAIRS OF BONDED ASYMMETRIC UNITS
SUBMIT FRACTIONAL COORDINATES FOR ONE COMPLETE ASYMMETRIC UNIT
INPUT LINES OF POSN COORDINATES AND 'THERMAL' PARAMETERS ARE READ
PAIRWISE FOR EACH ATOM, 1ST LINE COORDINATES, 2ND LINE U'S OR B'S
(EXCEPT FOR SHELX INPUT, IFMX=1, WHEN U11,U22 ARE ON FIRST LINE).
THE SEQUENCE OF THE ATOMS IS IRRELEVANT (EXCEPT FOR EASY INTER-
PRETATION OF THE MSDA MATRIX -- SEE COMMENTS ON 'NVIB' ON THE
CONTROL LINE)
NOTE: ATOMIC WEIGHTS WILL BE GENERATED AUTOMATICALLY FROM THE
ELEMENT SYMBOL IMPLIED BY FIRST TWO LETTERS IN ATOM'S NAME
FOR MOST COMMON ATOMS, UNLESS ON INPUT THE ATOM WAS
GIVEN ATOMIC WEIGHT 800.0, 999.9 OR A NEGATIVE WEIGHT.
(SEE DETAILED DISCUSSION UNDER IATWT , 2nd OPTION LINE)
ATOM NAME MAY BE UPPER CASE, lower case, OR MiXed.
(There are various SPECIAL weights that may be used for
special purposes; see the discussion and TABLE below).
WITH SHELX INPUT, IF MULT IS INPUT AS 10.0 OR GREATER, IT
WILL BE DIMINISHED BY 10.0; SIMILARLY, IF X,Y,Z, OR ANY U
VALUE HAS BEEN FIXED BY HAVING HAD 10.0 ADDED TO IT, IT
WILL BE AUTOMATICALLY CORRECTED BY THIS PROGRAM.
WITH SHELX INPUT, 'AFIX' LINES ARE AUTOMATICALLY SKIPPED,
SO THEY NEED NOT BE REMOVED FROM THE FILE.
STANDARD FORMAT (WHEN IFMX = 0) IS A4,23X,3F9.6,2F5.1
OTHER FORMATS POSSIBLE WHEN IFMX.NE.0. SEE ABOVE.
INPUT FORMAT CHANGES MAY BE MADE IN SUBROUTINE RDIN.
*****************************************************************
* NOTE: WHEN USING LIST-DIRECTED (FREE FORMAT) INPUT, *
* ALL ATOM-NAMES ON ATOM LINES AND OTHER LINES LATER *
* MUST BE ENCLOSED WITHIN APOSTROPHES *
* FOR EXAMPLE, 'C12' 'H19A' 'NA+' *
* *
* BE SURE SPACE(S), COMMA, OR BOTH BETWEEN EACH ITEM OF INPUT. *
* IF ITEMS FROM END OF LIST ARE TO BE OMITTED, STOP WITH / *
*****************************************************************
WEIGHTS: (These are NOT weightings for the LS calculation, but
rather either relative weights of atoms to be used in the
calculation of the INERTIA TENSOR, or signals to the
program to treat the atom in a special way.)
The following Table SUMMARIZES the way in which atoms with
different input weights are treated. Positions and U's or B's
must be input for all atoms, but the U or B values are irrele-
vant for those atoms not included in analysis of the motion,
except insofar as you may be interested in their comparison
with the U's calculated by the program. These will be listed,
for ALL input atoms, in the crystal system when NS is not
negative, and in the Cartesian crystal system (if different)
when NS is not -2 or -4. When IFU is positive (CONTROL LINE),
detailed atom-by-atom comparisons are made in the inertial
system. See discussion of IFU above.
Esds of
U's used Reprod. Incl. in U's of atom(#) U's (B's)
in analysis by inertial "interpreted" need be
Weight of motion sym opns system when IFU.NE.0 input(##)
------ ---------- -------- -------- ------------ -------
0.0(*) YES YES NO YES YES
Negative NO YES YES(**) YES(***) NO
800. NO YES NO NO NO
999.9 NO NO NO YES NO
Other YES YES YES YES YES
(*) If program is assigning at wts (IATWT = 0), you must
give an unrecognizable name to the atom to keep the
input weight = 0.0 (e.g., CX, NX, OX, ...)
(**) Negative weight is made positive by Subroutine INERT
(***) Isotropic atoms are given neg wt by program, but
they will not be "interpreted" by Subr ATINT
(#) U's corresponding to the derived motion will be cal-
culated for these atoms in the inertial system
and compared with those input when YES is entered
here, except for isotropic atoms
(##) When ISIG is non-zero, that is, when any esds input
NOTES: DUMMY ATOMS SHOULD BE GIVEN WEIGHT 800.0; SUCH ATOMS ARE
USEFUL FOR DEFINING LIBRATION AXES THAT DO NOT LIE ALONG
ANY INTERATOMIC LINE IN THE MOLECULE. ALTHOUGH WT 999.9
CAN BE USED FOR DUMMY ATOMS WHEN THE SYMMETRY IS ONLY 1
(NO = 1), ATOMS WITH WEIGHT 999.9 ARE NOT REPRODUCED BY
SYMMETRY OPERATIONS.
NOTE THAT ATOMS OF WT 800.0 WILL BE REPRODUCED BY THE
SYMMETRY OPERATIONS. U'S OR B'S MUST BE GIVEN FOR 800.0
ATOMS, BUT THE SPECIFIC VALUES ARE NOT USED (THEY MAY ALL
BE ZERO). ESD'S ARE OPTIONAL, EVEN IF INCLUDED FOR OTHERS.
(ALTERNATIVELY, DUMMY ATOMS MAY BE GIVEN WT 0.0, SO THAT
THEY DO NOT CONTRIBUTE TO THE INERTIAL TENSOR AND GIVEN
ESDS OF U'S (OR B'S) HIGHER BY A FACTOR OF 1000
OR MORE THAN THOSE OF OTHER ATOMS. THESE TWO STEPS
HAVE THE SAME EFFECT AS WEIGHT 800.0: THE ATOMS CONTRI-
BUTE NOTHING TO THE INERTIAL TENSOR AND NEGLIGIBLY TO
THE MATRIX OF NORMAL EQUATIONS, BUT THEY ARE REPRODUCED
BY THE SYMMETRY OPERATIONS BECAUSE THEY HAVE WT.GE.0.0).
IF THIS OPTION IS USED, HOWEVER, THESE ATOMS WILL ADD
TO THE 'NUMBER OF INDEPENDENT OBSERVATIONS' THROUGH
THEIR NUORB VALUES, SO ESD'S WILL BE ESTD TOO LOW.
IF THERE ARE NO ATOMS WITH EITHER POSITIVE OR ZERO WEIGHT
THE JOB WILL BE TERMINATED
ATOMS IN SPECIAL POSITIONS:
NOTE THAT ATOMS IN SPECIAL POSITIONS WILL BE GIVEN THEIR
NORMAL ATOMIC WEIGHTS, FOR THE WEIGHT OF EACH ATOM
IS ADJUSTED FOR MULTIPLICITY IN THE CALCULATION OF THE
INERTIA TENSOR. (DONE IN 'SYMPOS' BEFORE 'INERT')
THERE IS NO ADJUSTMENT FOR MULTIPLICITY IN CALCULATING THE
CONTRIBUTIONS TO THE NORMAL EQUATIONS, THAT IS, THE U'S OF
ATOMS IN SPECIAL POSITIONS ARE GIVEN THE SAME RELATIVE WEIGHT
FOR L.S. AS ATOMS IN GENERAL POSITIONS, TAKING INTO ACCOUNT
WHATEVER VARIATION THERE MAY BE IN THE SIGMAS OF INDIVIDUAL
COMPONENTS OF THE U'S IF SIGU IS USED FOR WEIGHTING.
A USER WHO WANTS TO EXCLUDE A PARTICULAR COMPONENT FROM THE
ANALYSIS CAN DO THIS WITH THE OPTION ISIG.LT.0 (ON CONTROL
LINE, (3)), INSERTING SIGU(I,J) = 0. FOR THIS COMPONENT;
FOR ALL THE OTHERS, SIGU = 1.
MULT THE MULTIPLICITY OF THE POSITION FOR THE ATOM.
ALL ATOMS IN GENERAL POSITIONS HAVE MULT = 1.0
IF MULT IS INPUT AS 0.0 OR BLANK, IT IS CHANGED TO 1.0, SO THAT
EFFECTIVE INPUT VALUE OF MULT IS ALWAYS GREATER THAN OR
EQUAL TO 1.0
FOR ATOMS IN SPECIAL POSITIONS, CALCULATE MULT AS
FOLLOWS: EXAMINE THE LISTING OF THE POSITIONS IN VOL
I OF THE INTERNATIONAL TABLES FOR THE SPACE GROUP
APPROPRIATE FOR THE POINT GROUP. IF NG = THE NUMBER
OF GENERAL POSITIONS (ALWAYS LISTED FIRST IN THE
TABLES) AND NS = THE NUMBER OF SPECIAL POSITIONS,
THEN
MULT = NG/NS
NOTE THAT THE PROGRAM IMMEDIATELY CONVERTS MULT
INTO ITS RECIPROCAL (STILL CALLING IT MULT(I)).
THIS IS WHY MULT (DESPITE ITS NAME) IS NOT REGARDED
BY THE PROGRAM AS AN INTEGER AND WHY IT IS TO BE
INPUT AS F5.1 (SEE FORMAT), E.G. AS 1.0, 4.0, ETC.
EXAMPLE D2h NUMBER 47, Pmmm, NG = 8)
ALL ATOMS IN GENERAL POSITIONS HAVE MULT = 1.0
(SINCE FOR THESE POSITIONS NS = NG)
AN ATOM IN A POSITION OF SITE-SYMMETRY m HAS
NS = 4, AND THUS HAS MULT = 8/4 = 2.0
AN ATOM IN A POSITION OF SITE-SYMMETRY mmm HAS
NS = 1 AND THUS HAS MULT = 8/1 = 8.0
EXAMPLE IN A CUBIC CRYSTAL: A GROUP WITH SYM D3d
[(3bar)m], USE NO = 166, AS SPECIFIED FOR NO (ON
CONTROL LINE) SINCE SPACE GROUP 166 IS R(3bar)m
NG = 12
AN ATOM IN A POSITION OF SITE-SYMMETRY 3m HAS
NS = 2, SO MULT = 12/2 = 6.0
(5B) 'THERMAL' (DISPLACEMENT, VIBRATION) PARAMETERS
STANDARD FORMAT IS (6F9.6,I1)
BUT IF IFMB IS NOT = 0, FORMAT IS 6F10.6,I1
(AGAIN, FORMAT CHANGES MAY BE MADE IN SUBROUTINE RDIN)
OR FREE-FORMAT INPUT (SEE EARLIER COMMENTS)
BETA'S OR U'S AS INDICATED WITH IB (LINE(3))
THE BETA'S ARE NOT USED IN THE PROGRAM. THEY ARE
IMMEDIATELY CONVERTED TO U'S (SUBROUTINE CONVER).
SEQUENCE B11,B22,B33,B12,B13,B23,NUORB(I)
OR U11,U22,U33,U12,U13,U23,NUORB(I)
OR (SHELX) U33,U23,U13,U12 (U11,U22,NUORB WITH x,y,z)
NUORB(I) NUMBER OF INDEPENDENT U'S OR B'S OF THE ATOM I
IF BLANK, 6 IS ASSUMED
NOTE: BE SURE TO END B-LINE (U-LINE) WITH A / IF USING
FREE FORMAT INPUT AND NOT GIVING NUORB (IT IS USUALLY
UNNECESSARY TO GIVE NUORB. IT NEED BE EXPLICITLY
INPUT ONLY FOR ATOMS IN SPECIAL POSITIONS.)
THE NUMBER OF INDEPENDENT OBSERVATIONS NINOBS = SUM(NUORB(I))
(NUORB IS USED ONLY IN CALCULATION OF ESD'S, SO IF THEY
HAVE NOT BEEN ADJUSTED FOR SYMMETRY THE ONLY EFFECT IS
THAT THE CALCULATED ESD'S ARE TOO LOW)
********************************************************************
* IF SIGMA U'S ARE PROVIDED, THEY FOLLOW AFTER THE COMPLETE SET OF *
* INPUT DATA FOR COORDINATES AND 'THERMAL' PARAMETERS *
********************************************************************
(5C) INPUT OF SIGMAS OF U (OR B), ATNAME FORMAT (6F10.5,A4)
SEQUENCE: SIGU11,SIGU22,SIGU33,SIGU12,SIGU13,SIGU23,ATNAME
FREE-FORMAT INPUT WILL BE USED HERE IF IT IS USED FOR
THE POSITION AND DISPLACEMENT PARAMETERS
NOTES: (1) |ISIG| INPUT LINES OF ESD's OF U'S (B'S) MUST BE GIVEN
(2) ATOM NAMES MUST BE IDENTICAL TO THOSE USED ABOVE.
SEQUENCE OF ATOMS IRRELEVANT. SORTED BY PROGRAM.
(3) IF ISIGX (1st OPTION LINE) IS NON-ZERO, SIGMAS
OF x,y,z INTERMIXED WITH SIGMAS OF U OR B,
SIGMAS OF x,y,z BEING FIRST LINE OF EACH PAIR.
THE SIGMAS OF x,y,z ARE NOT USED BY THE PROGRAM.
(4) FORMAT FOR SIGMAS OF U (OR B) IS NOT VARIABLE, BUT
IT COULD BE ALTERED IN SUBROUTINE RDIN (RDIN5)
(5) THE SIGMAS OF THE 'THERMAL' PARAMETERS WILL BE TAKEN
TO BE SIGMAS OF B'S IF IB = 0 OR 1 AND WILL BE
CONVERTED TO SIGMAS OF U'S. THEY ARE NOT LISTED
UNTIL AFTER THEY HAVE BEEN CONVERTED TO SIGMA(U)
(6) IF SIGU'S ARE TO BE USED TO CALCULATE L.S. WTS (ISIG
>0), ANY SIGMA = 0.0 IS SET = AVERAGE SIGMA
(7) IF NO SIGU'S INPUT, WU IS SET TO 1.0, ALL ATOMS, ALL U
(8) WHEN ISIG POSITIVE AND IWU.NE.1, SIGU'S FOR EQUIVALENT
ATOMS ARE GENERATED, AND SIGU'S ARE TRANSFORMED
TO CARTESIAN (WORKING) SYSTEM.
(6A, 6B, 6C)
INPUT CONCERNING ATTACHED RIGID GROUPS, ASSUMED TO BE
UNDERGOING TORSIONAL OR OTHER MOTION ('NON-RIGID' INPUT)
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ALL ATOMIC NAMES MUST BE IDENTICAL WITH THE NAMES USED IN THE
INPUT FOR THE COORDINATES, INCLUDING SPACING AND BLANKS. IF NOT
AN ERROR MESSAGE IS PRINTED AND CALCULATION STOPS.
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LIMITS AND DIMENSIONS:
NO ATOM MAY BE IN MORE THAN 3 ATTACHED RIGID GROUPS
A MAXIMUM OF 7 ATTACHED RIGID GROUPS IS ALLOWED, EACH CONTAINING
AT THE MOST 40 "AFFECTED ATOMS", I.E., ATOMS WHOSE POSITIONS
ARE AFFECTED BY MOTION OF THE GROUP ABOUT ITS PRESCRIBED AXIS
(An atom lying ON THE AXIS is not affected by the motion; thus
do NOT CONSIDER the axis-defining atoms as "affected atoms").
IF THESE DIMENSIONS ARE EXCEEDED , THE JOB WILL BE TERMINATED.
FOR EACH ARG, INPUT LINES 6A, 6B (AND 6C IF NEEDED). THEN
FOLLOW WITH SIMILAR LINES FOR THE NEXT ARG.
ALL INPUT FREE FORMAT. FOR EACH GROUP:
(6A) NAFA, LBAT1, LBAT2, NONSY, AXMOM
(NONSY, AXMOM USUALLY NOT NEEDED; USE / IF OMIT THEM)
NAFA - NUMBER OF AFFECTED ATOMS (NO MORE THAN 40)
NOTE ESPECIALLY THAT THIS NUMBER DOES NOT INCLUDE
THE TWO ATOMS THAT DEFINE THE LIBRATION AXIS AND
IT INCLUDES ONLY THE UNIQUE AFFECTED ATOMS, NOT
THOSE GENERATED BY ANY SYMMETRY OPERATIONS THAT
AFFECT THE ATTACHED RIGID GROUP.
IF NAFA IS INPUT AS A NEGATIVE NUMBER (IT IS
MADE POSITIVE), IT MEANS THAT THREE MORE ATOM NAMES
ARE TO BE READ (SEE LINE (6C) BELOW), AND THAT DIREC-
TION OF AXIS OF ATTACHED RIGID GROUP IS TO BE DEFINED
AS THE VECTOR PRODUCT OF THE VECTOR FROM LBAT1 TO
LBAT2 WITH THE VECTOR FROM LBAT3 TO LBAT4, THE AXIS
PASSING THROUGH THE ATOM WHOSE NAME IS GIVEN BY LBAT5.
i.e., (LBAT1-->LBAT2)x(LBAT3-->LBAT4), thru LBAT5
LBAT1 - NAME OF ATOM 1 DEFINING THE LIBRATION AXIS
LBAT2 - NAME OF ATOM 2 DEFINING THE LIBRATION AXIS
LBAT2 SHOULD BE THE AXIS-DEFINING ATOM THAT IS
CLOSEST TO THE OTHER ATOMS IN THE GROUP, SINCE
CORRECTED DISTANCES TO IT (BUT NOT TO LBAT1) ARE
CALCULATED AND PRINTED.
(PARAMETER 'NRBCON' WAS FORMERLY IN COLS 31-35; IT IS NO
LONGER USED. IF USING FREE FORMAT INPUT WITH A PRE-EXISTING
INPUT SET, BE SURE TO REMOVE IT)
NONSY
[ CAN IGNORE THIS PARAMETER IF DOING NO FREQUENCY CALCS,
(IFREQ = 0, 2nd OPTION LINE) OR IF SYMMETRY IS ONLY
P1 OR P1BAR ]
= 0 IF THIS 'ARG' LIES ON ANY SYMMETRY ELEMENT
NON-ZERO IF 'ARG' LIES ON NO SYMMETRY ELEMENT, WHEN
SYMMETRY IS HIGHER THAN P1BAR
(THIS IS USED ONLY IN SUBROUTINE NRCOR. THE PROGRAM USUALLY
CALCULATES THE MOMENT OF INERTIA FOR AN ARG IN MAKING
FREQUENCY AND FORCE CONSTANT CALCULATIONS. HOWEVER, WHEN
SYMMETRY IS HIGHER THAN P1BAR, MOMENT OF INERTIA CALCULATED
BY THE PROGRAM FOR A GROUP LYING ON A SYMMETRY ELEMENT WILL
BE WRONG, SO CALCULATION IS SKIPPED IN THESE CIRCUMSTANCES
UNLESS A NON-ZERO VALUE OF AXMOM HAS BEEN INPUT FOR THE
GROUP. )
AXMOM (ONLY USED WHEN NONSY IS ZERO). THE MOMENT
OF INERTIA OF THE ATTACHED GROUP, IN UNITS OF AT WTS AND
ANGSTROM SQUARED, ABOUT THE SYMMETRY AXIS. TYPICAL VALUES
ARE 2.9 FOR -NH3+; 3.2 FOR CH3; 40. FOR A CARBOXYLATE GROUP;
76. FOR T-BUTYL (NOT INCLUDING H'S); 88. FOR TRIFLUORO-
METHYL; 89. FOR PHENYL (INCLUDING H'S)
(6B) NAMES OF THE AFFECTED ATOMS
(UP TO 40 NAMES)
NOW THIS IS ALWAYS FREE FORMAT
- SUBMIT A TOTAL OF NAFA NAMES, EACH ENCLOSED IN
APOSTROPHES
(6C) WHEN NAFA INPUT AS NEGATIVE NUMBER FOR A GIVEN ARG, THREE
ATOM NAMES ARE READ HERE, FREE FORMAT:
LBAT3, LBAT4, LBAT5
(FOR EXAMPLE, 'C8' 'O4' 'N2' )
(SEE DISCUSSION UNDER NAFA ABOVE)
(6D, 6E, 6F)
(6D) WHEN IRIDE (1st OPTION LINE) IS NON-ZERO, READ HERE UP
TO 20 PAIRS OF ATOM NAMES, FREE FORMAT, FOR APPLICATION
OF RIDING CORRECTION. NO NEED FOR THIS FOR BONDS THAT
INVOLVE (ANISOTROPIC) H OR D; RIDING CORRECTIONS FOR
THESE WILL BE CALCULATED AUTOMATICALLY.
FIRST ATOM OF EACH PAIR IS THE ATOM ASSUMED TO BE RIDING
SECOND ATOM OF EACH PAIR IS THE ATOM THAT IS BEING RIDDEN
ENCLOSE EACH ATOM NAME IN APOSTROPHES, AND TERMINATE WITH /
EXAMPLE: 'C15' 'RU1' 'C16' 'RU1' 'O19' 'RU2' /
NOTE THAT EITHER SPACE(S) OR A COMMA MUST BE BETWEEN EACH
ITEM IN THE LIST.
(6E) WHEN IMIN (OPTION LINE) NE.0, READ HERE UP TO 20 PAIRS
OF ATOM NAMES, FREE FORMAT, FOR APPLICATION OF THE
'MINIMUM' THERMAL MOTION CORRECTION TO THE DISTANCE
BETWEEN THE ATOMS. THE ATOM NAMES MUST BE ENCLOSED
IN APOSTROPHES AND THE LIST TERMINATED WITH / (AS IN
THE EXAMPLE GIVEN UNDER (6B) ABOVE).
(6F) WHEN IUNC (OPTION LINE) NE.0, READ HERE UP TO 20 PAIRS
OF ATOM NAMES, WITH AN EQUIVALENT POSN FOR 2ND ATOM, FOR
CORRN OF A DISTANCE FOR UNCORREL'D (INDEPENDENT) MOTION.
THE EQUIV POSN MAY ONLY BE ONE RELATED BY TRANSL SYM OR
BY COMBINATION OF A CENTER OF SYM AT ORIGIN AND TRANSL.
THE DISTANCE MAY BE LARGER THAN THE LIMITING DISTANCE
SPECIFIED BY DIS ON THE CELL-DIMENSION LINE. ALL
INPUT FREE FORMAT. BE SURE ATOM NAMES ARE ENCLOSED IN
APOSTROPHES AND INPUT ENDS WITH A / AS IN THE
EXAMPLE BELOW. FOR EACH PAIR, THE FOLLOWING IS NEEDED:
ATOMNAME 1 ATOMNAME 2 NUNC (TUNC(I),I=1,3)
IF 2ND ATOM IS RELATED TO INPUT POSN BY A CENTER OF
SYM AT ORIGIN, NUNC IS NEGATIVE; IF NOT, NUNC IS
ZERO OR POSITIVE. TUNC(I) ARE TRANSL COMPONENTS,
WHICH MAY BE FRACTIONAL FOR CENTERED LATTICES AND
THUS ARE INPUT WITH DECIMAL PT, AS IN THIS EXAMPLE:
'C15' 'O17' 0 0. -1. 2. 'O18' 'N2' -1 0.5 2. 1.5
HERE FOR FIRST PAIR, O17 IS RELATED TO INPUT O17 BY
x, y - 1., z + 2. AND FOR THE SECOND PAIR, N2 IS
RELATED TO THE INPUT N2 BY 0.5 - x, 2. - y, 1.5 - z
(7) WHEN ISYM.NE.0 READ IN ONE LINE HERE (FREE FORMAT)
SYML(I), I = 1,3 (TERMINATE WITH / IF FEWER THAN 3
VALUES ENTERED)
SYML(I) ARE THE COORDINATES OF A POINT LYING ON ALL THE MOLECULAR
SYMMETRY ELEMENTS. IF THERE IS A UNIQUE POINT, THEY ARE THE
(CRYSTAL) COORDINATES OF THAT POINT, WHICH IS THE INVARIANT
POINT OF THE MOLECULAR POINT GROUP. IF NO UNIQUE POINT,
THEN THE ARBITRARY COORDINATES MAY BE GIVEN ANY VALUE, MOST
CONVENIENTLY 0. FOR EXAMPLE, FOR POINT GROUP Cs (m) WITH THE
m PERPENDICULAR TO THE b-AXIS, AT SAY y = 0.25, THE VALUES OF
SYML(I) WOULD BE 0.0, 0.25, 0.0 (ALTHOUGH ANY OTHER VALUES
COULD BE USED FOR x AND z). FOR POINT GROUP C2v WITH THE
PRINCIPAL AXIS ALONG THE a-AXIS OF THE CRYSTAL AT y = 0.25 AND
z = 0.50, WITH x ARBITRARY, SYML(I) WOULD BE 0.0, 0.25, 0.50.
(8A) IF NVIB.LE.0 (LINE 3), NO INPUT IS NEEDED HERE.
WHEN NVIB.LT.0, CALCULATION IS DONE FOR EVERY UNIQUE PAIR
OF ATOMS. WHEN NVIB.GT.0, SUCH CALCULATIONS DONE ONLY FOR
SPECIFIED PAIRS OF ATOMS.
EACH PAIR OF ATOMS DEFINES A DIRECTION FOR WHICH MEAN SQUARE
DISPLACEMENT AMPLITUDES WILL BE CALCULATED FOR THE ATOMS
FROM THE UOBS AND, FOR ATOMS IN THE ASYMMETRIC UNIT
INPUT, THE UCALC AS WELL. THE VALUES FROM THE
UOBS GIVE A MEASURE OF THE QUALITY OF THE DATA IF THE
ATOMS DEFINE A 'BOND' THAT WOULD BE EXPECTED TO BE
'RIGID'. THE VALUES FROM THE UCALC FOR ANY PAIR OF
ATOMS WITHIN A RIGID BODY OR WITHIN ANY LIBRATING
GROUP SHOULD BE IDENTICAL. THEY ARE OUTPUT FOR CHECKING
AND FOR COMPARISON WITH THE 'OBSERVED' AMPLITUDES.
MSDA CALCULATED BETWEEN AN ATOM IN THE FRAMEWORK AND
ONE IN A LIBRATING ATTACHED GROUP (OR BETWEEN ATOMS IN
DIFFERENT GROUPS OF THIS KIND) REFLECT THE INTERNAL MOTION
WHEN NVIB.GT.0 (LINE (3)), READ NVIB PAIRS OF ATOM NAMES,
EACH NAME BEING ACCOMPANIED BY THE NUMBER OF ITS EQUIVALENT
POSITION (= 1 IF ATOM IS IN THE ASYMMETRIC UNIT INPUT).
FREE FORMAT:
ATNAME1, EQPOSN1, ATNAME2, EQPOSN2
THE EQUIVALENT POSITIONS ARE LISTED
IN ORDER EARLY IN THE OUTPUT. IF UNSURE ABOUT THIS
ORDER, TRY ONE RUN WITH NVIB = 0 TO CHECK THE ORDER.
CAUTION: ATOM NAMES MUST BE IDENTICAL TO THOSE USED
ON ATOM PARAMETER LINES, INCLUDING BLANKS.
(8B) IF ICSVIB.NE.0 (ON LINE (3)), READ 2*ICSVIB LINES
HERE. ICSVIB MAY BE NO LARGER THAN 10. THE LINES
COME IN PAIRS.
- - FIRST LINE OF EACH PAIR CONTAINS DIRECTION COSINES
(RELATIVE TO THE CARTESIAN CRYSTAL AXES) AND THE
NUMBER OF ATOMS WHOSE NAMES ARE TO BE READ ON THE
FOLLOWING LINE (NO MORE THAN 12) AND FOR WHICH THE
DISPLACEMENT AMPLITUDES IN THE SPECIFIED DIRECTION ARE
TO BE CALCULATED.
FREE FORMAT
(FOUR VALUES: 3 DIR COS, AND NO. OF ATOMS TO BE READ)
- - SECOND LINE OF EACH PAIR CONTAINS THE NAMES OF UP TO 12
ATOMS FOR WHICH AMPLITUDES ARE TO BE CALCULATED IN THE
SPECIFIED DIRECTION. CALCULATIONS MAY BE MADE ONLY FOR
ATOMS IN THE ASYMMETRIC UNIT INPUT.
FREE FORMAT
(BE SURE TO ENCLOSE ATOM NAMES IN APOSTROPHES)