The X-ray system of crystallographic programs for any computer having a PIDGIN FORTRAN ...

284 Pages·2008·9.98 MB·English

https://ntrs.nasa.gov/search.jsp?R=19730005010 2018-01-30T04:59:26+00:00Z
TECHNICAL REPORT TR-igZ JUNE 1972
THE X-RAy SYSTEM
,OF CRYSTALUOGRAPHIC PROGRAMS
FOR ANY COMPUTER
HAVING A PIDGIN* FORTRAN COMPILER
VERSION OF JUNE 1972 EDITED By
j. M. STEWART* '
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TITLE 1 1
04/22/72
TECHNICAL REPORT TR-lg2 JUNE 1972
THE X-RAy SYSTEM
,,OF CRYSTALLOGRAPHIC PROGRAMS
FOR ANY COMPUTER
HAVING A PIDGIN* FORTRAN COMPILER
VERSION OF JUNE 1972 EDITED BY
J. M. STEWARTf
6, J. KRuGER, M. L. AMMON,
C. DICKINSON, AND S. R. HALL
COMPUTER SCIENCE CENTER
UNIVERSITY OF MARYLAND
*PiDGIN FORTR»N IS A NEUTRAL SUBSET OF FORTRAN I,V
AND IS DESCRIBED IN DETAIL IN AN APPENDIX
THE UNivtHsirTY OF MARYLAND CONTRIBUTION TO THIS WORK WAS IN PART
SUPPORTED BY tHE NATIONAL AERONAUTICS AND SPACE ADMINISTRATION UNDER
GRANT NGL-21-002-008 TO THE COMPUTER SCIENCE CENTER AND IN PART BY
THE ARPA GKANT TO THE UNIVERSITY OF MARYLAND
v-' TITLE 2 2
04/22/72
IN COLLABORATION WITH -
DEPARTMENT OF ENERGY, MINES AND RESOURCES
MINISTERE DE L'ENEKGIE DES MINES
ET DES RESSOURcES
CANADA
AND
SCIENCK RESEARCH COUNCIL (U.K.)
************
I SHALL TRY TO CORRECT ERRORS WHERE SHOWN
TO BE ERRORS. AND SHALL ADOPT NEW VIEWS
AS> FAST AS THEY APPEAR To BE THuE VIEWS
ABRAHAM LINCOLN...,.
************
TITLE 3 3
OH/22/72
ABSTRACT
THIS REPORT IS A MANUAL FOR THP USE OF A LIBRARY OF CRYSTALLOGRAPHIC PROGRAMS.
THIS LlBRARYf CALLED THE X-RAY SYSTEM, IS DESIGNED TO CARRY OUT THE
CALCULATIONS REQUIRtO TO SOLVE THE STRUCTURE OF CRYSTALS BY DIFFRACTION
TECHNIQUES. IT HAS BEEN IMPLEMhNTED AT THE UNIVERSITY OF MARYLAND ON THE
UNIVAC 1108 UNDER EXEC.yHI. H HAS» HOWEVER, BEEN DEVELOPED AND RUN ON A
VARIETY- OF MACHINES UNDER VARIOUS OPERATING SYSTEMS. HENCE WE CONSIDER IT
TO BE AN ESSENTIALLY MACHINE INDEPENDENT LIBRARY OF APPLICATIONS PROGRAMS.
THE REPORT INCLUDES DEFINITION OF CRYSTALLOGRAPHIC COMPUTING TERMS, PROGRAM
DESCRIPTIONS, WITH iOME TEXT TO SHOW THEIR APPLICATION TO SPECIFIC CRYSTAL :
PROBLEMS. DETAILED CARD INPUT DESCRIPTIONS, MASS STORAGE FILE STRUCTURE AND
SOME EXAMPLE RUN STKEAMS. NO PROGRAMS ARE SHOWN. THEY ARE SUPPLIED SEPARATELY
AS CA. 60000 CARDS UN A BLOCKED TAPE APPROPRIATE TO THE MACHINE ON WHICH ~
THEY ARE TO BE COMPILED AND RUN.
l.TOC
Ot/22/72
OF CONTENTS
THE wKITt-U^ OF EACH PROGRAM IS GIVEN IN TWO PARTS, THE FIRST
IS DESCRIPTIVE. THE SECOND IS « CARD ORDER SUMMARY. FILE HANDLING SUMMARY,
AND CARD FORMAT DESCRIPTION. IN EACH CAf£. THE WRITE-UP APPEARS
ALPHABETICALLY BY PKOGRAM CALLING CARD MNEMONIC. THE APPENDICES PROVIDE
FURTHER DETAILS ABOUT THE STRUCTURE OF THE SYSTEM.
GENERL GENERAL DESCRIPTION OF THE SYSTEM
ABSORB DIFFRACrOMETER ABSORPTION CORRECTION
APHASE SEARCH OF SIGMA-TWO RELATIONSHIPS FOR A SET OF POSSIBLE PHASES
BONDAT GENERA I ION OF BONUED ATOM POSITIONS
BONDLA DETERMINATION OF CONTACT AND BOND DISTANCES AND ANGLES WITH
ESTIMATED ERRORS
CRYLSQ GENERAL CRYSTALLOGHAPHIC LEAST SQUARES PROGRAM
DATC05 TREATMENT OF DIFFR«CTOMETER DA A
T
DATRDN PREPARAIION OF BINARY DATA FILE AND PRELIMINARY TREATMENT OF
DATA ANU SYMMETRY
DIFPCH PREPARAI10N OF SORTED DIFFRACTQMETER SETTING CARDS
DIFSET GENERATION OF SETTINGS FOR GATHERING DATA ON AN AUTOMATED
DIFFRACIOMETER
OUMCOP DUMP OR COPY THE BINARY DATA FILE
FC STRUCTURE FACTOR C»LCULATION
FOURR FOURIER TRANSFORMATIONS TO GIVE PATTERSON, VECTOR, ELECTRON
DENSITY. DIFFERENCt, OR E MAPS
LISTFC LISTS SIRUCTURE FACTORS FOR PUBLICATION '
LOADAT LOAD ATOMIC PARAMETERS INTO THE BINARY DATA FILE
LSOPL CALCULAIION OF EQUATIONS OF 3-DIMENSIONAL PLANES AND LINES
MODIFY BINARY UATA FILE EDITING AND GENERATION OF PSEUDO DATA
l.TOC 2 5
0<t/22/72
NORMsF PRELIMINARY DATA SCALING, CALCULATION OF QUASI-NORMALIZED
STRUCTURE FACTORS (E>, AND ESTIMATION OF OVERALL TEMPERATURE
FACTOR
PARAw LEAST SUUARES REFINEMENT OF CELL PARAMETERS FROM TwO THETA DATA
PEKPIK SEARCH COURIER MAPS FOR PEAKS
PHASE SEARCH UF SIGMA-TWO RELATIONSHIPS FOR A SET OF POSSIBLE PHASES
(CENTRIC CASE)
REVIEW EVALUATION OF DIRECT PHASE DETERMINATION
RLIST LISTS R VALUES FOR VARIOUS ZONES AND OTHER REFLECTION CLASSES
SIN&FN FORMS TRIPLES FOR PHASE DETERMlNATION(CENTRlC OR ACENTRIC)
STEPRF STEP REFINEMENT
TANGEN USE OF IANGENT FORMULA TO CALCULATE PHASES
WRITEU GENERATION OF WRITt-UP
WTANAL ANALYSIS OF LEAST SQUARES WEIGHTING SCHEMES
WTLSSQ REVISION OF LEAST SQUARES WEIGHTING SCHEMES
APENDX-1 CONTRIBUTORS TO THfe SYSTEM
APENDX-2 EXAMPLE DATA DECKS.
APENDX-3 DISTRIBUTION OF THP SYSTEM
APENDX-I+ PIDGIN I-OKTRAN
APENDX-5 THE STRUCTURE OF THE SYSTEM
APENDX-6 THE FORMAT OF THE BINARY DATA FILE
APENDX-7 INFORMAIION REQUIRED IN REPORT OF SUSPECTED ERRORS
l.GENERL- 1 6
0<*/22/72
PREFACE
THE X-RAY SYSTtM COMPRISES A COLI_EXTI N OF INTER-RELATED FORTRAN
P
PROGRAMS FOR THE STKUCTyRAL ANALYSIS OK CRYSTALS FROM DIFFRACTION DATA.
IT PROVIDES ROUTINES AT ALL LEVELS OF THE ANALYSIS - EXAMPLES ARE
UIFFRACTOMETEH SETTING PROGRAMS, PROGRAMS FOR APPLYING DIRECT METHODS OF
PHASE DETERMINATION IN THE PRODUCTION OF A TRIAL STRUCTURE* FOURIER
TRANSFORMS AND LEASI SQUARES RFFlNEMENTSt AND ALSO PROGRAMS TO AID IN THE
INTERPRETATION AND PUBLICATION OF THE REFINED RESULTS. IT OPERATES
UNDER ITS OWN FORTRAN SUB-SYSTKM MONITOR - THE 'NUCLEUS' - WHICH PERMITS
THE READY ADDITION OF EXTRA PROGRAMS INTO THE SYSTEM.
THE COURSE OF A JOB RUN ON THE SYSTEM IS DETERMINED BY THE INPUT -
DATA CARDS WHICH CALL THE APPROPRIATE PROGRAMS INTO THE STORE 0? THE
COMPUTER AS REOUIREU. AT THE SAME TIME, A 'BINARY DATA FILE' (WHICH IS
FULLY DESCRIBED LATtR) is CONTINUOUSLY UPDATED AS THE SOLUTION PROGRESSES,
THUS KEEPING THE SI^E OF AN IN^UT DATA DECK TO A MINIMUM. WHENEVER
POSSIBLE. THE SYSTEM WILL CONTINUE WITH A CALCULATION BUT, IN THE EVENT
OF AN IRRECOVERABLE SITUATION, IT WILL ABANDON ITS EFFORTS *ND CHASTISE
THE USER WITH AN EPIGRAMMATIC OUOTATION.
THIS WRITE-UP Ib DIVIDED I"TO THREE SECTIONS -
1. A DESCKIPT10N OF THE CALCULATIONS PERFORMED BY EACH PROGRAM
2. DETAILtO INSTRUCTIONS FOR THE PREPARATION OF INPUT DATA
3. A SERItS OF APPENDICES PROVIDING NECESSARY INFORMATION
FOR THOSE WHO REQUIRE A DETAILED KNOWLEDGE OF THE STRUCTURE
OF THE SYSTEM, KQK EXAMPLE IN ITS IMPLEMENTATION ON ANY
GIVEN COMPUTER.
DISCLAIMER
ALTHOUGH EACH PROGRAM OF THE X-RAY SYSTEM AND THE NUCLEUS HAS BEEN
TESTED BY ITS CONTRIBUTORS AND FURTHER TEStED ON A NUMBER OF DIFFERENT
COMPUTFRS, NO WARRANTY, EXPRESSED OR IMPLIED, IS MADE BY THE CONTRIBUTORS
OR THE SYSTEM'S PKOUKAMMEHS AS TO THE ACCURACY AND FUNCTIONING OF THE
PROGRAMS, THEIR SUBPROGRAMS, T^E RELATED PROGRAM MATERIAL, OR wRITE-UP.
NO RESPONSIBILITY Ib ASSUMED BY THE CONTRIBUTORS OR BY ANY MEMBER OF THE
X-RAY SYSTEM (iROUP UR SUPPORTERS OF THESE pERSONS IN CONNECTION WITH THE
USE OR ATTEMPTED USt OR APPLICATION OF THESE PROGRAMS.
l.GENERL- 2 7
04/22/72
NOTE TO USFRS
THE USUAL JOURNAL REFERENCE TO CALCULATIONS DONE WITH THE X-RAY SYSTEM IS
AS FOLLOWS
THE X-KAY SYSTEM - VERSION OF JUNE 1972. TECHNICAL REPORT TR-192
OF THE COMPUTER SCItNCE CENTER, UNIVERSITY OF MARYLAND, JUNE 1972.
l.GENERL- 3 8
OU/22/72
INTRODUCTION
THE OVERALL PLAN OF THE X-RAY SYSTEM iS SUCH THAT THE USER SHOULD
UNDERSTAND SEVERAL IOPICS, NAMhLY -
1. PREAMBLE CARDS NEtDED FOR THE LOCAL IMPLEMENTATION OF THE
SYSTEM
2. X-RAY SYSTEM CARD FORMAT CONVENTIONS AND FUNCTIONS
3. FORTRAN FORMAT CONVENTIONS
H. THE CONCEPT AND USE OF THE BINARY DATA FILE
5. THE STKUCTURE OF »N X-RAY SYSTEM DATA DECK
6. SYSTEM TERMINOLOGY.
PKEAMBLE CARL'S REQUIRED BUT NOT DESCRIBED
IT IS NOT POSSIBLE HERE T» TREAT ALL THE LOCAL LORE (EVEN IF IT .WERE
KNOWN) CONCERNING THE PREAMBLE CARDS REQUIRED TO GET A JOB RUN ON ANY
GIVtN COMPUTEK. APHtNL>IX 2 GIVES SEVERAL EXAMPLES OF RUNS OF
VARYING COMPLEXITY IN SYSTEM U^E. WHhN THE SYSTEM IS IMPLEMENTED ON A
SPECIFIC MACHINE. I I IS SUGGESTED THAT EACH OF THE EXAMPLES BE PREFACED
bY THE APPROPRIATE JOB CONTROL DECK REQUIRED FOR THAT MACHINE.
THE FOLLOWING UISCUSSION WILL ONLY BE CONCERNED WITH HOW THE USER
MUST PREPARE HIS DAI A FROM THE POINT AT WHICH THE SYSTEM ASSUMES CONTROL
OF THE JOB.
X-RAY bYSTEM CARD FORMAT CONVENTIONS AND FUNCTIONS
X-RAY SYSTEM UTILIZES 1-OUR TYPES OF INPUT DATA CARDS. EVERY CARDr
REGARDLESS OF TYPE, IS IDENTIFIED BY ITS FiRST SIX COLUMNS.
THE FOUR TYPES OF CARD ARfe AS FOLLOWS ...
i. PROGRAM CALLING C«RDS (WHICH ARE READ BOTH BY THE SYSTEM
AND BY THE CALLED PROGRAM) - E.G. =OATRDN=, =BONDLA=, =TANGEN=»
l.GENERL- 4 <»
04/22/72
=FC=, =CRYLSQ=
CARDS ACTUALLY CONTAINING CRYsTALLOGRAPHIC OR OTHER DATA
(READ WITHIN THE APPROPRIATE. PROGRAM) - E.G. =ATOM=,
=CELL=> =HKL=, =
3. THE =END= CARD, WHICH MARKS THE END OF A DATA SET FOR THE
SELECTED PROGRAM «ND USUALLY INITIATES THE ACTUAL CALCULATION
H, • OPERATION CARDS, ".'HICH ARE REcOGNIZtD AND ACTED UPON BY
THE SYSTEM. THESE ACHIEVE HOUSEKEEPING FUNCTIONS SUCH AS
PROVIDING A =TITLf= TO BE PRINTED AT THE TOP OF EACH PAGE OF
PRINTED OUTPUT, 0" =FINISH= WHICH TERMINATES THE RUN. OTHER
EXAMPLES ARE =REM"RK=, =S<WE=, =RESTART= ( AS ONLY THE FIRST
6 COLUMNS ARE CHECKED, THE FINAL T IS OPTIONAL),
IN ADDITION TO ITS IDENTIFICATION COLyMNSr EACH CARD HAS A FIXED
FORMAT WHICH IS SET IN THE PROGRAMS. EVERY CARD IS READ AT LEAST TWICE,
ONCE To IDENTIFY ITi> FUNCTION PND ONCE TO OPCODE IT ACCORDING TO ITS FORMAT
AND THE LIST OF ITEMS WHICH IT SHOULD CONTAIN. THIS DOUBLE READING MAKES
POSSIBLE FAIRLY FLEXIBLE CARD ORDERS AMD GIVES THE USER CONTROL OF THE
CALCULATIONS BY MEANS OF THE STRUCTURE OF HIS DATA DECK. THE WHOLE
PROCESS OF CONTROL LS BASED UPON THESE CARDS AND THEIR ORDER so THAT
THE UTMOST CARE SHOULD BE EXtRMSED IN THEIR PUNCHING AND ORDERING.
AS LONG AS NO 'INVALID' PUNCHING IS CONTAINED IN THE CARD, CHECKING AND
DIAGNOSTIC PRINT OUI ARE POSSIBLE WHEN UNA CEPTABLE CARD ORDER SEQUENCES
C
ARE ENCOUNTERED. 1H1S DIAGNOSTIC WHKH, UNFORTUNATELY' WILL BECOME
FAMILIAR TO MOST X-KAY SYSTEM USERS STATES -
CARD JUST RtAD.... (IMOGE OF CARD N QUESTION)
CARD i.D. EXPECTED.... xxxxxx TYYYYYY zzzzzz
WHERE XXXXXX=, =YYTYYY=, AND =ZZZZZZ= ARE THE ONLY ACCEPTABLE CARD
=
IDENTIFICATIONS EXPtCTED AT THF POINT AT WHICH THE 'CONDEMNED' CARD WAS
ENCOUNTERED. MANY TIMES THIS ERROR IS CA(jS£D BY SIMPLY NOT PUNCHING
WHAT IS SHOWN IN THt INSTRUCTIONS, E.G. =DATRON= FOR =OATRDN=, OR,
MORE COMMONLY, A CONFUSION BETWEEN THE LETTER 0 AND THE DIGIT 0.
THE 'INVALID' HUNCHING REt-ERRED TO ABOVE IS THE PLACING OF CHARACTERS
IN FIELDS WHICH DO NOT BELONG THERE UNU£R THE RULES OF FORTRAN. EXAMPLES
ARE THE PLACING OF « DECIMAL POINT WITHIN AN 'I' FIELD, OR A LETTER WITHIN
AN «F» FIELD.
FORTRAN FORMAT CONVENTIONS
THE FOLLOWING UISCUSSION IS NOT INTENDED TO BE EXHAUSTIVE, BUT RATHER
TO EMPHASIZE THE RULES OF FORTPAN FORMAT STATEMENTS WHICH ARE USUALLY
TROUBLESOME TO THE CRYSTALLOGRnPHER USING THE X-RAY SYSTEM WITH NO
PREVIOUS FORTRAN PROGRAMMING EXPERIENCE. SOME OF THE FOLLOWING MATERIAL
WILL REPRESENT AN OVERSIMPLIFICATION BUT HOPEFULLY WILL BE SUFFICIENT TO
INSURE FEWER TERMINATIONS DUE TO 'BAD' CARDS IN THE CRYSTALLOGRAPHIC