Computer Programs for Chemistry

293 Pages·1972·6.021 MB·English

by  DeLos DeTar (Eds.)

EDITORIAL BOARD
DeLos F. DeTar, EDITOR
STANLEY HAGSTROM
WALTER HAMILTON
ANDREW STREITWIESER
KENNETH WIBERG
C O M P U T ER P R O G R A MS
F OR C H E M I S T RY
Edited by DeLos F. DeTar
DEPARTMENT OF CHEMISTRY
AND INSTITUTE OF MOLECULAR BIOPHYSICS
THE FLORIDA STATE UNIVERSITY
TALLAHASSEE, FLORIDA
VOLUME] 4
ACADEMIC PRESS New York and London 1972
COPYRIGHT © 1972, BY ACADEMIC PRESS, INC.
ALL RIGHTS RESERVED
NO PART OF THIS BOOK MAY BE REPRODUCED IN ANY FORM,
BY PHOTOSTAT, MICROFILM, RETRIEVAL SYSTEM, OR ANY
OTHER MEANS, WITHOUT WRITTEN PERMISSION FROM
THE PUBLISHERS.
ACADEMIC PRESS, INC.
Ill Fifth Avenue, New York, New York 10003
United Kingdom Edition published by
ACADEMIC PRESS, INC. (LONDON) LTD.
24/28 Oval Road, London NW1
LIBRARY OF CONGRESS CATALOG CARD NUMBER: 68-19706
PRINTED IN THE UNITED STATES OF AMERICA
CONTRIBUTORS TO VOLUME 4
Contributors of Programs
DELOS F. DETAR, Department of Chemistry and Institute of Molecular
Biophysics, Florida State University, Tallahassee, Florida 32306
CAROL DEUTSCH, Department of Chemistry, Yale University, New Haven,
Connecticut 06520
MARK M. ROCHKIND, Bell Telephone Laboratories, Inc., Murray Hill, New
Jersey 07974
Contributors of Conversion Decks
CHARLES L. WILKINS, Department of Chemistry, University of Nebraska,
Lincoln, Nebraska 68508
Other Contributors
HARRY M. MURPHY, JR., Air Force Weapons Laboratory, Kirtland AFB,
New Mexico
(The program TIDY used to improve some of the FORTRAN listings
in Volume 4.)
ix
P R E F A CE
The purpose of Computers Programs for Chemistry is to make available
a useful collection of tested programs, which may be expected to have a
long useful life. Since the programs in each volume are represented by
considerably over 10,000 source cards, arrangements have been made to
provide a master tape for each volume. The tapes are available from the
publishers of Volumes I to III, W. A. Benjamin, Inc., and for Volume 4,
Academic Press, Inc. The tape for Volume 4 has about 16,000 card images
and a cumulative compilation of correction and conversion cards for the
previous volumes.
The programs in the series fall into two broad classes: complete
packages and subroutines. ANSI FORTRAN has been chosen as the
language since it provides adequate flexibility and excellent compatibility.
But where departures are needed for efBciency, the editors have not
hesitated to allow use of small subroutines in nonstandard FORTRAN
or in assembly language, with careful documentation.
Since computers still represent a relatively new tool, it will require
time to develop and to implement adequate standards for programs. It is
xi
xii PREFACE
the hope of the editorial board that Computer Programs for Chemistry
can encourage the continuing development of elegant programs useful
in many aspects of chemical research. There may be occasional overlap
between this series and the activities of the excellent program exchanges,
but for the most part, program publication and program exchange are
complementary and serve different needs. Exchange is the only practical
approach for programs that are experimental or that the author is willing
to make available to others only on an as is basis. Publication is better
for programs that accomplish important tasks by well-established algo­
rithms. Publication implies a commitment on the part of the author and
the editorial board to help solve problems due to bugs, it implies a
high standard of programming, and it implies careful and extensive
documentation.
Anyone who intends to use computer techniques will have to learn
about computer hardware and computer software. To use effectively
even the stand-alone programs in these volumes requires some under­
standing of FORTRAN. This volume also contains a number of convert­
ing subroutines that are useful primarily to the serious programmer.
These have proved especially useful as parts of programs presented in
previous volumes.
B R I EF DESCRIPTIONS
OF P R O G R A MS
BNJBCD
This is a FORTRAN subroutine to convert a binary integer into a
coded integer. It is compatible with REMECH (Volume II) PLOTLN
(Volume I), BNJBCD requires MSHIFT.
These routines give the FORTRAN programmer access to character
manipulation which is relatively machine independent; the assembly
language routines needed are trivial.
CDORD
CDORD treats circular dichroism and optical rotatory dispersion data.
The CD curve is approximated by any desired number of Gaussian
xiii
xiv BRIEF DESCRIPTIONS OF PROGRAMS
terms. Adjustment of the Gaussian parameters may be made on the CD
data, on the ORD data through the Kronig-Kramers transform, or on
both. There are extensive facilities for plotting the results.
EDITID
EDITID (Edit on Identifier) is a utility program for editing a file of
card images. Insertions and replacements are automatic and depend on
the identification in Cols. 78-80. EDITID was designed to edit the master
tapes of Computer Programs for Chemistry with the conversion and
correction decks.
EDITQ
EDITQ (Edit Sequential) is a utility program for editing a file of
card images, usually a tape file, by control cards which specify insertions
and deletions at sequential locations.
EQCENT
EQCENT computes the molecular weight of a protein or of a polymer
from equilibrium ultracentrifugation data based on Rayleigh interference
optics.
FRS3
This sorting subroutine physically sorts a master array and will reorder
a series of passive arrays so that corresponding elements in all arrays
remain in step. The algorithm has been extensively tested and shown
to be highly efficient. It may be used as a stand alone subroutine or the
code may be incorporated in other programs.
GBCDBN
This is a FORTRAN subroutine to convert a string of binary coded
characters representing a real number into binary real form. It requires
MSHIFT. GBCDBN is compatible with REMECH (Volume II).
Brief Descriptions of Programs xv
GENLSS
GENLSS is a general program for obtaining a least squares fit of
parameters of virtually any function. Convergence is based on the con­
ventional Taylor's series expansion of the function about the initial param­
eter estimates. The user supplies two subroutines DEFINE and FUNCT.
DATA statements in DEFINE identify the parameters, the variables, and
the expression being treated. The equation which relates the dependent
variable, the independent variables, and the parameters is coded in
FUNCT. There is provision for variable weighting, and any or all param­
eters can be held constant. Data may belong to a single set or to a
series of subsets characterized by individual constants. An example of the
latter would be kinetics runs where all data are characterized by a com­
mon rate constant but where each run involves different initial reactant
concentrations. Any number of dependent and independent variables may
be used.
IBCDBN
This is a FORTRAN subroutine to convert a string of binary coded
numerical characters to binary integer form. It requires MSHIFT.
IBCDBN is compatible with REMECH (Volume II).
INDEX
This is a FORTRAN program to provide an indexed listing of all
variables and all statement references. INDEX is the program used to
provide the listings published in these volumes.
LORAK
LORAK is a program for obtaining rate constants of consecutive first-
order reactions A-»B-»C based on measurements of optical absorbance
at a series of wavelengths over a series of time intervals. LORAK also
computes the molar absorbtivity of A, B, and C at each wavelength.
LSKIN2
LSKIN2 finds best parameters for a second-order equation, namely
the rate constant and initial concentrations of reactants a and h. It treats
xvi BRIEF DESCRIPTIONS OF PROGRAMS
all cases: disappearance of reactant or appearance of product with either
a single reactant or with two reactants having initial a equal or not equal
to initial b. It also handles nonintegral stoichiometry. The input variable
may be concentration, it may be proportional to concentration, it may be
optical transmittance, it may be resistance or other reciprocal variable,
or the user can code his own functions to relate concentration and
observed variable. There is provision to treat small nonlinearity between
the nominal concentration and the true concentration.
MSHIFT
This is a simple CDC 6400 assembly language (COMPASS) shifting
subroutine presented as a prototype for coding a similar program for
other computers.
PACK and PACKI, UNPACK and UNPCKI
These are FORTRAN subroutines for packing characters into words
and conversely for unpacking the characters. They require MSHIFT, a
simple assemply language shifting program, described above. They also
require very simple logical functions. PACKI and UNPCKI define the
formats.