write_h {crone} | R Documentation |
Write structure factors to a reflections file
Description
This function writes standardised structure factors data into an ASCII
file. The files includes cell size, space group character symbol and
Miller indices vector. It can include all of some of observed and/or
calculated structure factors amplitudes and phases, either for anomalous
or non-anomalous data.
Usage
write_h(filename, fdata)
Arguments
filename |
A character string. Prefix of the structure factors
file name. The file name has the form "[prefix]_h.dat".
|
fdata |
A names list, usually created with functions
standardise_fdata or read_h , and consisting of
the following fields:
a Real numeric. Unit cell length in angstroms. Always
included.
SG. Spacegroup 2-letters character string. There are only two
symmetries possible when working within 1D
crystallography, P1 (no symmetry) and P-1 (inversion
through the origin). SG can be either "P1" or "P-1".
Always included.
hidx. Real numeric array. 1D unique (positive in the 1D context)
Miller indices. Always included.
Fobs. Real numeric array. Amplitudes of observed structure
factors. Not always included.
sigFobs. Real numeric array. Errors associated with Fobs. Not
always included.
Fp. Real numeric vector. Amplitudes of the positive
component of Friedel (or Bijvoet) pairs (F+). Not
always included.
sigFp. Real numeric vector. Errors associated with Fp.
Not always included.
Fm. Real numeric vector. Amplitudes of the negative
component of Friedel (or Bijvoet) pairs (F-). Not always
included.
sigFm. Real numeric vector. Errors associated with Fm. Not
always included.
Phiobs. Real numeric array. Phases (in degrees) of structure
factors obtained with one of the methods used for
structure solution. Not always included.
Phicalc. Real numeric array. Phases (in degrees) of structure
factors calculated from the correct 1D structure.
They are normally used to check correctness of
Phiobs. Not always included.
|
Value
This function does not return anything, but will create an ASCII
file of name *_h.dat which contains structure factors and other type of
information.
Examples
# Data from thiocyanate structure
datadir <- system.file("extdata",package="crone")
filename <- file.path(datadir,"thiocyanate_x.dat")
sdata <- read_x(filename)
# Miller indices
hidx <- 1:10
# Observed structure factors with errors
ltmp <- sfobs(hidx,sdata)
Fobs <- ltmp$F
sigFobs <- ltmp$sF
# Phases from calculated structure factors
ftmp <- strufac(hidx,sdata)
phicalc <- ftmp$Fpha
# Create standardised fdata structure
fdata <- standardise_fdata(sdata$a,sdata$SG,hidx,Fobs=Fobs,
sigFobs=sigFobs,Phicalc=phicalc)
# Name of structure factors file (in temporary directory)
wd <- tempdir()
fname <- file.path(wd,"test")
# Write data to file
write_h(fname,fdata)
[Package
crone version 0.1.1
Index]