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Full Discussion: [BASH] Problem with a sed -n statement
Top Forums Shell Programming and Scripting [BASH] Problem with a sed -n statement Post 302599843 by agama on Saturday 18th of February 2012 11:45:25 PM
Old 02-19-2012
From your text, it seems that given input like this:

Code:
comment
comment
data
data
data
data
comment
comment
data
data
data
data

You want an output file (Cartesian.xyz) to contain:

Code:
Cartesian GeomOpt Video
transformed data
transformed data
transformed data
transformed data
Cartesian GeomOpt Video
transformed data
transformed data
transformed data
transformed data

I also assume that the transformation can be applied to each line independently (i.e. you don't need the whole frame's worth of data to do the transformation. If that is true, then might I suggest something along the lines of the following script to read and transform the data. Looking at your code, it seems to me you are doing a lot of unnecessary rereading of the input file with each loop skipping what has already been processed.

Code:
#!/usr/bin/env ksh

# converts coordinates from one form to another and
# echos translated values
function transform
{ 
    echo "$(( $1 * 300 ))  $(( $2 * 200 )) $(( $3 /42 ))"
}

natoms=5       # constant number of atoms/frame
nframes=2       # number of frames in the input data
data=t37.data   # name of the data file (my test file was t37.data)

for (( j = 0; j < nframes; j++ ))         # for each frame
do
    read junk       # read and ignore comment lines 
    read junk

    echo "Cartesian GeomOpt Video"  # looks like this marks the frame in new file????
    for (( i = 0; i < natoms; i++ ))     # for each atom in the frame
    do
        read atom_letter x y z           # read its data 
        echo "$atom_letter $(transform $x $y $z)"   # transform and wriite 
    done
done <$data >Cartesian.xyz   # all echos in the loop write to cart.xyz

Again, this was just a guess at what your goal is, and a big assumption that each atom's coords can be translated independently of the others in the frame.

As for the transformation. I stuck in a dummy function to illustrate it. I don't know if you have an external programme that needs to be called, or if it's a function in your script that computes the transformation. Regardless, the assumption that I made was that the process/function echoes the changed x,y,z values which can then be echoed by the statement in the while loop.

Hope this makes some sense, and that I'm not too far off the mark.
This User Gave Thanks to agama For This Post:
EdinburghLad
 

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LEARN ABOUT FREEBSD

gpioiic

GPIOIIC(4)						   BSD Kernel Interfaces Manual 						GPIOIIC(4)

NAME

     gpioiic -- GPIO I2C bit-banging device driver

SYNOPSIS

     To compile this driver into the kernel, place the following lines in your kernel configuration file:

	   device gpio
	   device gpioiic
	   device iic
	   device iicbb
	   device iicbus

DESCRIPTION

     The gpioiic driver provides an IIC bit-banging interface using two GPIO pins for the SCL and SDA on the gpiobus.  gpioiic implements an open
     collector kind of output, as recommended by the standard, when driving the pins on the gpiobus, i.e, they are never switched to the logical
     value of '1', or they are '0' or simply open (Hi-Z/tri-state).  So the pullup resistors are required so gpioiic can work.

     On a device.hints(5) based system, like MIPS, these values are configurable for the gpioiic:

     hint.gpioiic.%d.at     The gpiobus you are attaching to.  Normally just gpiobus0.

     hint.gpioiic.%d.pins   This is a bitmask of the pins on the gpiobus that are to be used for SCLOCK and SDATA from the GPIO IIC bit-banging
			    bus.  To configure pin 0 and 7, use the bitmask of 0b10000001 and convert it to a hexadecimal value of 0x0081.  Please
			    note that this mask should only ever have two bits set (any other bits - i.e., pins - will be ignored).

     hint.gpioiic.%d.scl    Indicates which bit in the hint.gpioiic.%d.pins should be used as the SCLOCK source.  Optional, defaults to 0.

     hint.gpioiic.%d.sda    Indicates which bit in the hint.gpioiic.%d.pins should be used as the SDATA source.  Optional, defaults to 1.

     On a FDT(4) based system, like ARM, the DTS part for a gpioiic device usually looks like:

     gpio: gpio {

	     gpio-controller;
	     ...

	     gpioiic0 {
		     compatible = "gpioiic";
		     /*
		      * Attach to GPIO pins 21 and 22.	Set them
		      * initially as inputs.
		      */
		     gpios = <&gpio 21 1 0
			      &gpio 22 1 0>;
		     scl = <0>; 	     /* GPIO pin 21 - optional */
		     sda = <1>; 	     /* GPIO pin 22 - optional */

		     /* This is an example of a gpioiic child. */
		     gpioiic-child0 {
			     compatible = "lm75";
			     i2c-address = <0x4f>;
		     };
	     };
     };

     Where:

     compatible  Should always be set to "gpioiic".

     gpios	 The gpios property indicates which GPIO pins should be used for SCLOCK and SDATA on the GPIO IIC bit-banging bus.  For more
		 details about the gpios property, please consult /usr/src/sys/boot/fdt/dts/bindings-gpio.txt.

     scl	 The scl option indicates which bit in the gpios should be used as the SCLOCK source.  Optional, defaults to 0.

     sda	 The sda option indicates which bit in the gpios should be used as the SDATA source.  Optional, defaults to 1.

SEE ALSO

     fdt(4), gpio(4), gpioled(4), iic(4), iicbb(4), iicbus(4)

HISTORY

     The gpioiic manual page first appeared in FreeBSD 10.1.

AUTHORS

     This manual page was written by Luiz Otavio O Souza.

BSD
								   May 14, 2014 							       BSD
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