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Full Discussion: Calculate root mean square?
Top Forums Shell Programming and Scripting Calculate root mean square? Post 302954481 by liuzhencc on Tuesday 8th of September 2015 10:48:22 AM
Old 09-08-2015
Calculate root mean square?
Dear friend,

I know for a single case, this could be finished quickly with Excel. But if we have hundreds of files, we definitely want to do it with a script or a FORTRAN code. Since I have no knowledge of FORTRAN, I tried to work out a script to do it. The math is very simple. we chose one atom (in x, y, z, Cartesian coordinate), and we calculate the distance from other atom to the reference atom with the simple math sqrt((x(i)-x(1))^2+(y(i)-y(1))^2+(z(i)-z(1))^2)
Problem explanation: we have a list of numbers
Code:
P               1.219142       0.637315      -0.824280
N              -0.265369       0.551699      -1.665314
P              -1.232957      -0.291982      -0.536350
C               1.550001       2.370502      -0.242803
C               0.756639       2.983923       0.747041
C               1.003518       4.293274       1.173466
C               2.045233       5.026004       0.616725
C               2.835510       4.452541      -0.372444
C               2.587869       3.143957      -0.800209
C               2.645951       0.045340      -1.859172

assume we set the P1 as the center atom, now we need to calculate all the distance of other atoms from P, respectively.
and we print out the results as follows,
Code:
N2-P1 P3-P1 C4-P1 C5-P1 C6-P1 C7-P1 C8-P1 C9-P1 C10-P1
1.708 2.638 1.858  2.862 4.172  4.692 4.168 2.856 1.859

Thank you very much in advance!
Zhen
Last edited by liuzhencc; 09-08-2015 at 11:54 AM..
 

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LEARN ABOUT OSF1

xlsatoms

xlsatoms(1X)															      xlsatoms(1X)

NAME

       xlsatoms - list interned atoms defined on server

SYNOPSIS

       xlsatoms [-options...]

OPTIONS

       This  option  specifies	the X server to which to connect.  This option specifies a printf-style string used to list each atom <value,name>
       pair, printed in that order (value is an unsigned long and name is a char *).  xlsatoms will supply a newline at the end of each line.  The
       default	is  %ld	%s.  This option specifies the range of atom values to check.	If low is not given, a value of 1 assumed.  If high is not
       given, xlsatoms will stop at the first undefined atom at or above low.  This option specifies the name of an atom to  list.   If  the  atom
       does not exist, a message will be printed on the standard error.

DESCRIPTION

       The  xlsatoms  command lists the interned atoms.  By default, all atoms starting from 1 (the lowest atom value defined by the protocol) are
       listed until unknown atom is found. If an explicit range is given, xlsatoms will try all atoms in the range, regardless of whether  or  not
       any are undefined.

ENVIRONMENT

       to get the default host and display to use.

SEE ALSO

       X(1X), Xserver(1X), xprop(1X)

AUTHOR

       Jim Fulton, MIT X Consortium

																      xlsatoms(1X)
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