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–
calc_lj_shift <lj_sigma> <lj_cutoff>
returns the value needed to shift the Lennard Jones potential to zero at the
cutoff.
• VECTOR OPERATIONS
A vector v is a tcl list of numbers with an arbitrary length Some functions are
provided only for three dimensional vectors. corresponding functions contain 3d
at the end of the name.
– veclen <v>
return the length of a vector
– veclensqr <v>
return the length of a vector squared
– vecadd <a> <b>
add vector a to vector b: return = (a+b)
– vecsub <a> <b>
subtract vector b from vector a: return = (a-b)
– vecscale <s> <v>
scale vector v with factor s: return = (s*v )
– vecdot_product <a> <b>
calculate dot product of vectors a and b: return = (a.b)
– veccross_product3d <a> <b>
calculate the cross product of vectors a and b: return = (a x b)
– vecnorm <v> [len]
normalize a vector to length len (default 1.0)
– unitvec <p1> <p2>
return unit vector pointing from position p1 to position p2
– orthovec3d <v> [len]
return orthogonal vector to v with length len (default 1.0) This vector does
not have a random orientation in the plane perpendicular to v
– create_dihedral_vec <v1> <v2> <theta> [phi] [len]
create last vector of a dihedral (v1 , v2 , res) with dihedral angle theta and
bond angle (v2 , res) phi and length len (default 1.0). If phi is ommited or
set to rnd then phi is assigned a random value between 0 and 2 Pi.
• TCL LIST OPERATIONS
– average <list>
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