Dear teacher Zhang and Nick
Maybe there's a little different between the two. First in the
subroutine, movement of the 20 atoms along the z aixs is allowed, but
for the first/last 10 atoms only uniform movement are existed , any
reletively movement between the 10 atoms are not allowed. While follow
Nick's idea, movement of the 20 atoms along the z aixs is allowed,
whenever the movement is uniform or relative.
Is that all right?
Best
Dexi Shao
2014-08-14 15:26 GMT+08:00 zgp121 <zgp...@126.com
<mailto:zgp...@126.com>>:
Dear Nick,
Thanks for your suggestion.
I have tried it, and it succeeded. If I want to fix atom 1 to 3
the x and y coordinates, I should write two lines,
position from 1 to 3 1.0 0.0 0.0 # no movement in x-direction
position from 1 to 3 0.0 1.0 0.0 # no movement in y-direction
which can not be written in one line,
position from 1 to 3 1.0 1.0 0.0
Dear Roberto,
Also, the method I mentioned first can achive the same thing. When
I run again for the same job, it succeeded.
Thanks very much for your suggestions and discussions.
/Guangping Zhang
2014-08-14
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*发件人：*"zgp121"<zgp...@126.com <mailto:zgp...@126.com>>
*发送时间：*2014-08-13 17:37
*主题：*Re: [SIESTA-L] can not constrain atom using constr.f (with
attched constr.f)
*收件人：*"siesta-l"<siesta-l@uam.es <mailto:siesta-l@uam.es>>
*抄送：*
Dear Nick,
Thanks very much for your suggestion.
I will try it.
With best regards.
Guangping
2014-08-13
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*发件人：*Nick Papior Andersen <nickpap...@gmail.com
<mailto:nickpap...@gmail.com>>
*发送时间：*2014-08-13 16:26
*主题：*Re: [SIESTA-L] can not constrain atom using constr.f (with
attched constr.f)
*收件人：*"siesta-l@uam.es
<mailto:siesta-l@uam.es>"<siesta-l@uam.es <mailto:siesta-l@uam.es>>
*抄送：*
In some versions of siesta you can do:
%block GeometryConstraints
position from 1 to 10 1. 0. 0. # no movement in x-direction
position from 1 to 10 0. 1. 0. # no movement in y-direction
position from -10 to -1 1. 0. 0.
position from -10 to -1 0. 1. 0.
%endblock GeometryConstraints
Try it out and see if it works.
2014-08-13 8:19 GMT+00:00 zgp121 <zgp...@126.com
<mailto:zgp...@126.com>>:
Dear all,
I wan to do molecular dynamics for part of my system. So I use
constr.f to constrain some of the atoms. As attached my
constr.f, during the molecular dynamics, I want only my first
10 and last 10 atoms rigidly move along z axis. So, there only
two dimensions unstricted for the 20 atoms.
But the results show that the x, y coodinates of the 20 atoms
also move.
So, can anyone give some suggestions?
Guangping Zhang
=========constr.f======
!
! This file is part of the SIESTA package.
!
! Copyright (c) Fundacion General Universidad Autonoma de Madrid:
! E.Artacho, J.Gale, A.Garcia, J.Junquera, P.Ordejon,
D.Sanchez-Portal
! and J.M.Soler, 1996- .
!
! Use of this software constitutes agreement with the full
conditions
! given in the SIESTA license, as signed by all legitimate users.
!
c $Id: constr.f,v 1.6 2003/06/23 09:46:16 ordejon Exp $
subroutine constr( cell, na, isa, amass, xa, stress, fa,
ntcon )
c
*****************************************************************
c User-written routine to implement specific geometric
constraints,
c by orthogonalizing the forces and stress to undesired changes.
c Arguments:
c real*8 cell(3,3) : input lattice vectors (Bohr)
c integer na : input number of atoms
c integer isa(na) : input species indexes
c real*8 amass(na) : input atomic masses
c real*8 xa(3,na) : input atomic cartesian coordinates (Bohr)
c real*8 stress( 3,3) : input/output stress tensor (Ry/Bohr**3)
c real*8 fa(3,na) : input/output atomic forces (Ry/Bohr)
c integer ntcon : total number of positions constr. imposed
c
*****************************************************************
implicit none
integer na, isa(na), ntcon
double precision amass(na), cell(3,3), fa(3,na),
. stress(3,3), xa(3,na), fz, tmass
c Write here your problem-specific code.
fz = fa(3,1)+fa(3,2)+fa(3,3)+fa(3,4)+fa(3,5)+fa(3,6)+fa(3,7)
& +fa(3,8)+fa(3,9)+fa(3,10)
tmass=amass(1)+amass(2)+amass(3)+amass(4)+amass(5)+amass(6)
& +amass(7)+amass(8)+amass(9)+amass(10)
fa(3,1) = fz * amass(1)/tmass
fa(3,2) = fz * amass(2)/tmass
fa(3,3) = fz * amass(3)/tmass
fa(3,4) = fz * amass(4)/tmass
fa(3,5) = fz * amass(5)/tmass
fa(3,6) = fz * amass(6)/tmass
fa(3,7) = fz * amass(7)/tmass
fa(3,8) = fz * amass(8)/tmass
fa(3,9) = fz * amass(9)/tmass
fa(3,10) = fz * amass(10)/tmass
fa(1,1) = 0.0d0
fa(1,2) = 0.0d0
fa(1,3) = 0.0d0
fa(1,4) = 0.0d0
fa(1,5) = 0.0d0
fa(1,6) = 0.0d0
fa(1,7) = 0.0d0
fa(1,8) = 0.0d0
fa(1,9) = 0.0d0
fa(1,10) = 0.0d0
fa(2,1) = 0.0d0
fa(2,2) = 0.0d0
fa(2,3) = 0.0d0
fa(2,4) = 0.0d0
fa(2,5) = 0.0d0
fa(2,6) = 0.0d0
fa(2,7) = 0.0d0
fa(2,8) = 0.0d0
fa(2,9) = 0.0d0
fa(2,10) = 0.0d0
fz = fa(3,92)+fa(3,93)+fa(3,94)+fa(3,95)+fa(3,96)+fa(3,97)
& +fa(3,98)+fa(3,99)+fa(3,100)+fa(3,101)
tmass=amass(92)+amass(93)+amass(94)+amass(95)+amass(96)+amass(97)
& +amass(98)+amass(99)+amass(100)+amass(101)
fa(3,92) = fz * amass(92)/tmass
fa(3,93) = fz * amass(93)/tmass
fa(3,94) = fz * amass(94)/tmass
fa(3,95) = fz * amass(95)/tmass
fa(3,96) = fz * amass(96)/tmass
fa(3,97) = fz * amass(97)/tmass
fa(3,98) = fz * amass(98)/tmass
fa(3,99) = fz * amass(99)/tmass
fa(3,100) = fz * amass(100)/tmass
fa(3,101) = fz * amass(101)/tmass
fa(1,92) = 0.0d0
fa(1,93) = 0.0d0
fa(1,94) = 0.0d0
fa(1,95) = 0.0d0
fa(1,96) = 0.0d0
fa(1,97) = 0.0d0
fa(1,98) = 0.0d0
fa(1,99) = 0.0d0
fa(1,100) = 0.0d0
fa(1,101) = 0.0d0
fa(2,92) = 0.0d0
fa(2,93) = 0.0d0
fa(2,94) = 0.0d0
fa(2,95) = 0.0d0
fa(2,96) = 0.0d0
fa(2,97) = 0.0d0
fa(2,98) = 0.0d0
fa(2,99) = 0.0d0
fa(2,100) = 0.0d0
fa(2,101) = 0.0d0
ntcon=58
end
2014-08-12
------------------------------------------------------------------------
--
Kind regards Nick
