root / src / CalcDist_cart.f90
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SUBROUTINE CalcDist_cart(iopt,s,dist,x0,y0,z0,xgeom,Coef) |
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! This subroutine computes the curvilinear distance of the images on the path |
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! It is adapted from Extrapol_cart |
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!---------------------------------------------------------------------- |
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! Copyright 2003-2014 Ecole Normale Supérieure de Lyon, |
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! Centre National de la Recherche Scientifique, |
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! Université Claude Bernard Lyon 1. All rights reserved. |
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! |
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! This work is registered with the Agency for the Protection of Programs |
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! as IDDN.FR.001.100009.000.S.P.2014.000.30625 |
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! |
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! Authors: P. Fleurat-Lessard, P. Dayal |
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! Contact: optnpath@gmail.com |
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! |
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! This file is part of "Opt'n Path". |
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! |
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! "Opt'n Path" is free software: you can redistribute it and/or modify |
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! it under the terms of the GNU Affero General Public License as |
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! published by the Free Software Foundation, either version 3 of the License, |
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! or (at your option) any later version. |
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! |
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! "Opt'n Path" is distributed in the hope that it will be useful, |
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! but WITHOUT ANY WARRANTY; without even the implied warranty of |
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! |
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! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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! GNU Affero General Public License for more details. |
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! |
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! You should have received a copy of the GNU Affero General Public License |
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! along with "Opt'n Path". If not, see <http://www.gnu.org/licenses/>. |
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! |
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! Contact The Office of Technology Licensing, valorisation@ens-lyon.fr, |
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! for commercial licensing opportunities. |
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!---------------------------------------------------------------------- |
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|
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use Path_module |
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use Io_module |
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|
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|
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IMPLICIT NONE |
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|
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REAL(KREAL), INTENT(OUT) :: s |
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! X0(Nat),Y0(Nat),Z0(Nat): reference geometry. |
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REAL(KREAL), INTENT(IN) :: dist,X0(Nat),Y0(Nat),Z0(Nat) |
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REAL(KREAL), INTENT(IN) :: Xgeom(NGeomI),Coef(NGeomI,NCoord) |
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! Iopt: Number of the cycles for the optimization |
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INTEGER(KINT), INTENT(IN) :: Iopt |
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INTEGER(KINT) :: IdxGeom, I, J, K, Idx,Iat, IGeom |
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! NSpline is the number of points along the interpolating path |
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INTEGER(KINT) :: NSpline |
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! FileSpline: Filename to save the interpolating path coordinates |
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CHARACTER(LCHARS) :: FileSpline,TmpChar |
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REAL(KREAL) :: Rmsd,MRot(3,3), ds, u, v |
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REAL(KREAL) :: a_val, d |
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|
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REAL(KREAL), ALLOCATABLE :: XyzTmp(:,:), XyzTmp2(:,:) ! (Nat,3) |
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REAL(KREAL), ALLOCATABLE :: DerXyz(:,:) ! Nat,3 |
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|
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|
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LOGICAL :: debug, print, printspline |
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LOGICAL, EXTERNAL :: valid |
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|
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!We will calculate the length of the path, in MW coordinates... |
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! this is done is a stupid way: we interpolate the zmatrix values, |
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! convert them into cartesian, weight the cartesian |
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! and calculate the evolution of the distance ! |
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! We have to follow the same procedure for every geometry |
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! so even for the first one, we have to convert it from zmat |
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! to cartesian ! |
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|
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debug=valid("pathcreate")
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print=valid("printgeom")
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printspline=(valid("printspline").AND.(dist<=1e30))
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|
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if (debug) Call Header("Entering CalcDist_cart")
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|
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! We want 100 points along the interpolating path |
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NSpline=int(NMaxPtPath/100) |
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|
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if (printspline) THEN |
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WRITE(TmpChar,'(I5)') Iopt |
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FileSpline=Trim(adjustL(PathName)) // '_spline.' // AdjustL(TRIM(TmpChar)) |
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OPEN(IOTMP,FILE=FileSpline) |
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|
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END IF |
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|
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|
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ALLOCATE(XyzTmp(Nat,3),XyzTmp2(Nat,3),DerXyz(Nat,3)) |
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|
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! XyzTmp2=Reshape(XyzGeomI(1,:,:),(/Nat,3/),ORDER=(/2,1/)) |
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|
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if (debug) THEN |
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WRITE(*,*) "DBG Extrapol_cart Initial geometries" |
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DO IGeom=1,NGeomI |
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WRITE(*,*) 'XyzGeomI, IGeom=',IGeom |
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DO I=1,Nat |
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WRITE(IOOUT,'(1X,A2,3(1X,F15.6))') Nom(Atome(I)), & |
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(XyzGeomI(IGeom,J,I),J=1,3) |
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END DO |
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END DO |
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END IF |
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|
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|
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! In order to mesure only the relevant distance between two points |
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! we align all geometries on the original one |
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DO IGeom=1,NGeomI |
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XyzTmp2=Reshape(XyzGeomI(IGeom,:,:),(/Nat,3/),ORDER=(/2,1/)) |
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! We align this geometry with the original one |
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! PFL 17/July/2006: only if we have more than 4 atoms. |
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! IF (Nat.GT.4) THEN |
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! PFL 24 Nov 2008 -> |
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! If we have frozen atoms we align only those ones. |
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! PFL 8 Feb 2011 -> |
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! I add a flag to see if we should align or not. |
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! For small systems, it might be better to let the user align himself |
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IF (Align) THEN |
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if (NFroz.GT.0) THEN |
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Call AlignPartial(Nat,x0,y0,z0, & |
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xyzTmp2(1,1),xyzTmp2(1,2),xyzTMP2(1,3), & |
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FrozAtoms,MRot) |
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ELSE |
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Call CalcRmsd(Nat, x0,y0,z0, & |
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xyzTmp2(1,1),xyzTmp2(1,2),xyzTMP2(1,3), & |
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MRot,rmsd,.TRUE.,.TRUE.) |
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END IF |
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! <- PFL 24 Nov 2008 |
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END IF |
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! -> PFL 8 Feb 2011 |
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! END IF |
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|
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XyzGeomI(IGeom,:,:)=Reshape(XyzTmp2(:,:),(/3,Nat/),ORDER=(/2,1/)) |
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END DO |
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|
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if (print) THEN |
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WRITE(*,*) "Aligned geometries" |
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DO J=1, NGeomI |
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WRITE(IOOUT,*) Nat |
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WRITE(IOOUT,*) " Aligned geometry ",J,"/",NGeomI |
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DO i=1,Nat |
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WRITE(IOOUT,'(1X,A2,3(1X,F15.6))') Nom(Atome(I)), & |
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XyzGeomI(J,1:3,I) |
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END DO |
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END DO |
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END IF |
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XyzGeomF(1,:,:)=XyzGeomI(1,:,:) |
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! We initialize the first geometry |
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XyzTmp=Reshape(XyzGeomI(1,:,:),(/Nat,3/),ORDER=(/2,1/)) |
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|
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! We align this geometry with the original one |
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! PFL 17/July/2006: only if we have more than 4 atoms. |
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! IF (Nat.GT.4) THEN |
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! PFL 24 Nov 2008 -> |
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! If we have frozen atoms we align only those ones. |
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! PFL 8 Feb 2011 -> |
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! I add a flag to see if we should align or not. |
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! For small systems, it might be better to let the user align himself |
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IF (Align) THEN |
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if (NFroz.GT.0) THEN |
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Call AlignPartial(Nat,x0,y0,z0, & |
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xyzTmp(1,1),xyzTmp(1,2),xyzTMP(1,3), & |
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FrozAtoms,MRot) |
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ELSE |
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Call CalcRmsd(Nat, x0,y0,z0, & |
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xyzTmp(1,1),xyzTmp(1,2),xyzTMP(1,3), & |
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MRot,rmsd,.TRUE.,.TRUE.) |
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END IF |
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! <- PFL 24 Nov 2008 |
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END IF |
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! -> PFL 8 Feb 2011 |
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! END IF |
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|
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|
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|
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s=0.d0 |
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SGeom(1)=0.d0 |
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|
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if (printspline) THEN |
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u=0.d0 |
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DO Iat=1,Nat |
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! We generate the interpolated coordinates |
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if (Linear) THEN |
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call LinearInt(u,XyzTmp2(Iat,1),DerXyz(Iat,1),NGeomI,xgeom(1),XyzGeomI(1,1,Iat)) |
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call LinearInt(u,XyzTmp2(Iat,2),DerXyz(Iat,2),NGeomI,xgeom(1),XyzGeomI(1,2,Iat)) |
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call LinearInt(u,XyzTmp2(Iat,3),DerXyz(Iat,3),NGeomI,xgeom(1),XyzGeomI(1,3,Iat)) |
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|
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ELSE |
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call splintder(u,XyzTmp2(Iat,1),DerXyz(Iat,1),NGeomI,xgeom(1),XyzGeomI(1,1,Iat),Coef(1,3*Iat-2)) |
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call splintder(u,XyzTmp2(Iat,2),DerXyz(Iat,2),NGeomI,xgeom(1),XyzGeomI(1,2,Iat),Coef(1,3*Iat-1)) |
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call splintder(u,XyzTmp2(Iat,3),DerXyz(Iat,3),NGeomI,xgeom(1),XyzGeomI(1,3,Iat),Coef(1,3*Iat)) |
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END IF |
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END DO |
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|
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WRITE(IOTMP,*) Nat |
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WRITE(IOTMP,'(1X,A,1X,F15.6)') "Debug Spline - Coord=Cart,s=",s |
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DO Iat=1,Nat |
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WRITE(IOTMP,'(1X,A2,3(1X,F15.6))') Nom(Atome(Iat)), & |
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(XyzTmp2(Iat,1:3)) |
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END DO |
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END IF |
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|
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IdxGeom=1 |
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|
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DO K=1,NMaxPtPath |
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u=real(K)/NMaxPtPath*(NGeomI-1.) |
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|
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DO Iat=1,Nat |
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! We generate the interpolated coordinates |
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if (Linear) THEN |
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call LinearInt(u,XyzTmp2(Iat,1),DerXyz(Iat,1),NGeomI,xgeom(1),XyzGeomI(1,1,Iat)) |
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call LinearInt(u,XyzTmp2(Iat,2),DerXyz(Iat,2),NGeomI,xgeom(1),XyzGeomI(1,2,Iat)) |
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call LinearInt(u,XyzTmp2(Iat,3),DerXyz(Iat,3),NGeomI,xgeom(1),XyzGeomI(1,3,Iat)) |
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|
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ELSE |
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call splintder(u,XyzTmp2(Iat,1),DerXyz(Iat,1),NGeomI,xgeom(1),XyzGeomI(1,1,Iat),Coef(1,3*Iat-2)) |
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call splintder(u,XyzTmp2(Iat,2),DerXyz(Iat,2),NGeomI,xgeom(1),XyzGeomI(1,2,Iat),Coef(1,3*Iat-1)) |
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call splintder(u,XyzTmp2(Iat,3),DerXyz(Iat,3),NGeomI,xgeom(1),XyzGeomI(1,3,Iat),Coef(1,3*Iat)) |
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END IF |
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END DO |
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|
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|
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! We align this geometry with the original one |
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! PFL 17/July/2006: only if we have more than 4 atoms. |
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! IF (Nat.GT.4) THEN |
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! PFL 24 Nov 2008 -> |
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! If we have frozen atoms we align only those ones. |
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! PFL 8 Feb 2011 -> |
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! I add a flag to see if we should align or not. |
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! For small systems, it might be better to let the user align himself |
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IF (Align) THEN |
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if (NFroz.GT.0) THEN |
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Call AlignPartial(Nat,x0,y0,z0, & |
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xyzTmp2(1,1),xyzTmp2(1,2),xyzTMP2(1,3), & |
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FrozAtoms,MRot) |
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ELSE |
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Call CalcRmsd(Nat, x0,y0,z0, & |
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xyzTmp2(1,1),xyzTmp2(1,2),xyzTMP2(1,3), & |
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MRot,rmsd,.TRUE.,.TRUE.) |
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END IF |
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! <- PFL 24 Nov 2008 |
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END IF |
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! -> PFL 8 Feb 2011 |
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! END IF |
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|
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|
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|
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ds=0. |
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DO I=1,Nat |
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DO J=1,3 |
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ds=ds+MassAt(I)*(XYZTMp2(I,J)-XYZTmp(I,J))**2 |
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XYZTmp(I,J)=XyzTMP2(I,J) |
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ENDDO |
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ENDDO |
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s=s+sqrt(ds) |
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|
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! if (debug) WRITE(*,*) "Debug u,s,dist",u,s,dist |
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|
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if ((printspline).AND.(MOD(K,NSpline).EQ.0)) THEN |
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WRITE(IOTMP,*) Nat |
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WRITE(IOTMP,'(1X,A,1X,F15.6)') "Debug Spline - Coord=Cart,s=",s |
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DO Iat=1,Nat |
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WRITE(IOTMP,'(1X,A2,3(1X,F15.6))') Nom(Atome(Iat)), & |
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(XyzTmp2(Iat,1:3)) |
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END DO |
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END IF |
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|
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|
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if (s>=dist) THEN |
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|
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if (debug) THEN |
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WRITE(*,*) "DBG Interpol_cart",s |
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DO i=1,Nat |
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WRITE(IOOUT,'(1X,A2,3(1X,F15.6))') Nom(Atome(I)), & |
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(XyzTmp2(I,J),J=1,3) |
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END DO |
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END IF |
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|
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s=s-dist |
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IdxGeom=IdxGeom+1 |
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SGeom(IdxGeom)=s+dist*(IdxGeom-1) |
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|
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! We align this geometry with the original one |
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! PFL 17/July/2006: only if we have more than 4 atoms. |
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! IF (Nat.GT.4) THEN |
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! PFL 24 Nov 2008 -> |
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! If we have frozen atoms we align only those ones. |
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! PFL 8 Feb 2011 -> |
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! I add a flag to see if we should align or not. |
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! For small systems, it might be better to let the user align himself |
| 298 |
IF (Align) THEN |
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if (NFroz.GT.0) THEN |
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Call AlignPartial(Nat,x0,y0,z0, & |
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xyzTmp2(1,1),xyzTmp2(1,2),xyzTMP2(1,3), & |
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FrozAtoms,MRot) |
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ELSE |
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Call CalcRmsd(Nat, x0,y0,z0, & |
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xyzTmp2(1,1),xyzTmp2(1,2),xyzTMP2(1,3), & |
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MRot,rmsd,.TRUE.,.TRUE.) |
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END IF |
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! <- PFL 24 Nov 2008 |
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END IF |
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! -> PFL 8 Feb 2011 |
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! END IF |
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|
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XyzGeomF(IdxGeom,:,:)=Reshape(XyzTmp2(:,:),(/3,Nat/),ORDER=(/2,1/)) |
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XyzTangent(IdxGeom,:)=Reshape(DerXyz(:,:),(/3*Nat/)) |
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|
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if (print) THEN |
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WRITE(IOOUT,'(1X,I5)') Nat |
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WRITE(IOOUT,*) "# Cartesian coord for Geometry ",IdxGeom,K |
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|
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DO i=1,Nat |
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WRITE(IOOUT,'(1X,A2,3(1X,F15.6))') Nom(Atome(I)), & |
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(XyzTmp2(I,J),J=1,3) |
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END DO |
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|
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END IF |
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END IF ! s>= dist |
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ENDDO ! K |
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|
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|
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if (s>=0.9*dist) THEN |
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s=s-dist |
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XyzTmp2=Reshape(XyzGeomI(NGeomI,:,:),(/Nat,3/),ORDER=(/2,1/)) |
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|
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if (printspline) THEN |
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WRITE(IOTMP,*) Nat |
| 336 |
WRITE(IOTMP,*) "Debug Spline - Coord=Cart,s=",s |
| 337 |
DO Iat=1,Nat |
| 338 |
WRITE(IOTMP,'(1X,A2,3(1X,F15.6))') Nom(Atome(Iat)), & |
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(XyzTmp2(Iat,1:3)) |
| 340 |
END DO |
| 341 |
END IF |
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|
| 343 |
|
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! We align this geometry with the original one |
| 345 |
! PFL 17/July/2006: only if we have more than 4 atoms. |
| 346 |
! IF (Nat.GT.4) THEN |
| 347 |
! PFL 24 Nov 2008 -> |
| 348 |
! If we have frozen atoms we align only those ones. |
| 349 |
! PFL 8 Feb 2011 -> |
| 350 |
! I add a flag to see if we should align or not. |
| 351 |
! For small systems, it might be better to let the user align himself |
| 352 |
IF (Align) THEN |
| 353 |
if (NFroz.GT.0) THEN |
| 354 |
Call AlignPartial(Nat,x0,y0,z0, & |
| 355 |
xyzTmp2(1,1),xyzTmp2(1,2),xyzTMP2(1,3), & |
| 356 |
FrozAtoms,MRot) |
| 357 |
ELSE |
| 358 |
Call CalcRmsd(Nat, x0,y0,z0, & |
| 359 |
xyzTmp2(1,1),xyzTmp2(1,2),xyzTMP2(1,3), & |
| 360 |
MRot,rmsd,.TRUE.,.TRUE.) |
| 361 |
END IF |
| 362 |
! <- PFL 24 Nov 2008 |
| 363 |
END IF |
| 364 |
! -> PFL 8 Feb 2011 |
| 365 |
! END IF |
| 366 |
|
| 367 |
IdxGeom=IdxGeom+1 |
| 368 |
SGeom(IdxGeom)=s+dist*(IdxGeom-1) |
| 369 |
|
| 370 |
IF (IdxGeom.GT.NGeomF) THEN |
| 371 |
WRITE(IOOUT,*) "!!! ERROR in Extrapol_cart !!!!" |
| 372 |
WRITE(IOOUT,*) "Too many structures. Increase NMaxPath" |
| 373 |
WRITE(*,*) "** PathCreate ***" |
| 374 |
WRITE(*,*) "Distribution of points along the path is wrong." |
| 375 |
WRITE(*,*) "Increase value of NMaxPtPath in the input file" |
| 376 |
WRITE(*,*) "Present value is:", NMaxPtPath |
| 377 |
STOP |
| 378 |
END IF |
| 379 |
|
| 380 |
|
| 381 |
! We align this geometry with the original one |
| 382 |
! PFL 17/July/2006: only if we have more than 4 atoms. |
| 383 |
! IF (Nat.GT.4) THEN |
| 384 |
! PFL 24 Nov 2008 -> |
| 385 |
! If we have frozen atoms we align only those ones. |
| 386 |
! PFL 8 Feb 2011 -> |
| 387 |
! I add a flag to see if we should align or not. |
| 388 |
! For small systems, it might be better to let the user align himself |
| 389 |
IF (Align) THEN |
| 390 |
if (NFroz.GT.0) THEN |
| 391 |
Call AlignPartial(Nat,x0,y0,z0, & |
| 392 |
xyzTmp2(1,1),xyzTmp2(1,2),xyzTMP2(1,3), & |
| 393 |
FrozAtoms,MRot) |
| 394 |
ELSE |
| 395 |
Call CalcRmsd(Nat, x0,y0,z0, & |
| 396 |
xyzTmp2(1,1),xyzTmp2(1,2),xyzTMP2(1,3), & |
| 397 |
MRot,rmsd,.TRUE.,.TRUE.) |
| 398 |
END IF |
| 399 |
! <- PFL 24 Nov 2008 |
| 400 |
END IF |
| 401 |
! -> PFL 8 Feb 2011 |
| 402 |
! END IF |
| 403 |
|
| 404 |
XyzGeomF(IdxGeom,:,:)=Reshape(XyzTmp2(:,:),(/3,Nat/),ORDER=(/2,1/)) |
| 405 |
XyzTangent(IdxGeom,:)=Reshape(DerXyz(:,:),(/3*Nat/)) |
| 406 |
|
| 407 |
if (print) THEN |
| 408 |
WRITE(IOOUT,'(1X,I5)') Nat |
| 409 |
WRITE(IOOUT,*) "# Cartesian coord for Geometry ",IdxGeom,K |
| 410 |
|
| 411 |
DO i=1,Nat |
| 412 |
WRITE(IOOUT,'(1X,A2,3(1X,F15.6))') Nom(Atome(I)), & |
| 413 |
(XyzTmp2(I,J),J=1,3) |
| 414 |
END DO |
| 415 |
END IF |
| 416 |
END IF |
| 417 |
|
| 418 |
DEALLOCATE(XyzTmp,XyzTmp2) |
| 419 |
|
| 420 |
if (debug) WRITE(*,*) 's final =',s |
| 421 |
|
| 422 |
if (printspline) CLOSE(IOTMP) |
| 423 |
|
| 424 |
if (debug) Call Header("Extrapol_cart over")
|
| 425 |
|
| 426 |
END SUBROUTINE EXTRAPOL_CART |