root / src / Calc_zmat_frag.f90
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SUBROUTINE Calc_Zmat_frag(na,atome,ind_zmat,val_zmat,x,y,z,r_cov,fact) |
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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! |
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! Goal: to compute a viable Z-Matrix starting from the |
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! cartesian coordinates of the atoms |
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! |
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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! |
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! Input: |
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! na : Number or atoms |
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! atome : Mass number of the atoms (H=1, He=2,...) |
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! x,y,z : cartesian coordinates of the atoms |
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! r_cov : array containing the covalent radii of the atoms |
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! fact : multiplicative factor used to determine if two atoms are linked. |
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! see CalcCnct for more details. |
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! |
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! Output: |
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! ind_zmat : INTEGER(na,5) contains the indices of the Z-matrix |
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! val_zmat : REAL(na,3) contains the values of the Z-matrix |
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! |
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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! History |
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! |
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! v1.0 written for Cart a long time ago. Does not use fragment analysis, but was quite good ! |
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! |
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! v2.0 12/2007 |
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! Comes from Calc_zmat_constr_frag, based on a fragment analysis of the |
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! system under study. |
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! It should be more flexible and robust. |
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! |
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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|
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!---------------------------------------------------------------------- |
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! Copyright 2003-2014 Ecole Normale Sup?rieure de Lyon, |
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! Centre National de la Recherche Scientifique, |
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! Universit? 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, only : max_Z, NMaxL, Nom, Pi |
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Use Io_module |
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|
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IMPLICIT NONE |
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|
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integer(KINT), INTENT(IN) :: na,atome(na) |
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real(KREAL), INTENT(IN) :: x(Na),y(Na),z(Na),fact |
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real(KREAL), INTENT(IN) :: r_cov(0:Max_Z) |
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|
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INTEGER(KINT), INTENT(OUT) :: ind_zmat(Na,5) |
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real(KREAL), INTENT(OUT) :: val_zmat(Na,3) |
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|
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INTEGER(KINT) :: idx_zmat(NA) |
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! Frozen contains the indices of frozen atoms |
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! INTEGER(KINT) Frozen(*),NFroz |
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! Number of fragment, Index of the current fragment for loops |
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INTEGER(KINT) :: NbFrag |
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! Fragment(I) contains the fragment index to which I belongs |
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! NbAtFrag(j) contains the number of atoms of fragment j |
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INTEGER(KINT), ALLOCATABLE :: Fragment(:),NbAtFrag(:) !na |
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! FragAt(i,:) lists the atoms of fragment i |
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INTEGER(KINT), ALLOCATABLE :: FragAt(:,:) !na,na |
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! MaxLFrag(i,1) contains the maximum of links for an atom for fragment i |
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! MaxLFrag(i,2) is the atom that has this number of linked atoms |
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INTEGER(KINT), ALLOCATABLE :: MaxLFrag(:,:) !na,2 |
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! INTEGER(KINT), ALLOCATABLE :: IdxFragAt(:) !na |
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! INTEGER(KINT), ALLOCATABLE :: FrozBlock(:,:) !(na,0:na) |
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! DistFrag contains the distance between a given atom and some other atoms |
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REAL(KREAL), ALLOCATABLE :: DistFrag(:) !na |
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! FragDist(I) contains the index of the atoms corresponding to DistFrag(I) |
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INTEGER(KINT), ALLOCATABLE :: FragDist(:) ! na |
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|
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INTEGER(KINT) :: IdxCaFaire, IAfaire |
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INTEGER(KINT), ALLOCATABLE :: LIAISONS(:,:) ! (Na,0:NMaxL) |
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! INTEGER(KINT), ALLOCATABLE :: LiaisonsIni(:,:) ! (Na,0:NMaxL) |
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INTEGER(KINT), ALLOCATABLE :: CAFaire(:) ! (Na) |
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|
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real(KREAL) :: vx1,vy1,vz1,norm1 |
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real(KREAL) :: vx2,vy2,vz2,norm2 |
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real(KREAL) :: vx3,vy3,vz3,norm3 |
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real(KREAL) :: vx4,vy4,vz4,norm4 |
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real(KREAL) :: vx5,vy5,vz5,norm5 |
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real(KREAL) :: val,val_d, d12, d13,d23,d |
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Logical Debug, FirstAt, DebugGaussian |
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LOGICAL, ALLOCATABLE :: DejaFait(:), FCaf(:) !(na) |
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! Logical, ALLOCATABLE :: FrozAt(:) !T if this atom is frozen |
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LOGICAL F1213, F1223,F1323 |
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|
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INTEGER(KINT) :: I,J,n0,n1,n2,n3,n4,IAt,IL,JL,IFrag,ITmp, K, KMax |
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INTEGER(KINT) :: I3, I1, Ip |
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INTEGER(KINT) :: I0, Izm, JAt |
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INTEGER(KINT) :: OrderZmat |
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|
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REAL(KREAL) :: sDihe |
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REAL(KREAL), PARAMETER :: LocalNCart=0.d0 |
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|
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INTERFACE |
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function valid(string) result (isValid) |
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CHARACTER(*), intent(in) :: string |
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logical :: isValid |
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END function VALID |
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|
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FUNCTION angle(v1x,v1y,v1z,norm1,v2x,v2y,v2z,norm2) |
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INTEGER, PARAMETER :: KREAL=KIND(1.0D0) |
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real(KREAL) :: v1x,v1y,v1z,norm1 |
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real(KREAL) :: v2x,v2y,v2z,norm2 |
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real(KREAL) :: angle |
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END FUNCTION ANGLE |
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|
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FUNCTION SinAngle(v1x,v1y,v1z,norm1,v2x,v2y,v2z,norm2) |
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INTEGER, PARAMETER :: KREAL=KIND(1.0D0) |
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real(KREAL) :: v1x,v1y,v1z,norm1 |
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real(KREAL) :: v2x,v2y,v2z,norm2 |
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real(KREAL) :: SinAngle |
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END FUNCTION SINANGLE |
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|
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FUNCTION angle_d(v1x,v1y,v1z,norm1,v2x,v2y,v2z,norm2,v3x,v3y,v3z,norm3) |
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INTEGER, PARAMETER :: KREAL=KIND(1.0D0) |
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real(KREAL) :: v1x,v1y,v1z,norm1 |
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real(KREAL) :: v2x,v2y,v2z,norm2 |
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real(KREAL) :: v3x,v3y,v3z,norm3 |
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real(KREAL) :: angle_d,ca,sa |
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END FUNCTION ANGLE_D |
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END INTERFACE |
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|
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debug=valid("calc_zmat").OR.valid("calc_zmat_frag")
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debugGaussian=valid("zmat_gaussian")
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|
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if (debug) WRITE(*,*) "=============================== Entering Calc_zmat_frag ========================" |
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if (na.le.2) THEN |
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WRITE(*,*) "I do not work for less than 2 atoms :-p" |
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RETURN |
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END IF |
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|
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ALLOCATE(FragDist(Na),Fragment(na), NbAtFrag(na),FragAt(na,na)) |
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! ALLOCATE(FrozFrag(na,3), IdxFragAt(na), FrozBlock(na,0:na)) |
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! ALLOCATE(FrozFrag(na,3)) |
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ALLOCATE(DistFrag(na),Liaisons(na,0:NMaxL)) |
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! ALLOCATE(Liaisons(na,0:NMaxL),LiaisonsIni(na,0:NMaxL)) |
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! ALLOCATE(CaFaire(na),DejaFait(Na),FCaf(na),FrozAt(na)) |
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ALLOCATE(CaFaire(na+1),DejaFait(Na),FCaf(na)) |
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|
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if (debug) THEN |
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WRITE(*,*) "DBG Calc_zmat_frag - Cartesian coordinates" |
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DO I=1,na |
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WRITE(*,'(1X,A3,3(1X,F15.8))') Nom(atome(i)),x(i),y(i),z(i) |
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END DO |
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END if |
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|
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DO I=1,na |
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DO J=1,5 |
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Ind_Zmat(I,J)=0 |
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END DO |
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END DO |
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|
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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! |
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! Easy case : 3 or less atoms |
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! |
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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if (Na.eq.3) THEN |
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d12=sqrt((x(1)-x(2))**2+(y(1)-y(2))**2+(z(1)-z(2))**2) |
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d13=sqrt((x(1)-x(3))**2+(y(1)-y(3))**2+(z(1)-z(3))**2) |
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d23=sqrt((x(3)-x(2))**2+(y(3)-y(2))**2+(z(3)-z(2))**2) |
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F1213=(d12<=d13) |
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F1323=(d13<=d23) |
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F1223=(d12<=d23) |
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if (debug) THEN |
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WRITE(*,*) "DEBUG Calc_Zmat 3 atoms" |
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WRITE(*,*) "d12,d13,d23:",d12,d13,d23 |
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WRITE(*,*) "F1213,F1323,F1223:",F1213,F1323,F1223 |
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END IF |
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OrderZmat=0 |
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if (F1213) orderZmat=OrderZmat+4 |
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if (F1323) orderZmat=OrderZmat+2 |
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if (F1223) orderZmat=OrderZmat+1 |
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if (debug) WRITE(*,*) 'OrderZmat=',OrderZmat |
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SELECT CASE (OrderZmat) |
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CASE (0) |
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! F F F ordre 2-3----1 |
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ind_zmat(1,1)=3 |
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ind_zmat(2,1)=2 |
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ind_zmat(2,2)=3 |
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ind_zmat(3,1)=1 |
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ind_zmat(3,2)=3 |
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ind_zmat(3,3)=2 |
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CASE (2) |
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! F T F ordre 1-3----2 |
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ind_zmat(1,1)=3 |
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ind_zmat(2,1)=1 |
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ind_zmat(2,2)=3 |
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ind_zmat(3,1)=2 |
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ind_zmat(3,2)=3 |
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ind_zmat(3,3)=1 |
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CASE (3) |
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! F T T ordre 2---1-3 |
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ind_zmat(1,1)=1 |
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ind_zmat(2,1)=3 |
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ind_zmat(2,2)=1 |
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ind_zmat(3,1)=2 |
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ind_zmat(3,2)=1 |
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ind_zmat(3,3)=3 |
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CASE (5) |
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! T F T ordre 1-2----3 |
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ind_zmat(1,1)=2 |
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ind_zmat(2,1)=1 |
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ind_zmat(2,2)=2 |
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ind_zmat(3,1)=3 |
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ind_zmat(3,2)=2 |
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ind_zmat(3,3)=1 |
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CASE (7) |
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! T T T ordre 3----1-2 |
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ind_zmat(1,1)=1 |
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ind_zmat(2,1)=2 |
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ind_zmat(2,2)=1 |
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ind_zmat(3,1)=3 |
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ind_zmat(3,2)=1 |
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ind_zmat(3,3)=2 |
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END SELECT |
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|
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IF (debug) THEN |
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WRITE(*,*) "DBG Calc_zmat_frag - Nat=3 -" |
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DO i=1,na |
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WRITE(*,'(1X,A3,5(1X,I5))') Nom(Atome(ind_zmat(i,1))),(ind_zmat(i,j),j=1,5) |
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END DO |
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END IF |
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|
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! We have ind_zmat, we fill val_zmat |
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val_zmat=0.d0 |
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n2=ind_zmat(2,1) |
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n1=ind_zmat(2,2) |
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d=sqrt((x(n1)-x(n2))**2+(y(n1)-y(n2))**2+(z(n1)-z(n2))**2) |
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val_zmat(2,1)=d |
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n1=ind_zmat(3,1) |
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n2=ind_zmat(3,2) |
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n3=ind_zmat(3,3) |
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CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
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if (debug) write(*,*) n1,n2,norm1 |
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val_zmat(3,1)=norm1 |
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|
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CALL vecteur(n2,n3,x,y,z,vx2,vy2,vz2,norm2) |
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val=angle(vx1,vy1,vz1,norm1,vx2,vy2,vz2,norm2) |
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if (debug) write(*,*) n2,n3,norm2,val |
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val_zmat(3,2)=val |
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|
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RETURN |
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END IF !matches if (Na.eq.3) THEN |
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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! |
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! End of Easy case : 3 or less atoms |
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! |
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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! |
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! General Case |
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! |
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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! |
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|
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! Initialization |
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DejaFait=.False. |
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Liaisons=0 |
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ind_zmat=0 |
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val_zmat=0.d0 |
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|
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if (debug) WRITE(*,*) "Coucou from Calc_zmat_frag.f90; L240" |
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|
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if (debug) THEN |
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WRITE(*,*) "Bonds initialized" |
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WRITE(*,*) 'Covalent radii used' |
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DO iat=1,na |
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i=atome(iat) |
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WRITE(*,*) Nom(I),Iat,r_cov(i),r_cov(i)*fact |
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END DO |
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END IF |
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|
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1003 FORMAT(1X,I4,' - ',25(I5)) |
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|
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! First step : connectivity are calculated |
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|
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Call CalcCnct(na,atome,x,y,z,LIAISONS,r_cov,fact) |
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|
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if (debug) THEN |
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WRITE(*,*) "Connections calculated" |
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DO IL=1,na |
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WRITE(IOOUT,1003) Il,(LIAISONS(IL,JL),JL=0,NMaxL) |
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END DO |
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END IF |
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|
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FCaf=.TRUE. |
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Call Decomp_frag(na,liaisons,FCaf,nbfrag,Fragment,NbAtFrag,FragAt) |
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|
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IF (debug) THEN |
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WRITE(*,*) 'I found ',NbFrag, 'fragments' |
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WRITE(*,*) (NbAtFrag(I),I=1,NbFrag) |
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DO I=1,NbFrag |
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WRITE(*,*) NbAtFrag(I) |
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WRITE(*,*) 'Fragment ', i |
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DO J=1,Na |
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IF (Fragment(J).EQ.I) WRITE(*,'(1X,I3,1X,A5,3(1X,F10.6))') J,Nom(Atome(J)) & |
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,X(J),Y(J),Z(J) |
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END DO |
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WRITE(*,*) "FragAt:",(FragAt(I,j),j=1,NbAtFrag(I)) |
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END DO |
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END IF |
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|
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ALLOCATE(MaxLFrag(NbFrag,2)) |
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|
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MaxLFrag=0 |
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|
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DO I=1,NbFrag |
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MaxLFrag(I,1)=Liaisons(FragAt(I,1),0) |
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MaxLFrag(I,2)=FragAt(I,1) |
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|
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DO J=1,NbAtFrag(I) |
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Iat=FragAt(I,J) |
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IF (Liaisons(IAt,0).GT.MaxLFrag(I,1)) THEN |
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MaxLFrag(I,1)=Liaisons(Iat,0) |
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MaxLFrag(I,2)=Iat |
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END IF |
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END DO |
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IF (debug) WRITE(*,*) 'Frag :',I,', atom ',MaxLFrag(I,2), ' has ',MaxLFrag(I,2),' links' |
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END DO |
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|
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! We will now build the molecule fragment by fragment |
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! We choose the starting fragment with two criteria: |
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! 1- Number of linked atoms: |
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! * >=3 is good as it fully defines the coordinate space |
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! * 2 is ok as we can either use a 3rd atom from the same fragment |
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! or add a X atom somewhere but this complicates quite a lot the way |
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! to treat the conversion from cartesian to zmat latter |
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! * 1 is bad... |
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! 2- Size of the fragment |
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! this allows us to deal more easily with cases 1- when number of |
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! directly linked atoms is less than 3 |
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|
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IFrag=0 |
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! I0 is the number of connections of the best fragment |
| 362 |
I0=0 |
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! I1 is the number of atoms of the best fragment |
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I1=0 |
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IAt=0 |
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DO I=1,NbFrag |
| 367 |
SELECT CASE(MaxLFrag(I,1)-I0) |
| 368 |
CASE (1:) |
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IFrag=I |
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I0=MaxLFrag(I,1) |
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I1=NbAtFrag(I) |
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IAt=MaxLFrag(I,2) |
| 373 |
CASE (0) |
| 374 |
if (NbAtFrag(I).GT.I1) THEN |
| 375 |
IFrag=I |
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I0=MaxLFrag(I,1) |
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I1=NbAtFrag(I) |
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IAt=MaxLFrag(I,2) |
| 379 |
END IF |
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END SELECT |
| 381 |
END DO |
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|
| 383 |
if (debug) WRITE(*,'(1X,A,I5,A,I5,A,I5,A,I5)') 'Starting with fragment:',IFrag,' with ',I0 & |
| 384 |
,' max links for atom',IAt,' fragment size',NbAtFrag(IFrag) |
| 385 |
|
| 386 |
! We will build the first fragment in a special way, as it will |
| 387 |
! set the coordinates system |
| 388 |
|
| 389 |
if (debug) WRITE(*,*) 'Fragment 1, starting with atom:',IAt, & |
| 390 |
'with ',I0,' connections' |
| 391 |
|
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DejaFait=.FALSE. |
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FCaf=.FALSE. |
| 394 |
|
| 395 |
izm=0 |
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SELECT CASE (I0) |
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CASE(3:) |
| 398 |
if (debug) WRITE(*,*) 'DBG select case I0 3' |
| 399 |
n0=Iat |
| 400 |
|
| 401 |
ITmp=2 |
| 402 |
sDihe=0. |
| 403 |
n2=IAt |
| 404 |
n3=Liaisons(Iat,1) |
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! We search for the third atom while making sure that it is not aligned with first two ! |
| 406 |
DO While ((ITmp.LE.Liaisons(Iat,0)).AND.(sDihe.LE.0.09d0)) |
| 407 |
n4=Liaisons(Iat,Itmp) |
| 408 |
CALL vecteur(n2,n3,x,y,z,vx2,vy2,vz2,norm2) |
| 409 |
CALL vecteur(n3,n4,x,y,z,vx3,vy3,vz3,norm3) |
| 410 |
val_d=angle(vx3,vy3,vz3,norm3,vx2,vy2,vz2,norm2) |
| 411 |
sDiHe=abs(sin(val_d*pi/180.d0)) |
| 412 |
if (debug) Write(*,*) 'Trying n2,n3,n4,sdihe,val_d',n2,n3,n4,sdihe,val_d |
| 413 |
Itmp=Itmp+1 |
| 414 |
END DO |
| 415 |
If (debug) WRITE(*,*) 'Itmp,Liaisons',Itmp,Liaisons(Iat,1:NMaxL) |
| 416 |
Liaisons(Iat,Itmp-1)=Liaisons(iat,2) |
| 417 |
Liaisons(Iat,2)=n4 |
| 418 |
If (debug) WRITE(*,*) 'Itmp,Liaisons',Itmp,Liaisons(Iat,1:NMaxL) |
| 419 |
|
| 420 |
if (sDihe.LE.0.09d0) THEN |
| 421 |
WRITE(*,*) "PROBLEM !!! All atoms linked to ",n0," are aligned..." |
| 422 |
WRITE(*,*) "Surprising as this atom has at least three bonds... For NOW STOP" |
| 423 |
STOP |
| 424 |
END IF |
| 425 |
|
| 426 |
CALL produit_vect(vx3,vy3,vz3,vx2,vy2,vz2, vx5,vy5,vz5,norm5) |
| 427 |
|
| 428 |
|
| 429 |
! We search for the fourth atom while checking that it is not aligned with 1st and 2nd atoms. |
| 430 |
Itmp=3 |
| 431 |
sDiHe=0. |
| 432 |
! PFL 28 Dec 2007 -> |
| 433 |
! I had a test on the dihedral angle, but I cannot see why it is important to have |
| 434 |
! a non planar fragment at the begining... ethylene works and is fully planar |
| 435 |
! I thus suppress this test |
| 436 |
! |
| 437 |
! DO While ((ITmp.LE.Liaisons(Iat,0)).AND.(sDihe.LE.0.09d0)) |
| 438 |
! ITmp=ITmp+1 |
| 439 |
n1=Liaisons(Iat,Itmp) |
| 440 |
if (debug) WRITe(*,*) 'trying n1,n2,n3,n4',n1,n2,n3,n4 |
| 441 |
CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
| 442 |
! Is this atom aligned with n2-n3 ? |
| 443 |
val_d=angle(vx1,vy1,vz1,norm1,vx2,vy2,vz2,norm2) |
| 444 |
sDiHe=abs(sin(val_d*pi/180.d0)) |
| 445 |
if (debug) Write(*,*) 'Angle n3-n2-n1',val_d |
| 446 |
if (sDiHe.le.0.09d0) THEN |
| 447 |
! As atoms n2,n3 and n4 are not aligned, we interchange n3 and n4 so that n1,n2 and n3 are not aligned |
| 448 |
if (debug) WRITE(*,*) "n3-n2-n1 aligned, we interchange n3 and n4" |
| 449 |
n1=n3 |
| 450 |
n3=n4 |
| 451 |
n4=n1 |
| 452 |
n1=Liaisons(Iat,ITmp) |
| 453 |
CALL vecteur(n2,n3,x,y,z,vx2,vy2,vz2,norm2) |
| 454 |
CALL vecteur(n2,n4,x,y,z,vx3,vy3,vz3,norm3) |
| 455 |
val_d=angle(vx1,vy1,vz1,norm1,vx2,vy2,vz2,norm2) |
| 456 |
if (debug) Write(*,*) 'NEW Angle n3-n2-n1',val_d |
| 457 |
END IF |
| 458 |
|
| 459 |
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
| 460 |
! avant de tester l'angle diedre, il faut verifier que ce 4e atome n'est pas |
| 461 |
! aligne avec les 2 premiers. |
| 462 |
! comme on a deja test? que les 3 premiers ne sont pas alignes, |
| 463 |
! s'il est align? avec les 2 premiers, on peut inverser le role de 2 et 3. |
| 464 |
! On pourrait tout simplier en faisant une bete recherche parmi tous les atomes geles |
| 465 |
! de ce bloc (au moins 4 ?) avec le critere 1) on les range par distance croissante |
| 466 |
! 2) on les scanne tant que l'angle valence n'est pas bon, puis tant que diehedre pas bon |
| 467 |
! on pourrait comme ca faire un tableau avec les atomes ranges d'abord pour le fragment s?lectionn? |
| 468 |
! puis les atomes des autres fragment par distance croissante. |
| 469 |
! les autres fragments ne seraient additonn?s que si l'on ne trouve pas notre bonheur dans le premier bloc |
| 470 |
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
| 471 |
|
| 472 |
CALL produit_vect(vx1,vy1,vz1,vx2,vy2,vz2, vx4,vy4,vz4,norm4) |
| 473 |
val_d=angle_d(vx4,vy4,vz4,norm4,vx5,vy5,vz5,norm5, & |
| 474 |
vx2,vy2,vz2,norm2) |
| 475 |
sDihe=abs(sin(val_d*pi/180.d0)) |
| 476 |
if (debug) WRITE(*,*) 'n2,n3,n4,n1, angle_d',n2,n3,n4,n1,val_d |
| 477 |
! END DO |
| 478 |
|
| 479 |
DejaFait(n2)=.TRUE. |
| 480 |
DejaFait(n3)=.TRUE. |
| 481 |
DejaFait(n4)=.TRUE. |
| 482 |
|
| 483 |
! if (sDihe.LE.0.09d0) THEN |
| 484 |
! ! None of the atoms linked to IAt are good to define the third |
| 485 |
! ! direction in space... |
| 486 |
! ! We will look at the other atoms |
| 487 |
! ! we might improve the search so as to take the atom closest to IAt |
| 488 |
! if (debug) WRITE(*,*) "All atoms linked to ",Iat," are in a plane. Looking for other atoms" |
| 489 |
! ITmp=0 |
| 490 |
! DO I=1,NbAtFrag(IFrag) |
| 491 |
! JAt=FragAt(IFrag,I) |
| 492 |
! if (FrozAt(Jat).AND.(.NOT.DejaFait(JAt))) THEN |
| 493 |
! n1=JAt |
| 494 |
! CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
| 495 |
! CALL produit_vect(vx1,vy1,vz1,vx2,vy2,vz2,vx4,vy4,vz4,norm4) |
| 496 |
! val_d=angle_d(vx4,vy4,vz4,norm4, & |
| 497 |
! vx5,vy5,vz5,norm5, & |
| 498 |
! vx2,vy2,vz2,norm2) |
| 499 |
! if (abs(sin(val_d)).GE.0.09D0) THEN |
| 500 |
! ITmp=ITmp+1 |
| 501 |
! DistFrag(ITmp)=Norm1 |
| 502 |
! FragDist(ITmp)=JAt |
| 503 |
! END IF |
| 504 |
! END IF |
| 505 |
! END DO |
| 506 |
|
| 507 |
! IF (ITmp.EQ.0) THEN |
| 508 |
! ! All dihedral angles between frozen atoms are less than 5? |
| 509 |
! ! (or more than 175?). We have to look at other fragments :-( |
| 510 |
! DO I=1,NFroz |
| 511 |
! Jat=Frozen(I) |
| 512 |
! if (.NOT.DejaFait(JAt)) THEN |
| 513 |
! n1=JAt |
| 514 |
! CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
| 515 |
! CALL produit_vect(vx1,vy1,vz1,vx2,vy2,vz2,vx4,vy4,vz4,norm4) |
| 516 |
! val_d=angle_d(vx4,vy4,vz4,norm4, & |
| 517 |
! vx5,vy5,vz5,norm5, & |
| 518 |
! vx2,vy2,vz2,norm2) |
| 519 |
! if (abs(sin(val_d)).GE.0.09D0) THEN |
| 520 |
! ITmp=ITmp+1 |
| 521 |
! DistFrag(ITmp)=Norm1 |
| 522 |
! FragDist(ITmp)=JAt |
| 523 |
! END IF |
| 524 |
! END IF |
| 525 |
! END DO |
| 526 |
! IF (ITmp.EQ.0) THEN |
| 527 |
! ! All frozen atoms are in a plane... too bad |
| 528 |
! WRITE(*,*) 'ERROR: It seems that all frozen atoms are in a plane' |
| 529 |
! WRITE(*,*) 'For now, I do not treat this case' |
| 530 |
! STOP |
| 531 |
! END IF |
| 532 |
! END IF |
| 533 |
! I1=0 |
| 534 |
! d=1e9 |
| 535 |
! DO I=1,ITmp |
| 536 |
! IF (DistFrag(I).LE.d) THEN |
| 537 |
! d=DistFrag(I) |
| 538 |
! I1=FragDist(I) |
| 539 |
! END IF |
| 540 |
! END DO |
| 541 |
! ELSE !(sDihe.LE.0.09d0) |
| 542 |
! I1=FrozBlock(IAt,ITmp) |
| 543 |
! if (debug) WRITE(*,*) 'I1,n1:',I1,n1 |
| 544 |
! END IF !(sDihe.LE.0.09d0) |
| 545 |
! ! we now have the atom that is closer to the first one and that |
| 546 |
! ! forms a non 0/Pi dihedral angle |
| 547 |
! |
| 548 |
! <- PFL 28 Dec 2007 |
| 549 |
|
| 550 |
! We construct the begining of the Z-Matrix |
| 551 |
|
| 552 |
ind_zmat(1,1)=n2 |
| 553 |
ind_zmat(2,1)=n3 |
| 554 |
ind_zmat(2,2)=n2 |
| 555 |
ind_zmat(3,1)=n4 |
| 556 |
ind_zmat(3,2)=n2 |
| 557 |
ind_zmat(3,3)=n3 |
| 558 |
DejaFait(n2)=.TRUE. |
| 559 |
DejaFait(n3)=.TRUE. |
| 560 |
DejaFait(n4)=.TRUE. |
| 561 |
CaFaire(1)=n3 |
| 562 |
CaFaire(2)=n4 |
| 563 |
|
| 564 |
! PFL 28 Dec 2007 |
| 565 |
! We have not selected a fourth atom, so that the following is not needed |
| 566 |
! ind_zmat(4,1)=I1 |
| 567 |
! ind_zmat(4,2)=n2 |
| 568 |
! ind_zmat(4,3)=n3 |
| 569 |
! ind_zmat(4,4)=n4 |
| 570 |
! DejaFait(I1)=.TRUE. |
| 571 |
! CaFaire(3)=I1 |
| 572 |
! CaFaire(4)=0 |
| 573 |
! IdxCaFaire=4 |
| 574 |
! izm=4 |
| 575 |
! FCaf(I1)=.TRUE. |
| 576 |
!!!!!!! |
| 577 |
! and replaced by: |
| 578 |
CaFaire(3)=0 |
| 579 |
IdxCaFaire=3 |
| 580 |
izm=3 |
| 581 |
! |
| 582 |
! <- PFL 28 Dec 2007 |
| 583 |
|
| 584 |
FCaf(n2)=.TRUE. |
| 585 |
FCaf(n3)=.TRUE. |
| 586 |
FirstAt=.TRUE. |
| 587 |
DO I=3,Liaisons(Iat,0) |
| 588 |
IF (.NOT.DejaFait(Liaisons(Iat,I))) THEN |
| 589 |
izm=izm+1 |
| 590 |
! ind_zmat(izm,1)=Liaisons(Iat,I) |
| 591 |
! ind_zmat(izm,2)=n2 |
| 592 |
! ind_zmat(izm,3)=n3 |
| 593 |
! ind_zmat(izm,4)=n4 |
| 594 |
Call add2indzmat(na,izm,Liaisons(Iat,I),n2,n3,n4,ind_zmat,x,y,z) |
| 595 |
if (FirstAt) THEN |
| 596 |
n4=Liaisons(Iat,I) |
| 597 |
FirstAt=.FALSE. |
| 598 |
END IF |
| 599 |
IF (.NOT.FCaf(Liaisons(Iat,I))) THEN |
| 600 |
CaFaire(IdxCaFaire)=Liaisons(Iat,I) |
| 601 |
IdxCaFaire=IdxCaFaire+1 |
| 602 |
CaFaire(IdxCaFaire)=0 |
| 603 |
FCaf(Liaisons(Iat,I))=.TRUE. |
| 604 |
END IF |
| 605 |
DejaFait(Liaisons(Iat,I))=.TRUE. |
| 606 |
END IF |
| 607 |
END DO |
| 608 |
|
| 609 |
if (debug) THEN |
| 610 |
WRITE(*,*) "Ind_zmat 0 - SELECT CASE I0 3: -- izm=",izm |
| 611 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(1,1) |
| 612 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(2,1), ind_zmat(2,2) |
| 613 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(3,1), ind_zmat(3,2), ind_zmat(3,3) |
| 614 |
DO I=4,izm |
| 615 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(I,1), ind_zmat(I,2), & |
| 616 |
ind_zmat(I,3), ind_zmat(I,4) |
| 617 |
END DO |
| 618 |
END IF |
| 619 |
|
| 620 |
|
| 621 |
! First four atoms (at least) have been put we go on with next parts |
| 622 |
! of this fragment... later |
| 623 |
|
| 624 |
|
| 625 |
CASE(2) |
| 626 |
if (debug) WRITE(*,*) 'DBG select case I0 2' |
| 627 |
WRITE(*,*) "PFL 28 Dec 2007: No test of alignment here :( TO DO TO DO TO DO" |
| 628 |
ind_zmat(1,1)=IAt |
| 629 |
ind_zmat(2,1)=Liaisons(IAt,1) |
| 630 |
ind_zmat(2,2)=IAt |
| 631 |
ind_zmat(3,1)=Liaisons(IAt,2) |
| 632 |
ind_zmat(3,2)=IAt |
| 633 |
ind_zmat(3,3)=Liaisons(IAt,1) |
| 634 |
DejaFait(IAt)=.TRUE. |
| 635 |
DejaFait(Liaisons(Iat,1))=.TRUE. |
| 636 |
DejaFait(Liaisons(Iat,2))=.TRUE. |
| 637 |
CaFaire(1)=Liaisons(Iat,1) |
| 638 |
CaFaire(2)=Liaisons(Iat,2) |
| 639 |
FCaf(Liaisons(Iat,1))=.TRUE. |
| 640 |
FCaf(Liaisons(Iat,2))=.TRUE. |
| 641 |
|
| 642 |
! PFL 28 Dec 2007 -> |
| 643 |
! We do NOT need a fourth atom !!! The third direction in space is defined by the cross |
| 644 |
! product of the first two directions |
| 645 |
! |
| 646 |
! the following is thus commented |
| 647 |
! |
| 648 |
! ! We search for a fourth atom, first in the FrozBlock atoms |
| 649 |
! ITmp=2 |
| 650 |
! sDihe=0. |
| 651 |
! n2=IAt |
| 652 |
! n3=Liaisons(Iat,1) |
| 653 |
! n4=Liaisons(Iat,2) |
| 654 |
! CALL vecteur(n2,n3,x,y,z,vx2,vy2,vz2,norm2) |
| 655 |
! CALL vecteur(n3,n4,x,y,z,vx3,vy3,vz3,norm3) |
| 656 |
! CALL produit_vect(vx3,vy3,vz3, vx2,vy2,vz2, vx5,vy5,vz5,norm5) |
| 657 |
! |
| 658 |
! DO While ((ITmp.LE.FrozBlock(Iat,0)).AND.(sDihe.LE.0.09d0)) |
| 659 |
! ITmp=ITmp+1 |
| 660 |
! n1=FrozBlock(Iat,Itmp) |
| 661 |
! CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
| 662 |
! CALL produit_vect(vx1,vy1,vz1,vx2,vy2,vz2, vx4,vy4,vz4,norm4) |
| 663 |
! val_d=angle_d(vx4,vy4,vz4,norm4, & |
| 664 |
! vx5,vy5,vz5,norm5, & |
| 665 |
! vx2,vy2,vz2,norm2) |
| 666 |
! sDihe=abs(sin(val_d)) |
| 667 |
! END DO |
| 668 |
! IF (debug) WRITE(*,*) 'DBG 4th atom, ITmp, sDihe',ITmp, sDihe |
| 669 |
! if (sDihe.LE.0.09d0) THEN |
| 670 |
! ! None of the frozen atoms linked to IAt are good to define the third |
| 671 |
! ! direction in space... |
| 672 |
! ! We will look at the other frozen atoms |
| 673 |
! ! we might improve the search so as to take the atom closest to IAt |
| 674 |
! ITmp=0 |
| 675 |
! DO I=1,NbAtFrag(IFrag) |
| 676 |
! JAt=FragAt(IFrag,I) |
| 677 |
! if (FrozAt(Jat).AND.(.NOT.DejaFait(JAt))) THEN |
| 678 |
! n1=JAt |
| 679 |
! CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
| 680 |
! CALL produit_vect(vx1,vy1,vz1, vx2,vy2,vz2, vx4,vy4,vz4,norm4) |
| 681 |
! val_d=angle_d(vx4,vy4,vz4,norm4, & |
| 682 |
! vx5,vy5,vz5,norm5, & |
| 683 |
! vx2,vy2,vz2,norm2) |
| 684 |
! if (abs(sin(val_d)).GE.0.09D0) THEN |
| 685 |
! ITmp=ITmp+1 |
| 686 |
! DistFrag(ITmp)=Norm1 |
| 687 |
! FragDist(ITmp)=JAt |
| 688 |
! END IF |
| 689 |
! END IF |
| 690 |
! END DO |
| 691 |
! IF (ITmp.EQ.0) THEN |
| 692 |
! ! All dihedral angles between frozen atoms are less than 5? |
| 693 |
! ! (or more than 175?). We have to look at other fragments :-( |
| 694 |
! DO I=1,NFroz |
| 695 |
! Jat=Frozen(I) |
| 696 |
! if (.NOT.DejaFait(JAt)) THEN |
| 697 |
! n1=JAt |
| 698 |
! CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
| 699 |
! CALL produit_vect(vx1,vy1,vz1, vx2,vy2,vz2, vx4,vy4,vz4,norm4) |
| 700 |
! val_d=angle_d(vx4,vy4,vz4,norm4, & |
| 701 |
! vx5,vy5,vz5,norm5, & |
| 702 |
! vx2,vy2,vz2,norm2) |
| 703 |
! if (abs(sin(val_d)).GE.0.09D0) THEN |
| 704 |
! ITmp=ITmp+1 |
| 705 |
! DistFrag(ITmp)=Norm1 |
| 706 |
! FragDist(ITmp)=JAt |
| 707 |
! END IF |
| 708 |
! END IF |
| 709 |
! END DO |
| 710 |
! IF (ITmp.EQ.0) THEN |
| 711 |
! ! All frozen atoms are in a plane... too bad |
| 712 |
! WRITE(*,*) 'ERROR: It seems that all frozen atoms are in a plane' |
| 713 |
! WRITE(*,*) 'For now, I do not treat this case' |
| 714 |
! STOP |
| 715 |
! END IF |
| 716 |
! END IF |
| 717 |
! I1=0 |
| 718 |
! d=1e9 |
| 719 |
! DO I=1,ITmp |
| 720 |
! IF (DistFrag(I).LE.d) THEN |
| 721 |
! d=DistFrag(I) |
| 722 |
! I1=FragDist(I) |
| 723 |
! END IF |
| 724 |
! END DO |
| 725 |
! ELSE !(sDihe.LE.0.09d0) |
| 726 |
! I1=FrozBlock(IAt,ITmp) |
| 727 |
! END IF !(sDihe.LE.0.09d0) |
| 728 |
! ! we now have the atom that is closer to the first one and that |
| 729 |
! ! forms a non 0/Pi dihedral angle |
| 730 |
! ! ind_zmat(4,1)=I1 |
| 731 |
! ! ind_zmat(4,2)=IAt |
| 732 |
! ! ind_zmat(4,3)=Liaisons(Iat,1) |
| 733 |
! ! ind_zmat(4,4)=Liaisons(Iat,2) |
| 734 |
! n3=Liaisons(Iat,1) |
| 735 |
! n4=Liaisons(Iat,2) |
| 736 |
! Call add2indzmat(na,4,I1,Iat,n3,n4,ind_zmat,x,y,z) |
| 737 |
! Liaisons(Iat,1)=n3 |
| 738 |
! Liaisons(Iat,2)=n4 |
| 739 |
! DejaFait(I1)=.TRUE. |
| 740 |
! CaFaire(3)=I1 |
| 741 |
! CaFaire(4)=0 |
| 742 |
! IdxCaFaire=4 |
| 743 |
! izm=4 |
| 744 |
! FCaf(I1)=.TRUE. |
| 745 |
! |
| 746 |
!!!!!! <- PFL 28 Dec 2007 |
| 747 |
|
| 748 |
CaFaire(3)=0 |
| 749 |
IdxCaFaire=3 |
| 750 |
izm=3 |
| 751 |
|
| 752 |
CASE(1) |
| 753 |
if (debug) WRITE(*,*) 'DBG select case I0 1, NbAtFrag=',NbAtFrag(IFrag) |
| 754 |
ind_zmat(1,1)=IAt |
| 755 |
ind_zmat(2,1)=Liaisons(IAt,1) |
| 756 |
ind_zmat(2,2)=IAt |
| 757 |
DejaFait(IAt)=.TRUE. |
| 758 |
DejaFait(Liaisons(Iat,1))=.TRUE. |
| 759 |
IdxCaFaire=2 |
| 760 |
CaFaire(1)=Liaisons(Iat,1) |
| 761 |
CaFaire(2)=0 |
| 762 |
FCaf(Liaisons(Iat,1))=.TRUE. |
| 763 |
|
| 764 |
! PFL 28 Dec 2007 -> |
| 765 |
! We do NOT need a fourth atom. So we will look only for a third atom |
| 766 |
! |
| 767 |
!!!! |
| 768 |
! |
| 769 |
! We search for a third and fourth atoms, first in the FrozBlock atoms |
| 770 |
! It should not be possible to have (FrozBlock(Iat,0).GT.2) and |
| 771 |
! iat linked to only one atom ! |
| 772 |
|
| 773 |
|
| 774 |
! we calculate the distances between Iat and all other frozen |
| 775 |
! atoms of this fragment, and store only those for which |
| 776 |
! valence angles are not too close to 0/Pi. (limit:5?) |
| 777 |
|
| 778 |
ITmp=0 |
| 779 |
CALL vecteur(Liaisons(Iat,1),IAt,x,y,z,vx2,vy2,vz2,norm2) |
| 780 |
|
| 781 |
! PFL 28 Dec 2007: As MaxL=1 I think that there is at most 2 atoms in this fragment... |
| 782 |
! so that the following loop is useless... this should be tested more carefully |
| 783 |
DO I=1,NbAtFrag(IFrag) |
| 784 |
JAt=FragAt(IFrag,I) |
| 785 |
if (.NOT.DejaFait(JAt)) THEN |
| 786 |
CALL vecteur(JAt,IAt,x,y,z,vx1,vy1,vz1,norm1) |
| 787 |
if (abs(cos(angle(vx1,vy1,vz1,norm1, & |
| 788 |
vx2,vy2,vz2,norm2))).LE.0.996d0) THEN |
| 789 |
ITmp=ITmp+1 |
| 790 |
DistFrag(ITmp)=Norm1 |
| 791 |
FragDist(ITmp)=JAt |
| 792 |
END IF |
| 793 |
END IF |
| 794 |
END DO |
| 795 |
|
| 796 |
IF (ITMP.EQ.0) THEN |
| 797 |
! We have no atoms correct in this fragment, we use |
| 798 |
! atoms from other fragments |
| 799 |
DO Jat=1,Na |
| 800 |
! DejaFait(Iat)=.TRUE. so that we do not need to test Jat/=Iat |
| 801 |
if (.NOT.DejaFait(JAt)) THEN |
| 802 |
CALL vecteur(JAt,IAt,x,y,z,vx1,vy1,vz1,norm1) |
| 803 |
if (abs(cos(angle(vx1,vy1,vz1,norm1, & |
| 804 |
vx2,vy2,vz2,norm2))).LE.0.996d0) THEN |
| 805 |
ITmp=ITmp+1 |
| 806 |
DistFrag(ITmp)=Norm1 |
| 807 |
FragDist(ITmp)=JAt |
| 808 |
END IF |
| 809 |
END IF |
| 810 |
END DO |
| 811 |
IF (ITMP.EQ.0) THEN |
| 812 |
WRITE(*,*) 'It seems all atoms are aligned' |
| 813 |
WRITE(*,*) 'Case non treated for now :-( ' |
| 814 |
STOP |
| 815 |
END IF |
| 816 |
END IF |
| 817 |
|
| 818 |
I1=0 |
| 819 |
d=1e9 |
| 820 |
! PFL 28 Dec 2007: There exists some F90 intrinsics to find the smallest element of an array. |
| 821 |
! The following loop should be replaced by it ! |
| 822 |
DO I=1,ITmp |
| 823 |
IF (DistFrag(I).LE.d) THEN |
| 824 |
I1=FragDist(I) |
| 825 |
d=DistFrag(I) |
| 826 |
END IF |
| 827 |
END DO |
| 828 |
|
| 829 |
! we now have the atom that is closer to the first one and that |
| 830 |
! forms a non 0/Pi valence angle |
| 831 |
ind_zmat(3,1)=I1 |
| 832 |
ind_zmat(3,2)=IAt |
| 833 |
ind_zmat(3,3)=Liaisons(Iat,1) |
| 834 |
DejaFait(I1)=.TRUE. |
| 835 |
CaFaire(2)=I1 |
| 836 |
FCaf(I1)=.TRUE. |
| 837 |
|
| 838 |
|
| 839 |
! PFL 28 Dec 2007 -> |
| 840 |
! We do NOT need a fourth atom so that the following is suppressed |
| 841 |
! |
| 842 |
! ! we search for a fourth atom ! |
| 843 |
! ! We search for a fourth atom, first in the FrozBlock atoms |
| 844 |
! ITmp=2 |
| 845 |
! sDihe=0. |
| 846 |
! n2=IAt |
| 847 |
! n3=Liaisons(Iat,1) |
| 848 |
! n4=I1 |
| 849 |
! CALL vecteur(n2,n3,x,y,z,vx2,vy2,vz2,norm2) |
| 850 |
! CALL vecteur(n3,n4,x,y,z,vx3,vy3,vz3,norm3) |
| 851 |
! CALL produit_vect(vx3,vy3,vz3, vx2,vy2,vz2,vx5,vy5,vz5,norm5) |
| 852 |
! |
| 853 |
! ! We will look at the other frozen atoms |
| 854 |
! ! we might improve the search so as to take the atom closest to IAt |
| 855 |
! ITmp=0 |
| 856 |
! DO I=1,NbAtFrag(IFrag) |
| 857 |
! JAt=FragAt(IFrag,I) |
| 858 |
! if (FrozAt(Jat).AND.(.NOT.DejaFait(JAt))) THEN |
| 859 |
! n1=JAt |
| 860 |
! CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
| 861 |
! CALL produit_vect(vx1,vy1,vz1, vx2,vy2,vz2, vx4,vy4,vz4,norm4) |
| 862 |
! val_d=angle_d(vx4,vy4,vz4,norm4, & |
| 863 |
! vx5,vy5,vz5,norm5, & |
| 864 |
! vx2,vy2,vz2,norm2) |
| 865 |
! if (abs(sin(val_d)).GE.0.09D0) THEN |
| 866 |
! ITmp=ITmp+1 |
| 867 |
! DistFrag(ITmp)=Norm1 |
| 868 |
! FragDist(ITmp)=JAt |
| 869 |
! END IF |
| 870 |
! END IF |
| 871 |
! END DO |
| 872 |
! IF (ITmp.EQ.0) THEN |
| 873 |
! ! All dihedral angles between frozen atoms are less than 5? |
| 874 |
! ! (or more than 175?). We have to look at other fragments :-( |
| 875 |
! DO I=1,NFroz |
| 876 |
! Jat=Frozen(I) |
| 877 |
! if (.NOT.DejaFait(JAt)) THEN |
| 878 |
! n1=JAt |
| 879 |
! CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
| 880 |
! CALL produit_vect(vx1,vy1,vz1,vx2,vy2,vz2, vx4,vy4,vz4,norm4) |
| 881 |
! val_d=angle_d(vx4,vy4,vz4,norm4, & |
| 882 |
! vx5,vy5,vz5,norm5, & |
| 883 |
! vx2,vy2,vz2,norm2) |
| 884 |
! if (abs(sin(val_d)).GE.0.09D0) THEN |
| 885 |
! ITmp=ITmp+1 |
| 886 |
! DistFrag(ITmp)=Norm1 |
| 887 |
! FragDist(ITmp)=JAt |
| 888 |
! END IF |
| 889 |
! END IF |
| 890 |
! END DO |
| 891 |
! IF (ITmp.EQ.0) THEN |
| 892 |
! ! All frozen atoms are in a plane... too bad |
| 893 |
! WRITE(*,*) 'ERROR: It seems that all frozen atoms are in a plane' |
| 894 |
! WRITE(*,*) 'For now, I do not treat this case' |
| 895 |
! STOP |
| 896 |
! END IF |
| 897 |
! END IF ! ITmp.EQ.0 after scaning fragment |
| 898 |
! I1=0 |
| 899 |
! d=1e9 |
| 900 |
! DO I=1,ITmp |
| 901 |
! IF (DistFrag(I).LE.d) THEN |
| 902 |
! d=DistFrag(I) |
| 903 |
! I1=FragDist(I) |
| 904 |
! END IF |
| 905 |
! END DO |
| 906 |
! |
| 907 |
! ! we now have the atom that is closer to the first one and that |
| 908 |
! ! forms a non 0/Pi dihedral angle |
| 909 |
! ! ind_zmat(4,1)=I1 |
| 910 |
! ! ind_zmat(4,2)=IAt |
| 911 |
! ! ind_zmat(4,3)=ind_zmat(2,1) |
| 912 |
! ! ind_zmat(4,4)=ind_zmat(3,1) |
| 913 |
! n3=ind_zmat(2,1) |
| 914 |
! n4=ind_zmat(3,1) |
| 915 |
! Call add2indzmat(na,4,I1,IAt,n3,n4,ind_zmat,x,y,z) |
| 916 |
! ind_zmat(2,1)=n3 |
| 917 |
! ind_zmat(3,1)=n4 |
| 918 |
! DejaFait(I1)=.TRUE. |
| 919 |
! CaFaire(3)=I1 |
| 920 |
! CaFaire(4)=0 |
| 921 |
! IdxCaFaire=4 |
| 922 |
! izm=4 |
| 923 |
! FCaf(I1)=.TRUE. |
| 924 |
!!!!!!!!!!! |
| 925 |
! |
| 926 |
! <- PFL 28 Dec 2007 |
| 927 |
|
| 928 |
CaFaire(3)=0 |
| 929 |
IdxCaFaire=3 |
| 930 |
|
| 931 |
CASE(0) |
| 932 |
WRITE(*,*) 'All atoms are separated .. ' |
| 933 |
WRITE(*,*) 'this case should be treated separately !' |
| 934 |
STOP |
| 935 |
END SELECT |
| 936 |
|
| 937 |
if (debug) THEN |
| 938 |
WRITE(*,*) 'ind_zmat 1 izm=',izm |
| 939 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(1,1) |
| 940 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(2,1), ind_zmat(2,2) |
| 941 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(3,1), ind_zmat(3,2), ind_zmat(3,3) |
| 942 |
DO I=4,izm |
| 943 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(I,1), ind_zmat(I,2), & |
| 944 |
ind_zmat(I,3), ind_zmat(I,4) |
| 945 |
END DO |
| 946 |
END IF |
| 947 |
|
| 948 |
DO I=1,izm |
| 949 |
Idx_zmat(ind_zmat(I,1))=i |
| 950 |
END Do |
| 951 |
|
| 952 |
! at least first three atoms of this fragment done... |
| 953 |
! we empty the 'cafaire' array before going on |
| 954 |
IAFaire=1 |
| 955 |
DO WHILE (CaFaire(IaFaire).NE.0) |
| 956 |
n1=CaFaire(IaFaire) |
| 957 |
n2=ind_zmat(idx_zmat(N1),2) |
| 958 |
if (idx_zmat(N1).EQ.2) THEN |
| 959 |
! We have a (small) problem: we have to add atoms linked to the 2nd |
| 960 |
! atom of the zmat. This is a pb because we do not know |
| 961 |
! which atom to use to define the dihedral angle |
| 962 |
! we take the third atom of the zmat |
| 963 |
n3=ind_zmat(3,1) |
| 964 |
ELSE |
| 965 |
n3=ind_zmat(idx_zmat(n1),3) |
| 966 |
END IF |
| 967 |
|
| 968 |
FirstAt=.TRUE. |
| 969 |
DO I=1,Liaisons(n1,0) |
| 970 |
IAt=Liaisons(n1,I) |
| 971 |
! PFL 29.Aug.2008 -> |
| 972 |
! We dissociate the test on 'DejaFait' that indicates that this atom |
| 973 |
! has already been put in the Zmat |
| 974 |
! from the test on FCaf that indicates that this atom has been put in the |
| 975 |
! 'CAFaire' list that deals with identifying its connectivity. |
| 976 |
! Those two test might differ in some cases. |
| 977 |
IF (.NOT.DejaFait(Iat)) THEN |
| 978 |
izm=izm+1 |
| 979 |
if (debug) WRITE(*,*) ">1< Adding atom ",Iat,"position izm=",izm |
| 980 |
! ind_zmat(izm,1)=iat |
| 981 |
! ind_zmat(izm,2)=n1 |
| 982 |
! ind_zmat(izm,3)=n2 |
| 983 |
! ind_zmat(izm,4)=n3 |
| 984 |
Call add2indzmat(na,izm,iat,n1,n2,n3,ind_zmat,x,y,z) |
| 985 |
if (FirstAt) THEN |
| 986 |
n3=Iat |
| 987 |
FirstAt=.FALSE. |
| 988 |
END IF |
| 989 |
idx_zmat(iat)=izm |
| 990 |
DejaFait(iat)=.TRUE. |
| 991 |
END IF |
| 992 |
IF (.NOT.FCaf(Iat)) THEN |
| 993 |
CaFaire(IdxCaFaire)=iat |
| 994 |
IdxCaFaire=IdxCaFaire+1 |
| 995 |
CaFaire(IdxCaFaire)=0 |
| 996 |
FCaf(Iat)=.TRUE. |
| 997 |
END IF |
| 998 |
! <- PFL 29.Aug.2008 |
| 999 |
END DO |
| 1000 |
IaFaire=IaFaire+1 |
| 1001 |
END Do ! DO WHILE CaFaire |
| 1002 |
|
| 1003 |
if (debug) THEN |
| 1004 |
WRITE(*,*) 'ind_zmat 2, izm=',izm |
| 1005 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(1,1) |
| 1006 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(2,1), ind_zmat(2,2) |
| 1007 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(3,1), ind_zmat(3,2), ind_zmat(3,3) |
| 1008 |
DO I=4,izm |
| 1009 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(I,1), ind_zmat(I,2), & |
| 1010 |
ind_zmat(I,3), ind_zmat(I,4) |
| 1011 |
END DO |
| 1012 |
END IF |
| 1013 |
|
| 1014 |
! We have finished putting atoms linked to the first one |
| 1015 |
! There should not be any atom left from this fragment. We check: |
| 1016 |
! we will add other atoms of this fragment |
| 1017 |
DO I=1,NbAtFrag(IFrag) |
| 1018 |
Iat=FragAt(IFrag,I) |
| 1019 |
if (debug) WRITE(*,*) "DBG: I,Iat,dejafait",I,Iat,DejaFait(Iat) |
| 1020 |
IF (.NOT.DejaFait(Iat)) THEN |
| 1021 |
WRITE(*,*) 'Treating atom I,Iat',I,Iat |
| 1022 |
|
| 1023 |
END IF |
| 1024 |
|
| 1025 |
END DO |
| 1026 |
|
| 1027 |
NbAtFrag(Ifrag)=0 |
| 1028 |
MaxLFrag(IFrag,1)=0 |
| 1029 |
|
| 1030 |
! we start again with the rest of the molecule... |
| 1031 |
! v 1.01 We add the fragment in the order corresponding to NbAtFrag |
| 1032 |
KMax=NbFrag-1 |
| 1033 |
|
| 1034 |
IF (DEBUG) WRITE(*,*) "Adding the ",Kmax," remaining fragments" |
| 1035 |
DO K=1, KMax |
| 1036 |
IFrag=0 |
| 1037 |
I0=0 |
| 1038 |
IAt=0 |
| 1039 |
I1=0 |
| 1040 |
DO I=1,NbFrag |
| 1041 |
SELECT CASE(MaxLFrag(I,1)-I0) |
| 1042 |
CASE (1:) |
| 1043 |
IFrag=I |
| 1044 |
I0=MaxLFrag(I,1) |
| 1045 |
IAt=MaxLFrag(I,2) |
| 1046 |
I1=NbAtFrag(I) |
| 1047 |
CASE (0) |
| 1048 |
if (NbAtFrag(I).GT.I1) THEN |
| 1049 |
IFrag=I |
| 1050 |
I0=MaxLFrag(I,1) |
| 1051 |
IAt=MaxLFrag(I,2) |
| 1052 |
I1=NbAtFrag(I) |
| 1053 |
END IF |
| 1054 |
END SELECT |
| 1055 |
|
| 1056 |
END DO |
| 1057 |
|
| 1058 |
if (debug) WRITE(*,'(1X,A,I5,A,I5,A,I5,A,I5)') 'Adding fragment:',IFrag,' with ',I0 & |
| 1059 |
,' max links for atom',IAt,' fragment size',NbAtFrag(IFrag) |
| 1060 |
|
| 1061 |
MaxLFrag(IFrag,1)=0 |
| 1062 |
|
| 1063 |
! We search for the closest atoms of the previous fragments to the atom with max links |
| 1064 |
d=1e9 |
| 1065 |
DO J=1,izm |
| 1066 |
Call vecteur(iat,ind_zmat(j,1),x,y,z,vx1,vy1,vz1,norm1) |
| 1067 |
if (norm1.le.d) THEN |
| 1068 |
Jat=j |
| 1069 |
d=norm1 |
| 1070 |
END IF |
| 1071 |
END DO |
| 1072 |
n2=ind_zmat(jat,1) |
| 1073 |
SELECT CASE(jat) |
| 1074 |
CASE (1) |
| 1075 |
n3=ind_zmat(2,1) |
| 1076 |
n4=ind_zmat(3,1) |
| 1077 |
CASE (2) |
| 1078 |
n3=ind_zmat(1,1) |
| 1079 |
n4=ind_zmat(3,1) |
| 1080 |
CASE DEFAULT |
| 1081 |
n3=ind_zmat(jAt,2) |
| 1082 |
n4=ind_zmat(jat,3) |
| 1083 |
END SELECT |
| 1084 |
izm=izm+1 |
| 1085 |
Call add2indzmat(na,izm,iat,n2,n3,n4,ind_zmat,x,y,z) |
| 1086 |
idx_zmat(iat)=izm |
| 1087 |
DejaFait(iat)=.TRUE. |
| 1088 |
IdxCaFaire=2 |
| 1089 |
CaFaire(1)=iat |
| 1090 |
CaFaire(2)=0 |
| 1091 |
FCaf(Iat)=.TRUE. |
| 1092 |
IaFaire=1 |
| 1093 |
DO WHILE (CaFaire(IaFaire).NE.0) |
| 1094 |
n1=CaFaire(IaFaire) |
| 1095 |
n2=ind_zmat(idx_zmat(N1),2) |
| 1096 |
if (idx_zmat(N1).EQ.2) THEN |
| 1097 |
! We have a (small) problem: we have to add atoms linked to the 2nd |
| 1098 |
! atom of the zmat. This is a pb because we do not know |
| 1099 |
! which atom to use to define the dihedral angle |
| 1100 |
! we take the third atom of the zmat |
| 1101 |
n3=ind_zmat(3,1) |
| 1102 |
ELSE |
| 1103 |
n3=ind_zmat(idx_zmat(n1),3) |
| 1104 |
END IF |
| 1105 |
DO I3=1,Liaisons(n1,0) |
| 1106 |
IAt=Liaisons(n1,I3) |
| 1107 |
! PFL 29.Aug.2008 -> |
| 1108 |
! We dissociate the test on 'DejaFait' that indicates that this atom |
| 1109 |
! has already been put in the Zmat |
| 1110 |
! from the test on FCaf that indicates that this atom has been put in the |
| 1111 |
! 'CAFaire' list that deals with identifying its connectivity. |
| 1112 |
! Those two test might differ for a frozen atom linked to non frozen atoms. |
| 1113 |
IF (.NOT.DejaFait(Iat)) THEN |
| 1114 |
izm=izm+1 |
| 1115 |
Call add2indzmat(na,izm,Iat,n1,n2,n3,ind_zmat,x,y,z) |
| 1116 |
idx_zmat(iat)=izm |
| 1117 |
n3=iat |
| 1118 |
DejaFait(Iat)=.TRUE. |
| 1119 |
END IF |
| 1120 |
IF (.NOT.FCaf(Iat)) THEN |
| 1121 |
CaFaire(IdxCaFaire)=iat |
| 1122 |
IdxCaFaire=IdxCaFaire+1 |
| 1123 |
CaFaire(IdxCaFaire)=0 |
| 1124 |
FCaf(Iat)=.TRUE. |
| 1125 |
END IF |
| 1126 |
! <- PFL 29.Aug.2008 |
| 1127 |
END DO |
| 1128 |
IaFaire=IaFaire+1 |
| 1129 |
END Do ! DO WHILE CaFaire |
| 1130 |
|
| 1131 |
if (debug) THEN |
| 1132 |
WRITE(*,*) 'ind_zmat 4' |
| 1133 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(1,1) |
| 1134 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(2,1), ind_zmat(2,2) |
| 1135 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(3,1), ind_zmat(3,2), ind_zmat(3,3) |
| 1136 |
DO Ip=4,izm |
| 1137 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(Ip,1), ind_zmat(Ip,2), & |
| 1138 |
ind_zmat(Ip,3), ind_zmat(Ip,4) |
| 1139 |
END DO |
| 1140 |
END IF |
| 1141 |
|
| 1142 |
END DO ! Loop on all fragments |
| 1143 |
|
| 1144 |
|
| 1145 |
! We have ind_zmat. We calculate val_zmat :-) |
| 1146 |
if (debug) WRITE(*,*) "Calculating val_zmat" |
| 1147 |
|
| 1148 |
val_zmat(1,1)=0.d0 |
| 1149 |
val_zmat(1,2)=0.d0 |
| 1150 |
val_zmat(1,3)=0.d0 |
| 1151 |
val_zmat(2,2)=0.d0 |
| 1152 |
val_zmat(2,3)=0.d0 |
| 1153 |
val_zmat(3,3)=0.d0 |
| 1154 |
|
| 1155 |
n1=ind_zmat(2,1) |
| 1156 |
n2=ind_zmat(2,2) |
| 1157 |
|
| 1158 |
CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
| 1159 |
|
| 1160 |
val_zmat(2,1)=norm1 |
| 1161 |
|
| 1162 |
|
| 1163 |
n1=ind_zmat(3,1) |
| 1164 |
n2=ind_zmat(3,2) |
| 1165 |
n3=ind_zmat(3,3) |
| 1166 |
|
| 1167 |
CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
| 1168 |
|
| 1169 |
val_zmat(3,1)=norm1 |
| 1170 |
|
| 1171 |
CALL vecteur(n2,n3,x,y,z,vx2,vy2,vz2,norm2) |
| 1172 |
val=angle(vx1,vy1,vz1,norm1,vx2,vy2,vz2,norm2) |
| 1173 |
|
| 1174 |
val_zmat(3,2)=val |
| 1175 |
|
| 1176 |
DO i=4,na |
| 1177 |
|
| 1178 |
n1=ind_zmat(i,1) |
| 1179 |
n2=ind_zmat(i,2) |
| 1180 |
n3=ind_zmat(i,3) |
| 1181 |
n4=ind_zmat(i,4) |
| 1182 |
|
| 1183 |
if (debug) WRITE(*,*) "Doing i,n1,n2,n3,n4",i,n1,n2,n3,n4 |
| 1184 |
CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
| 1185 |
|
| 1186 |
CALL vecteur(n2,n3,x,y,z,vx2,vy2,vz2,norm2) |
| 1187 |
val=angle(vx1,vy1,vz1,norm1,vx2,vy2,vz2,norm2) |
| 1188 |
|
| 1189 |
CALL vecteur(n3,n4,x,y,z,vx3,vy3,vz3,norm3) |
| 1190 |
CALL produit_vect(vx1,vy1,vz1,vx2,vy2,vz2,vx4,vy4,vz4,norm4) |
| 1191 |
CALL produit_vect(vx3,vy3,vz3,vx2,vy2,vz2,vx5,vy5,vz5,norm5) |
| 1192 |
|
| 1193 |
val_d=angle_d(vx4,vy4,vz4,norm4, vx5,vy5,vz5,norm5, & |
| 1194 |
vx2,vy2,vz2,norm2) |
| 1195 |
|
| 1196 |
! write(*,11) n1,n2,norm1,n3,val,n4,val_d |
| 1197 |
!11 format (2(1x,i3),1x,f8.4,2(1x,i3,1x,f8.3)) |
| 1198 |
|
| 1199 |
val_zmat(i,1)=norm1 |
| 1200 |
val_zmat(i,2)=val |
| 1201 |
val_zmat(i,3)=val_d |
| 1202 |
|
| 1203 |
END DO |
| 1204 |
|
| 1205 |
if (debug) THEN |
| 1206 |
WRITE(*,*) 'DBG Cre_Zmat_Frag: ind_zmat' |
| 1207 |
DO I=1,na |
| 1208 |
WRITE(*,'(1X,5I5)') (ind_zmat(i,j),j=1,5) |
| 1209 |
END DO |
| 1210 |
|
| 1211 |
WRITE(*,*) 'DBG Cre_Zmat_Frag: Full zmat' |
| 1212 |
DO I=1,na |
| 1213 |
WRITE(*,'(1X,I5,1X,I5,F8.4,2(1X,I5,1X,F7.2))') ind_zmat(i,1),(ind_zmat(i,j+1),val_zmat(i,j),j=1,3) |
| 1214 |
END DO |
| 1215 |
|
| 1216 |
END IF |
| 1217 |
|
| 1218 |
if (debugGaussian) THEN |
| 1219 |
WRITE(*,*) 'DBG Cre_Zmat_Frag: Gaussian Zmat - START' |
| 1220 |
Call WriteMixed_Gaussian(na,atome,LocalNCart,ind_zmat,val_zmat) |
| 1221 |
WRITE(*,*) 'DBG Cre_Zmat_Frag: Gaussian Zmat - END' |
| 1222 |
END IF |
| 1223 |
|
| 1224 |
|
| 1225 |
if (debug) WRITE(*,*) "Deallocate (FragDist,Fragment, NbAtFrag,FragAt)" |
| 1226 |
DEALLOCATE(FragDist,Fragment, NbAtFrag,FragAt) |
| 1227 |
if (debug) WRITE(*,*) "Deallocate (DistFrag,Liaisons)" |
| 1228 |
DEALLOCATE(DistFrag,Liaisons) |
| 1229 |
if (debug) WRITE(*,*) "Deallocate(CaFaire,DejaFait)" |
| 1230 |
DEALLOCATE(CaFaire,DejaFait,FCaf,MaxLFrag) |
| 1231 |
|
| 1232 |
|
| 1233 |
|
| 1234 |
if (debug) WRITE(*,*) "=============================== Exiting Calc_zmat_frag ========================" |
| 1235 |
|
| 1236 |
END SUBROUTINE Calc_Zmat_frag |
| 1237 |
|