root / src / Calc_zmat_constr_frag.f90
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SUBROUTINE Calc_Zmat_const_frag(na,atome,ind_zmat,val_zmat,x,y,z, & |
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r_cov,fact,frozen) |
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|
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! |
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! This second version enables the user to freeze some atoms |
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! the frozen atoms indices are listed in the frozen array. |
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! |
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! The idea is surely too stupid to work all the time... but here it is |
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! we first construct the zmat using only the frozen atoms, and then |
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! we add the other atoms on top of the first ones... |
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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 |
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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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|
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CHARACTER(5) :: AtName |
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integer(KINT) :: na,atome(na),ind_zmat(Na,5) |
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INTEGER(KINT) :: idx_zmat(NA) |
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real(KREAL) :: x(Na),y(Na),z(Na),fact |
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real(KREAL) :: val_zmat(Na,3) |
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real(KREAL) :: r_cov(0:Max_Z) |
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! Frozen contains the indices of frozen atoms |
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INTEGER(KINT) :: Frozen(*),NFroz |
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INTEGER(KINT), ALLOCATABLE :: FrozDist(:) ! na |
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INTEGER(KINT) :: NbFrag,IdxFrag |
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INTEGER(KINT), ALLOCATABLE :: Fragment(:),NbAtFrag(:) !na |
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INTEGER(KINT), ALLOCATABLE :: FragAt(:,:) !na,na |
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INTEGER(KINT), ALLOCATABLE :: FrozFrag(:,:) !na,3 |
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! INTEGER(KINT), ALLOCATABLE :: IdxFragAt(:) !na |
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INTEGER(KINT), ALLOCATABLE :: FrozBlock(:,:) !(na,0:na) |
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REAL(KREAL), ALLOCATABLE :: DistFroz(:) !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 :: LiaisonsBis(:,:) ! (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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|
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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, 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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|
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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) :: IMax, I3,I1,Ip, IFragFroz |
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INTEGER(KINT) :: I0, Izm, JAt,Izm0 |
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|
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REAL(KREAL), PARAMETER :: LocalNCart=0.d0 |
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REAL(KREAL) :: sDihe, Pi |
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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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use Path_module, only : Pi,KINT, KREAL |
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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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use Path_module, only : Pi,KINT, KREAL |
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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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|
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FUNCTION angle_d(v1x,v1y,v1z,norm1,v2x,v2y,v2z,norm2,v3x,v3y,v3z,norm3) |
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use Path_module, only : Pi,KINT, KREAL |
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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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|
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END INTERFACE |
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|
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|
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|
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Pi=dacos(-1.d0) |
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debug=valid("calc_zmat_constr").OR.valid("calc_zmat_contr_frag")
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debugGaussian=valid("zmat_gaussian")
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|
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if (debug) WRITE(*,*) "=============================== Entering Calc_zmat_contr_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(FrozDist(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), FrozBlock(na,0:na)) |
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ALLOCATE(DistFroz(na),Liaisons(na,0:NMaxL)) |
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ALLOCATE(LiaisonsBis(na,0:NMaxL),LiaisonsIni(na,0:NMaxL)) |
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ALLOCATE(CaFaire(na),DejaFait(Na),FCaf(na),FrozAt(na)) |
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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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if (F1213) THEN |
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if (F1323) THEN |
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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)=1 |
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ind_zmat(3,3)=3 |
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ELSE |
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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)=2 |
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ind_zmat(3,3)=1 |
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END IF |
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ELSE |
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IF (F1223) THEN |
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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)=1 |
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ind_zmat(3,3)=2 |
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ELSE |
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ind_zmat(1,1)=2 |
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ind_zmat(2,1)=3 |
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ind_zmat(2,2)=2 |
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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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END IF |
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END IF |
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IF (debug) THEN |
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DO i=1,na |
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WRITE(*,'(1X,5(1X,I5))') (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(1,1)=0. |
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val_zmat(1,2)=0. |
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val_zmat(1,3)=0. |
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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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val_zmat(2,2)=0. |
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val_zmat(2,3)=0. |
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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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val_zmat(3,3)=0. |
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|
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RETURN |
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END IF |
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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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! 1 - Frozen Atoms |
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|
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! Initialization |
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DejaFait=.False. |
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FrozAt=.False. |
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Liaisons=0 |
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LiaisonsBis=0 |
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ind_zmat=0 |
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val_zmat=0.d0 |
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|
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NFroz=0 |
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I=1 |
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DO WHILE (Frozen(I).NE.0) |
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If (Frozen(I).LT.0) THEN |
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DO J=Frozen(I-1),abs(Frozen(I)) |
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IF (.NOT.FrozAt(J)) THEN |
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NFroz=NFroz+1 |
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FrozAt(J)=.TRUE. |
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END IF |
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END DO |
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ELSEIF (.NOT.FrozAt(Frozen(I))) THEN |
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FrozAt(Frozen(I))=.TRUE. |
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NFroz=NFroz+1 |
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END IF |
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I=I+1 |
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END DO |
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|
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if (debug) WRITE(*,*) 'DGB zmtc NFroz=', NFroz |
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if (debug) WRITE(*,*) 'DGB zmtc FrozAt=',(FrozAt(I),I=1,na) |
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|
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if (debug) THEN |
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WRITE(*,*) "Liaisons 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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! DO IL=1,na |
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! WRITE(IOOUT,1003) Il,(LIAISONS(IL,JL),JL=0,NMaxL) |
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! WRITE(IOOUT,1003) Il,(LIAISONSBis(IL,JL),JL=0,NMaxL) |
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! END DO |
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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(*,'(20(1X,I4))') (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) THEN |
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if (FrozAt(J)) THEN |
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WRITE(*,'(1X,I3,"f",1X,A5,3(1X,F10.6))') J,Nom(Atome(J)) & |
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,X(J),Y(J),Z(J) |
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ELSE |
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WRITE(*,'(1X,I3,2X,A5,3(1X,F10.6))') J,Nom(Atome(J)) & |
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,X(J),Y(J),Z(J) |
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END IF |
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END IF |
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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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|
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! First, we decompose the connectivity into Frozen atoms and non frozen atoms |
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DO I=1,na |
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LiaisonsBis(I,0)=0 |
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DO J=1,Liaisons(I,0) |
| 324 |
IF (FrozAt(Liaisons(I,J))) THEN |
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LiaisonsBis(I,0)=LiaisonsBis(I,0)+1 |
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LiaisonsBis(I,LiaisonsBis(I,0))=Liaisons(I,J) |
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END IF |
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END DO |
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IMax=LiaisonsBis(I,0)+1 |
| 330 |
LiaisonsBis(I,Imax)=0 |
| 331 |
DO J=1,Liaisons(I,0) |
| 332 |
IF (.NOT.FrozAt(Liaisons(I,J))) THEN |
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LiaisonsBis(I,IMax)=LiaisonsBis(I,Imax)+1 |
| 334 |
LiaisonsBis(I,LiaisonsBis(I,Imax)+Imax)=Liaisons(I,J) |
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END IF |
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END DO |
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END DO |
| 338 |
|
| 339 |
if (debug) THEN |
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WRITE(*,*) "Liaisons and LiaisonsBis" |
| 341 |
DO I=1,Na |
| 342 |
WRITE(*,'(1X,I3," -",I3,":",15(1X,I3))') I, & |
| 343 |
(Liaisons(I,J),J=0,NMaxL) |
| 344 |
WRITE(*,'(1X,I3," +",I3,":",15(1X,I3))') I, & |
| 345 |
(LiaisonsBis(I,J),J=0,NMaxL) |
| 346 |
END DO |
| 347 |
END IF |
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|
| 349 |
! Now, for each frozen atom, we count the length of the frozen block |
| 350 |
! FrozBlock(I,0) contains the number of frozen atoms forming a frozen |
| 351 |
! fragment containing atom I |
| 352 |
! FrozBlock(I,:) is the list of the frozen atoms of this fragment. |
| 353 |
Do I=1,na |
| 354 |
FrozBlock(I,0)=-1 |
| 355 |
END DO |
| 356 |
DO I=1,na |
| 357 |
IF (FrozAt(I).AND.(FrozBlock(I,0).EQ.-1)) THEN |
| 358 |
if (debug) WRITE(*,*) 'Treating atom ',I |
| 359 |
FrozBlock(I,0)=1 |
| 360 |
FrozBlock(I,1)=I |
| 361 |
DO J=1,na |
| 362 |
DejaFait(J)=.FALSE. |
| 363 |
END DO |
| 364 |
DejaFait(I)=.TRUE. |
| 365 |
DO J=1,LiaisonsBis(I,0) |
| 366 |
CaFaire(J)=LiaisonsBis(I,J) |
| 367 |
END DO |
| 368 |
IdxCaFaire=LiaisonsBis(I,0)+1 |
| 369 |
CaFaire(IdxCaFaire)=0 |
| 370 |
IAfaire=1 |
| 371 |
FCaf=DejaFait |
| 372 |
DO WHILE (CaFaire(IAfaire).NE.0) |
| 373 |
Iat=CaFaire(IAFAire) |
| 374 |
if (debug) WRITE(*,*) 'IaFaire; Iat:', IaFaire, Iat, DejaFait(Iat) |
| 375 |
IF (.NOT.DejaFait(Iat)) THEN |
| 376 |
FrozBlock(I,0)=FrozBlock(I,0)+1 |
| 377 |
FrozBlock(I,FrozBlock(I,0))=Iat |
| 378 |
DO J=1,LiaisonsBis(Iat,0) |
| 379 |
IF ((.NOT.DejaFait(LiaisonsBis(Iat,J))).AND.(.NOT.FCaf(LiaisonsBis(Iat,J)))) THEN |
| 380 |
CaFaire(IdxCaFaire)=LiaisonsBis(Iat,J) |
| 381 |
IdxCaFaire=IdxCaFaire+1 |
| 382 |
CaFaire(IdxCaFaire)=0 |
| 383 |
FCaf(LiaisonsBis(Iat,J))=.TRUE. |
| 384 |
END IF |
| 385 |
END DO |
| 386 |
! WRITE(*,*) 'liaisonbis(Iat,0),FrozBlick(I,0)',& |
| 387 |
! LiaisonsBis(Iat,0), FrozBlock(I,0) |
| 388 |
END IF |
| 389 |
DejaFait(Iat)=.TRUE. |
| 390 |
IaFaire=IaFaire+1 |
| 391 |
END DO |
| 392 |
if (debug) WRITE(*,*) 'I,FrozBlock(0),IaFaire',I,FrozBlock(I,0),IaFaire |
| 393 |
if (debug) WRITE(*,*) 'FrozBlock:',FrozBlock(I,1:FrozBlock(I,0)) |
| 394 |
! FrozBlock(I,1)=I |
| 395 |
! DO J=2,IaFaire |
| 396 |
! FrozBlock(I,J)=CaFaire(J-1) |
| 397 |
! END DO |
| 398 |
! We copy this block into all frozen atoms that belongs to it |
| 399 |
DO J=2,Frozblock(I,0) |
| 400 |
Iat=FrozBlock(I,J) |
| 401 |
DO K=0,FrozBlock(I,0) |
| 402 |
FrozBlock(Iat,K)=FrozBlock(I,K) |
| 403 |
END DO |
| 404 |
END DO |
| 405 |
ELSE |
| 406 |
IF (.NOT.FrozAt(I)) FrozBlock(I,0)=0 |
| 407 |
END IF |
| 408 |
END DO |
| 409 |
|
| 410 |
if (debug) THEN |
| 411 |
WRITE(*,*) "FrozBlock" |
| 412 |
DO I=1,Na |
| 413 |
If (FrozAt(I)) WRITE(*,'(1X,I3," -",I3,":",15(1X,I3))') I, & |
| 414 |
(FrozBlock(I,J),J=0,FrozBlock(I,0)) |
| 415 |
END DO |
| 416 |
END IF |
| 417 |
|
| 418 |
DO I=1,NbFrag |
| 419 |
FrozFrag(I,1)=0 |
| 420 |
FrozFrag(I,2)=0 |
| 421 |
DO J=1,NbAtFrag(I) |
| 422 |
IF (FrozAt(FragAt(I,J))) THEN |
| 423 |
FrozFrag(I,1)=FrozFrag(I,1)+1 |
| 424 |
IF (FrozBlock(FragAt(I,J),0).GE.FrozFrag(I,2)) & |
| 425 |
FrozFrag(I,2)=FrozBlock(FragAt(I,J),0) |
| 426 |
if (FrozFrag(I,3).LE.LiaisonsBis(FragAt(I,J),0))& |
| 427 |
FrozFrag(I,3)=LiaisonsBis(FragAt(I,J),0) |
| 428 |
END IF |
| 429 |
END DO |
| 430 |
IF (debug) WRITE(*,*) 'Frag :',I,FrozFrag(I,1), & |
| 431 |
' frozen atoms,max linked:' & |
| 432 |
,FrozFrag(I,2),' with at most',FrozFrag(I,3),' frozen' |
| 433 |
END DO |
| 434 |
|
| 435 |
! We will now build the molecule fragment by fragment |
| 436 |
! First the frozen atoms, then the rest of the fragment |
| 437 |
! We choose the starting fragment with two criteria: |
| 438 |
! 1- Number of linked frozen atoms: |
| 439 |
! * >=3 is good as it fully defines the coordinate space |
| 440 |
! * 2 is ok as we can either use a 3rd atom from the same fragment |
| 441 |
! or add a X atom somewhere but this complicates quite a lot the way |
| 442 |
! to treat the conversion from cartesian to zmat latter |
| 443 |
! * 1 is bad... |
| 444 |
! 2- Max number of linked frozen atoms |
| 445 |
! this allows us to deal more easily with cases 1- when number of |
| 446 |
! directly linked frozen atoms is less than 3 |
| 447 |
|
| 448 |
IFrag=0 |
| 449 |
I0=0 |
| 450 |
I1=0 |
| 451 |
DO I=1,NbFrag |
| 452 |
SELECT CASE(FrozFrag(I,3)-I0) |
| 453 |
CASE (1:) |
| 454 |
IFrag=I |
| 455 |
I0=FrozFrag(I,3) |
| 456 |
I1=FrozFrag(I,2) |
| 457 |
CASE (0) |
| 458 |
if (FrozFrag(I,2).GT.I1) THEN |
| 459 |
IFrag=I |
| 460 |
I0=FrozFrag(I,3) |
| 461 |
I1=FrozFrag(I,2) |
| 462 |
END IF |
| 463 |
END SELECT |
| 464 |
END DO |
| 465 |
|
| 466 |
if (debug) WRITE(*,'(1X,A,I5,A,I5,A,I5,A)') 'Starting with fragment:',IFrag,' with ',I0,' frozen linked and overall',I1,' linked' |
| 467 |
|
| 468 |
! We will build the first fragment in a special way, as it will |
| 469 |
! set the coordinates system |
| 470 |
! We look for the frozen atom that is linked to the maximum frozen atom, |
| 471 |
! and belongs to the longer fragment |
| 472 |
I0=0 |
| 473 |
I1=0 |
| 474 |
DO I=1,NbAtFrag(IFrag) |
| 475 |
IF (FrozAt(FragAt(IFrag,I))) THEN |
| 476 |
SELECT CASE(LiaisonsBis(FragAt(IFrag,I),0)-I0) |
| 477 |
CASE (1:) |
| 478 |
IAt=FragAt(IFrag,I) |
| 479 |
I0=LiaisonsBis(IAt,0) |
| 480 |
I1=FrozBlock(IAt,0) |
| 481 |
CASE (0) |
| 482 |
IF (FrozBlock(FragAt(IFrag,I),0).GT.I1) THEN |
| 483 |
IAt=FragAt(IFrag,I) |
| 484 |
I0=LiaisonsBis(Iat,0) |
| 485 |
I1=FrozBlock(Iat,0) |
| 486 |
END IF |
| 487 |
END SELECT |
| 488 |
END IF |
| 489 |
if (debug) WRITE(*,*) 'DBG: I,FragAt(IFrag,I),IAt,I0,I1',I,FragAt(IFrag,I),IAt,I0,I1 |
| 490 |
END DO |
| 491 |
|
| 492 |
if (debug) WRITE(*,*) 'Fragment 1, starting with atom:',IAt,I0,I1 |
| 493 |
|
| 494 |
DO I=1,na |
| 495 |
DejaFait(I)=.FALSE. |
| 496 |
FCaf(I)=.FALSE. |
| 497 |
END DO |
| 498 |
|
| 499 |
izm=0 |
| 500 |
SELECT CASE (I0) |
| 501 |
CASE(3:) |
| 502 |
if (debug) WRITE(*,*) 'DBG select case I0 3' |
| 503 |
n0=Iat |
| 504 |
! We search for the fourth atom while making sure that the dihedral angle |
| 505 |
! is not 0 or Pi |
| 506 |
ITmp=2 |
| 507 |
sDihe=0. |
| 508 |
n2=IAt |
| 509 |
n3=LiaisonsBis(Iat,1) |
| 510 |
! We search for the third atom while making sure that it is not aligned with first two ! |
| 511 |
DO While ((ITmp.LE.LiaisonsBis(Iat,0)).AND.(sDihe.LE.0.09d0)) |
| 512 |
n4=LiaisonsBis(Iat,Itmp) |
| 513 |
CALL vecteur(n2,n3,x,y,z,vx2,vy2,vz2,norm2) |
| 514 |
CALL vecteur(n3,n4,x,y,z,vx3,vy3,vz3,norm3) |
| 515 |
val_d=angle(vx3,vy3,vz3,norm3,vx2,vy2,vz2,norm2) |
| 516 |
sDiHe=abs(sin(val_d*pi/180.d0)) |
| 517 |
if (debug) Write(*,*) 'Trying n2,n3,n4,sdihe,val_d',n2,n3,n4,sdihe,val_d |
| 518 |
Itmp=Itmp+1 |
| 519 |
END DO |
| 520 |
If (debug) WRITE(*,*) 'Itmp,LiaisonsBis',Itmp,LiaisonsBis(Iat,1:NMaxL) |
| 521 |
LiaisonsBis(Iat,Itmp-1)=LiaisonsBis(iat,2) |
| 522 |
LiaisonsBis(Iat,2)=n4 |
| 523 |
If (debug) WRITE(*,*) 'Itmp,LiaisonsBis',Itmp,LiaisonsBis(Iat,1:NMaxL) |
| 524 |
|
| 525 |
if (sDihe.LE.0.09d0) THEN |
| 526 |
WRITE(*,*) "Dans le caca car tous les atoms de ce block sont align?s!" |
| 527 |
END IF |
| 528 |
|
| 529 |
CALL produit_vect(vx3,vy3,vz3,vx2,vy2,vz2, & |
| 530 |
vx5,vy5,vz5,norm5) |
| 531 |
|
| 532 |
|
| 533 |
Itmp=2 |
| 534 |
sDiHe=0. |
| 535 |
|
| 536 |
DO While ((ITmp.LT.LiaisonsBis(Iat,0)).AND.(sDihe.LE.0.09d0)) |
| 537 |
ITmp=ITmp+1 |
| 538 |
n1=LiaisonsBis(Iat,Itmp) |
| 539 |
if (debug) WRITe(*,*) 'trying n1,n2,n3,n4',n1,n2,n3,n4 |
| 540 |
CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
| 541 |
! Is this atom aligned with n2-n3 ? |
| 542 |
val_d=angle(vx1,vy1,vz1,norm1,vx2,vy2,vz2,norm2) |
| 543 |
sDiHe=abs(sin(val_d*pi/180.d0)) |
| 544 |
if (debug) Write(*,*) 'Angle n3-n2-n1',val_d |
| 545 |
if (sDiHe.le.0.09d0) THEN |
| 546 |
! As atoms n2,n3 and n4 are not aligned, we interchange n3 and n4 so that n1,n2 and n3 are not aligned |
| 547 |
if (debug) WRITE(*,*) "n3-n2-n1 aligned, we interchange n3 and n4" |
| 548 |
n1=n3 |
| 549 |
n3=n4 |
| 550 |
n4=n1 |
| 551 |
n1=LiaisonsBis(Iat,ITmp) |
| 552 |
CALL vecteur(n2,n3,x,y,z,vx2,vy2,vz2,norm2) |
| 553 |
CALL vecteur(n2,n4,x,y,z,vx3,vy3,vz3,norm3) |
| 554 |
val_d=angle(vx1,vy1,vz1,norm1,vx2,vy2,vz2,norm2) |
| 555 |
if (debug) Write(*,*) 'NEW Angle n3-n2-n1',val_d |
| 556 |
END IF |
| 557 |
|
| 558 |
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
| 559 |
! avant de tester l'angle diedre, il faut verifier que ce 4e atome n'est pas |
| 560 |
! aligne avec les 2 premiers. |
| 561 |
! comme on a deja test? que les 3 premiers ne sont pas alignes, |
| 562 |
! s'il est align? avec les 2 premiers, on peut inverser le role de 2 et 3. |
| 563 |
! On pourrait tout simplier en faisant une bete recherche parmi tous les atomes geles |
| 564 |
! de ce bloc (au moins 4 ?) avec le critere 1) on les range par distance croissante |
| 565 |
! 2) on les scanne tant que l'angle valence n'est pas bon, puis tant que diehedre pas bon |
| 566 |
! on pourrait comme ca faire un tableau avec les atomes ranges d'abord pour le fragment s?lectionn? |
| 567 |
! puis les atomes des autres fragment par distance croissante. |
| 568 |
! les autres fragments ne seraient additonn?s que si l'on ne trouve pas notre bonheur dans le premier bloc |
| 569 |
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
| 570 |
|
| 571 |
CALL produit_vect(vx1,vy1,vz1,vx2,vy2,vz2, & |
| 572 |
vx4,vy4,vz4,norm4) |
| 573 |
val_d=angle_d(vx4,vy4,vz4,norm4,vx5,vy5,vz5,norm5, & |
| 574 |
vx2,vy2,vz2,norm2) |
| 575 |
sDihe=abs(sin(val_d*pi/180.d0)) |
| 576 |
if (debug) WRITE(*,*) 'n2,n3,n4,n1, angle_d',n2,n3,n4,n1,val_d |
| 577 |
END DO |
| 578 |
|
| 579 |
DejaFait(n2)=.TRUE. |
| 580 |
DejaFait(n3)=.TRUE. |
| 581 |
DejaFait(n4)=.TRUE. |
| 582 |
|
| 583 |
if (sDihe.LE.0.09d0) THEN |
| 584 |
! None of the frozen atoms linked to IAt are good to define the third |
| 585 |
! direction in space... |
| 586 |
! We will look at the other frozen atoms |
| 587 |
! we might improve the search so as to take the atom closest to IAt |
| 588 |
if (debug) WRITE(*,*) "All atoms linked to ",Iat," are in a plane. Looking for other frozen atoms" |
| 589 |
ITmp=0 |
| 590 |
DO I=1,NbAtFrag(IFrag) |
| 591 |
JAt=FragAt(IFrag,I) |
| 592 |
if (FrozAt(Jat).AND.(.NOT.DejaFait(JAt))) THEN |
| 593 |
n1=JAt |
| 594 |
CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
| 595 |
CALL produit_vect(vx1,vy1,vz1,vx2,vy2,vz2, & |
| 596 |
vx4,vy4,vz4,norm4) |
| 597 |
val_d=angle_d(vx4,vy4,vz4,norm4, & |
| 598 |
vx5,vy5,vz5,norm5, & |
| 599 |
vx2,vy2,vz2,norm2) |
| 600 |
if (abs(sin(val_d)).GE.0.09D0) THEN |
| 601 |
ITmp=ITmp+1 |
| 602 |
DistFroz(ITmp)=Norm1 |
| 603 |
FrozDist(ITmp)=JAt |
| 604 |
END IF |
| 605 |
END IF |
| 606 |
END DO |
| 607 |
IF (ITmp.EQ.0) THEN |
| 608 |
! All dihedral angles between frozen atoms are less than 5? |
| 609 |
! (or more than 175?). We have to look at other fragments :-( |
| 610 |
DO I=1,NFroz |
| 611 |
Jat=Frozen(I) |
| 612 |
if (.NOT.DejaFait(JAt)) THEN |
| 613 |
n1=JAt |
| 614 |
CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
| 615 |
CALL produit_vect(vx1,vy1,vz1,vx2,vy2,vz2, & |
| 616 |
vx4,vy4,vz4,norm4) |
| 617 |
val_d=angle_d(vx4,vy4,vz4,norm4, & |
| 618 |
vx5,vy5,vz5,norm5, & |
| 619 |
vx2,vy2,vz2,norm2) |
| 620 |
if (abs(sin(val_d)).GE.0.09D0) THEN |
| 621 |
ITmp=ITmp+1 |
| 622 |
DistFroz(ITmp)=Norm1 |
| 623 |
FrozDist(ITmp)=JAt |
| 624 |
END IF |
| 625 |
END IF |
| 626 |
END DO |
| 627 |
IF (ITmp.EQ.0) THEN |
| 628 |
! All frozen atoms are in a plane... too bad |
| 629 |
WRITE(*,*) 'ERROR: It seems that all frozen atoms are in a plane' |
| 630 |
WRITE(*,*) 'For now, I do not treat this case' |
| 631 |
STOP |
| 632 |
END IF |
| 633 |
END IF |
| 634 |
I1=0 |
| 635 |
d=1e9 |
| 636 |
DO I=1,ITmp |
| 637 |
IF (DistFroz(I).LE.d) THEN |
| 638 |
d=DistFroz(I) |
| 639 |
I1=FrozDist(I) |
| 640 |
END IF |
| 641 |
END DO |
| 642 |
ELSE !(sDihe.LE.0.09d0) |
| 643 |
I1=FrozBlock(IAt,ITmp) |
| 644 |
if (debug) WRITE(*,*) 'I1,n1:',I1,n1 |
| 645 |
END IF !(sDihe.LE.0.09d0) |
| 646 |
! we now have the atom that is closer to the first one and that |
| 647 |
! forms a non 0/Pi dihedral angle |
| 648 |
|
| 649 |
ind_zmat(1,1)=n2 |
| 650 |
ind_zmat(2,1)=n3 |
| 651 |
ind_zmat(2,2)=n2 |
| 652 |
ind_zmat(3,1)=n4 |
| 653 |
ind_zmat(3,2)=n2 |
| 654 |
ind_zmat(3,3)=n3 |
| 655 |
DejaFait(n2)=.TRUE. |
| 656 |
DejaFait(n3)=.TRUE. |
| 657 |
DejaFait(n4)=.TRUE. |
| 658 |
CaFaire(1)=n3 |
| 659 |
CaFaire(2)=n4 |
| 660 |
|
| 661 |
ind_zmat(4,1)=I1 |
| 662 |
ind_zmat(4,2)=n2 |
| 663 |
ind_zmat(4,3)=n3 |
| 664 |
ind_zmat(4,4)=n4 |
| 665 |
DejaFait(I1)=.TRUE. |
| 666 |
CaFaire(3)=I1 |
| 667 |
CaFaire(4)=0 |
| 668 |
IdxCaFaire=4 |
| 669 |
|
| 670 |
FCaf(n2)=.TRUE. |
| 671 |
FCaf(n3)=.TRUE. |
| 672 |
FCaf(I1)=.TRUE. |
| 673 |
izm=4 |
| 674 |
DO I=3,LiaisonsBis(Iat,0) |
| 675 |
IF (.NOT.DejaFait(LiaisonsBis(Iat,I))) THEN |
| 676 |
izm=izm+1 |
| 677 |
! ind_zmat(izm,1)=LiaisonsBis(Iat,I) |
| 678 |
! ind_zmat(izm,2)=n2 |
| 679 |
! ind_zmat(izm,3)=n3 |
| 680 |
! ind_zmat(izm,4)=n4 |
| 681 |
Call add2indzmat(na,izm,LiaisonsBis(Iat,I),n2,n3,n4,ind_zmat,x,y,z) |
| 682 |
IF (.NOT.FCaf(LiaisonsBis(Iat,I))) THEN |
| 683 |
CaFaire(IdxCaFaire)=LiaisonsBis(Iat,I) |
| 684 |
IdxCaFaire=IdxCaFaire+1 |
| 685 |
CaFaire(IdxCaFaire)=0 |
| 686 |
FCaf(LiaisonsBis(Iat,I))=.TRUE. |
| 687 |
END IF |
| 688 |
DejaFait(LiaisonsBis(Iat,I))=.TRUE. |
| 689 |
END IF |
| 690 |
END DO |
| 691 |
|
| 692 |
if (debug) THEN |
| 693 |
WRITE(*,*) "Ind_zmat 0 - SELECT CASE I0 3: -- izm=",izm |
| 694 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(1,1) |
| 695 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(2,1), ind_zmat(2,2) |
| 696 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(3,1), ind_zmat(3,2), ind_zmat(3,3) |
| 697 |
DO I=4,izm |
| 698 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(I,1), ind_zmat(I,2), & |
| 699 |
ind_zmat(I,3), ind_zmat(I,4) |
| 700 |
END DO |
| 701 |
END IF |
| 702 |
|
| 703 |
|
| 704 |
! First four atoms (at least) have been put we go on with next parts |
| 705 |
! of this fragment... later |
| 706 |
|
| 707 |
|
| 708 |
CASE(2) |
| 709 |
if (debug) WRITE(*,*) 'DBG select case I0 2' |
| 710 |
if (debug) WRITE(*,*) 'ATTENTION For now, case with only 3 frozen atoms non treated' |
| 711 |
ind_zmat(1,1)=IAt |
| 712 |
ind_zmat(2,1)=liaisonsBis(IAt,1) |
| 713 |
ind_zmat(2,2)=IAt |
| 714 |
ind_zmat(3,1)=LiaisonsBis(IAt,2) |
| 715 |
ind_zmat(3,2)=IAt |
| 716 |
ind_zmat(3,3)=LiaisonsBis(IAt,1) |
| 717 |
DejaFait(IAt)=.TRUE. |
| 718 |
DejaFait(LiaisonsBis(Iat,1))=.TRUE. |
| 719 |
DejaFait(LiaisonsBis(Iat,2))=.TRUE. |
| 720 |
CaFaire(1)=LiaisonsBis(Iat,1) |
| 721 |
CaFaire(2)=LiaisonsBis(Iat,2) |
| 722 |
FCaf(LiaisonsBis(Iat,1))=.TRUE. |
| 723 |
FCaf(LiaisonsBis(Iat,2))=.TRUE. |
| 724 |
|
| 725 |
! We search for a fourth atom, first in the FrozBlock atoms |
| 726 |
ITmp=2 |
| 727 |
sDihe=0. |
| 728 |
n2=IAt |
| 729 |
n3=LiaisonsBis(Iat,1) |
| 730 |
n4=LiaisonsBis(Iat,2) |
| 731 |
CALL vecteur(n2,n3,x,y,z,vx2,vy2,vz2,norm2) |
| 732 |
CALL vecteur(n3,n4,x,y,z,vx3,vy3,vz3,norm3) |
| 733 |
CALL produit_vect(vx3,vy3,vz3,vx2,vy2,vz2, & |
| 734 |
vx5,vy5,vz5,norm5) |
| 735 |
|
| 736 |
DO While ((ITmp.LE.FrozBlock(Iat,0)).AND.(sDihe.LE.0.09d0)) |
| 737 |
ITmp=ITmp+1 |
| 738 |
n1=FrozBlock(Iat,Itmp) |
| 739 |
CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
| 740 |
CALL produit_vect(vx1,vy1,vz1, vx2,vy2,vz2, & |
| 741 |
vx4,vy4,vz4,norm4) |
| 742 |
val_d=angle_d(vx4,vy4,vz4,norm4, & |
| 743 |
vx5,vy5,vz5,norm5, & |
| 744 |
vx2,vy2,vz2,norm2) |
| 745 |
sDihe=abs(sin(val_d)) |
| 746 |
END DO |
| 747 |
IF (debug) WRITE(*,*) 'DBG 4th atom, ITmp, sDihe',ITmp, sDihe |
| 748 |
if (sDihe.LE.0.09d0) THEN |
| 749 |
! None of the frozen atoms linked to IAt are good to define the third |
| 750 |
! direction in space... |
| 751 |
! We will look at the other frozen atoms |
| 752 |
! we might improve the search so as to take the atom closest to IAt |
| 753 |
ITmp=0 |
| 754 |
DO I=1,NbAtFrag(IFrag) |
| 755 |
JAt=FragAt(IFrag,I) |
| 756 |
if (FrozAt(Jat).AND.(.NOT.DejaFait(JAt))) THEN |
| 757 |
n1=JAt |
| 758 |
CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
| 759 |
CALL produit_vect(vx1,vy1,vz1, vx2,vy2,vz2, & |
| 760 |
vx4,vy4,vz4,norm4) |
| 761 |
val_d=angle_d(vx4,vy4,vz4,norm4, & |
| 762 |
vx5,vy5,vz5,norm5, & |
| 763 |
vx2,vy2,vz2,norm2) |
| 764 |
if (abs(sin(val_d)).GE.0.09D0) THEN |
| 765 |
ITmp=ITmp+1 |
| 766 |
DistFroz(ITmp)=Norm1 |
| 767 |
FrozDist(ITmp)=JAt |
| 768 |
END IF |
| 769 |
END IF |
| 770 |
END DO |
| 771 |
IF (ITmp.EQ.0) THEN |
| 772 |
! All dihedral angles between frozen atoms are less than 5? |
| 773 |
! (or more than 175?). We have to look at other fragments :-( |
| 774 |
DO I=1,NFroz |
| 775 |
Jat=Frozen(I) |
| 776 |
if (.NOT.DejaFait(JAt)) THEN |
| 777 |
n1=JAt |
| 778 |
CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
| 779 |
CALL produit_vect(vx1,vy1,vz1, vx2,vy2,vz2, & |
| 780 |
vx4,vy4,vz4,norm4) |
| 781 |
val_d=angle_d(vx4,vy4,vz4,norm4, & |
| 782 |
vx5,vy5,vz5,norm5, & |
| 783 |
vx2,vy2,vz2,norm2) |
| 784 |
if (abs(sin(val_d)).GE.0.09D0) THEN |
| 785 |
ITmp=ITmp+1 |
| 786 |
DistFroz(ITmp)=Norm1 |
| 787 |
FrozDist(ITmp)=JAt |
| 788 |
END IF |
| 789 |
END IF |
| 790 |
END DO |
| 791 |
IF (ITmp.EQ.0) THEN |
| 792 |
! All frozen atoms are in a plane... too bad |
| 793 |
WRITE(*,*) 'ERROR: It seems that all frozen atoms are in a plane' |
| 794 |
WRITE(*,*) 'For now, I do not treat this case' |
| 795 |
STOP |
| 796 |
END IF |
| 797 |
END IF |
| 798 |
I1=0 |
| 799 |
d=1e9 |
| 800 |
DO I=1,ITmp |
| 801 |
IF (DistFroz(I).LE.d) THEN |
| 802 |
d=DistFroz(I) |
| 803 |
I1=FrozDist(I) |
| 804 |
END IF |
| 805 |
END DO |
| 806 |
ELSE !(sDihe.LE.0.09d0) |
| 807 |
I1=FrozBlock(IAt,ITmp) |
| 808 |
END IF !(sDihe.LE.0.09d0) |
| 809 |
! we now have the atom that is closer to the first one and that |
| 810 |
! forms a non 0/Pi dihedral angle |
| 811 |
! ind_zmat(4,1)=I1 |
| 812 |
! ind_zmat(4,2)=IAt |
| 813 |
! ind_zmat(4,3)=LiaisonsBis(Iat,1) |
| 814 |
! ind_zmat(4,4)=LiaisonsBis(Iat,2) |
| 815 |
n3=LiaisonsBis(Iat,1) |
| 816 |
n4=LiaisonsBis(Iat,2) |
| 817 |
Call add2indzmat(na,4,I1,Iat,n3,n4,ind_zmat,x,y,z) |
| 818 |
LiaisonsBis(Iat,1)=n3 |
| 819 |
LiaisonsBis(Iat,2)=n4 |
| 820 |
DejaFait(I1)=.TRUE. |
| 821 |
CaFaire(3)=I1 |
| 822 |
CaFaire(4)=0 |
| 823 |
IdxCaFaire=4 |
| 824 |
izm=4 |
| 825 |
FCaf(I1)=.TRUE. |
| 826 |
|
| 827 |
CASE(1) |
| 828 |
if (debug) WRITE(*,*) 'DBG select case I0 1' |
| 829 |
ind_zmat(1,1)=IAt |
| 830 |
ind_zmat(2,1)=liaisonsBis(IAt,1) |
| 831 |
ind_zmat(2,2)=IAt |
| 832 |
DejaFait(IAt)=.TRUE. |
| 833 |
DejaFait(LiaisonsBis(Iat,1))=.TRUE. |
| 834 |
IdxCaFaire=2 |
| 835 |
CaFaire(1)=LiaisonsBis(Iat,1) |
| 836 |
CaFaire(2)=0 |
| 837 |
FCaf(LiaisonsBis(Iat,1))=.TRUE. |
| 838 |
|
| 839 |
! We search for a third and fourth atoms, first in the FrozBlock atoms |
| 840 |
! It should not be possible to have (FrozBlock(Iat,0).GT.2) and |
| 841 |
! iat linked to only one atom ! |
| 842 |
|
| 843 |
IF (FrozBlock(Iat,0).GT.2) THEN |
| 844 |
WRITE(*,*) 'I found some inconsistancy: IAt linked to 1' |
| 845 |
WRITE(*,*) 'Atom only, but belongs to a frozblock of at ' |
| 846 |
WRITE(*,*) 'least 3 atoms. IAt, FrozBlock' |
| 847 |
WRITE(*,*) Iat,(FrozBlock(IAt,J),J=0,FrozBlock(Iat,0)) |
| 848 |
STOP |
| 849 |
END IF |
| 850 |
|
| 851 |
! we calculate the distances between Iat and all other frozen |
| 852 |
! atoms of this fragment, and store only those for which |
| 853 |
! valence angles are not too close to 0/Pi. (limit:5?) |
| 854 |
|
| 855 |
ITmp=0 |
| 856 |
CALL vecteur(LiaisonsBis(Iat,1),IAt,x,y,z,vx2,vy2,vz2,norm2) |
| 857 |
|
| 858 |
DO I=1,NbAtFrag(IFrag) |
| 859 |
JAt=FragAt(IFrag,I) |
| 860 |
if (FrozAt(Jat).AND.(.NOT.DejaFait(JAt))) THEN |
| 861 |
CALL vecteur(JAt,IAt,x,y,z,vx1,vy1,vz1,norm1) |
| 862 |
if (abs(cos(angle(vx1,vy1,vz1,norm1, & |
| 863 |
vx2,vy2,vz2,norm2))).LE.0.996d0) THEN |
| 864 |
ITmp=ITmp+1 |
| 865 |
DistFroz(ITmp)=Norm1 |
| 866 |
FrozDist(ITmp)=JAt |
| 867 |
END IF |
| 868 |
END IF |
| 869 |
END DO |
| 870 |
|
| 871 |
IF (ITMP.EQ.0) THEN |
| 872 |
! We have no frozen atoms correct in this fragment, we use |
| 873 |
! atoms from other fragments |
| 874 |
DO I=1,NFroz |
| 875 |
Jat=Frozen(I) |
| 876 |
if (.NOT.DejaFait(JAt)) THEN |
| 877 |
CALL vecteur(JAt,IAt,x,y,z,vx1,vy1,vz1,norm1) |
| 878 |
if (abs(cos(angle(vx1,vy1,vz1,norm1, & |
| 879 |
vx2,vy2,vz2,norm2))).LE.0.996d0) THEN |
| 880 |
ITmp=ITmp+1 |
| 881 |
DistFroz(ITmp)=Norm1 |
| 882 |
FrozDist(ITmp)=JAt |
| 883 |
END IF |
| 884 |
END IF |
| 885 |
END DO |
| 886 |
IF (ITMP.EQ.0) THEN |
| 887 |
WRITE(*,*) 'It seems all frozen atoms are aligned' |
| 888 |
WRITE(*,*) 'Case non treated for now :-( ' |
| 889 |
STOP |
| 890 |
END IF |
| 891 |
END IF |
| 892 |
|
| 893 |
I1=0 |
| 894 |
d=1e9 |
| 895 |
DO I=1,ITmp |
| 896 |
IF (DistFroz(I).LE.d) THEN |
| 897 |
I1=FrozDist(I) |
| 898 |
d=DistFroz(I) |
| 899 |
END IF |
| 900 |
END DO |
| 901 |
|
| 902 |
! we now have the atom that is closer to the first one and that |
| 903 |
! forms a non 0/Pi valence angle |
| 904 |
ind_zmat(3,1)=I1 |
| 905 |
ind_zmat(3,2)=IAt |
| 906 |
ind_zmat(3,3)=LiaisonsBis(Iat,1) |
| 907 |
DejaFait(I1)=.TRUE. |
| 908 |
CaFaire(2)=I1 |
| 909 |
FCaf(I1)=.TRUE. |
| 910 |
|
| 911 |
|
| 912 |
! we search for a fourth atom ! |
| 913 |
! We search for a fourth atom, first in the FrozBlock atoms |
| 914 |
ITmp=2 |
| 915 |
sDihe=0. |
| 916 |
n2=IAt |
| 917 |
n3=LiaisonsBis(Iat,1) |
| 918 |
n4=I1 |
| 919 |
CALL vecteur(n2,n3,x,y,z,vx2,vy2,vz2,norm2) |
| 920 |
CALL vecteur(n3,n4,x,y,z,vx3,vy3,vz3,norm3) |
| 921 |
CALL produit_vect(vx3,vy3,vz3, vx2,vy2,vz2, & |
| 922 |
vx5,vy5,vz5,norm5) |
| 923 |
|
| 924 |
! We will look at the other frozen atoms |
| 925 |
! we might improve the search so as to take the atom closest to IAt |
| 926 |
ITmp=0 |
| 927 |
DO I=1,NbAtFrag(IFrag) |
| 928 |
JAt=FragAt(IFrag,I) |
| 929 |
if (FrozAt(Jat).AND.(.NOT.DejaFait(JAt))) THEN |
| 930 |
n1=JAt |
| 931 |
CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
| 932 |
CALL produit_vect(vx1,vy1,vz1, vx2,vy2,vz2, & |
| 933 |
vx4,vy4,vz4,norm4) |
| 934 |
val_d=angle_d(vx4,vy4,vz4,norm4, & |
| 935 |
vx5,vy5,vz5,norm5, & |
| 936 |
vx2,vy2,vz2,norm2) |
| 937 |
if (abs(sin(val_d)).GE.0.09D0) THEN |
| 938 |
ITmp=ITmp+1 |
| 939 |
DistFroz(ITmp)=Norm1 |
| 940 |
FrozDist(ITmp)=JAt |
| 941 |
END IF |
| 942 |
END IF |
| 943 |
END DO |
| 944 |
IF (ITmp.EQ.0) THEN |
| 945 |
! All dihedral angles between frozen atoms are less than 5? |
| 946 |
! (or more than 175?). We have to look at other fragments :-( |
| 947 |
DO I=1,NFroz |
| 948 |
Jat=Frozen(I) |
| 949 |
if (.NOT.DejaFait(JAt)) THEN |
| 950 |
n1=JAt |
| 951 |
CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
| 952 |
CALL produit_vect(vx1,vy1,vz1, vx2,vy2,vz2, & |
| 953 |
vx4,vy4,vz4,norm4) |
| 954 |
val_d=angle_d(vx4,vy4,vz4,norm4, & |
| 955 |
vx5,vy5,vz5,norm5, & |
| 956 |
vx2,vy2,vz2,norm2) |
| 957 |
if (abs(sin(val_d)).GE.0.09D0) THEN |
| 958 |
ITmp=ITmp+1 |
| 959 |
DistFroz(ITmp)=Norm1 |
| 960 |
FrozDist(ITmp)=JAt |
| 961 |
END IF |
| 962 |
END IF |
| 963 |
END DO |
| 964 |
IF (ITmp.EQ.0) THEN |
| 965 |
! All frozen atoms are in a plane... too bad |
| 966 |
WRITE(*,*) 'ERROR: It seems that all frozen atoms are in a plane' |
| 967 |
WRITE(*,*) 'For now, I do not treat this case' |
| 968 |
STOP |
| 969 |
END IF |
| 970 |
END IF ! ITmp.EQ.0 after scaning fragment |
| 971 |
I1=0 |
| 972 |
d=1e9 |
| 973 |
DO I=1,ITmp |
| 974 |
IF (DistFroz(I).LE.d) THEN |
| 975 |
d=DistFroz(I) |
| 976 |
I1=FrozDist(I) |
| 977 |
END IF |
| 978 |
END DO |
| 979 |
|
| 980 |
! we now have the atom that is closer to the first one and that |
| 981 |
! forms a non 0/Pi dihedral angle |
| 982 |
! ind_zmat(4,1)=I1 |
| 983 |
! ind_zmat(4,2)=IAt |
| 984 |
! ind_zmat(4,3)=ind_zmat(2,1) |
| 985 |
! ind_zmat(4,4)=ind_zmat(3,1) |
| 986 |
n3=ind_zmat(2,1) |
| 987 |
n4=ind_zmat(3,1) |
| 988 |
Call add2indzmat(na,4,I1,IAt,n3,n4,ind_zmat,x,y,z) |
| 989 |
ind_zmat(2,1)=n3 |
| 990 |
ind_zmat(3,1)=n4 |
| 991 |
DejaFait(I1)=.TRUE. |
| 992 |
CaFaire(3)=I1 |
| 993 |
CaFaire(4)=0 |
| 994 |
IdxCaFaire=4 |
| 995 |
izm=4 |
| 996 |
FCaf(I1)=.TRUE. |
| 997 |
|
| 998 |
CASE(0) |
| 999 |
WRITE(*,*) 'All frozen atoms are separated .. ' |
| 1000 |
WRITE(*,*) 'this case should be treated separately !' |
| 1001 |
STOP |
| 1002 |
END SELECT |
| 1003 |
|
| 1004 |
if (debug) THEN |
| 1005 |
WRITE(*,*) 'ind_zmat 1' |
| 1006 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(1,1) |
| 1007 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(2,1), ind_zmat(2,2) |
| 1008 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(3,1), ind_zmat(3,2), ind_zmat(3,3) |
| 1009 |
DO I=4,izm |
| 1010 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(I,1), ind_zmat(I,2), & |
| 1011 |
ind_zmat(I,3), ind_zmat(I,4) |
| 1012 |
END DO |
| 1013 |
END IF |
| 1014 |
|
| 1015 |
DO I=1,izm |
| 1016 |
Idx_zmat(ind_zmat(I,1))=i |
| 1017 |
END Do |
| 1018 |
|
| 1019 |
! at least first four (frozen) atoms of this fragment done... |
| 1020 |
! we empty the 'cafaire' array before pursuing |
| 1021 |
IAFaire=1 |
| 1022 |
DO WHILE (CaFaire(IaFaire).NE.0) |
| 1023 |
n1=CaFaire(IaFaire) |
| 1024 |
n2=ind_zmat(idx_zmat(N1),2) |
| 1025 |
if (idx_zmat(N1).EQ.2) THEN |
| 1026 |
! We have a (small) problem: we have to add atoms linked to the 2nd |
| 1027 |
! atom of the zmat. This is a pb because we do not know |
| 1028 |
! which atom to use to define the dihedral angle |
| 1029 |
! we take the third atom of the zmat |
| 1030 |
n3=ind_zmat(3,1) |
| 1031 |
ELSE |
| 1032 |
n3=ind_zmat(idx_zmat(n1),3) |
| 1033 |
END IF |
| 1034 |
IF (LiaisonsBis(n1,0).GE.1) THEN |
| 1035 |
IAt=LiaisonsBis(n1,1) |
| 1036 |
if (.NOT.DejaFait(Iat)) THEN |
| 1037 |
izm=izm+1 |
| 1038 |
if (debug) WRITE(*,*) ">0< Adding atom ",Iat,"position izm=",izm |
| 1039 |
! ind_zmat(izm,1)=iat |
| 1040 |
! ind_zmat(izm,2)=n1 |
| 1041 |
! ind_zmat(izm,3)=n2 |
| 1042 |
! ind_zmat(izm,4)=n3 |
| 1043 |
Call add2indzmat(na,izm,iat,n1,n2,n3,ind_zmat,x,y,z) |
| 1044 |
Idx_zmat(iat)=izm |
| 1045 |
n3=iat |
| 1046 |
IF (.NOT.FCaf(Iat)) THEN |
| 1047 |
CaFaire(IdxCaFaire)=iat |
| 1048 |
IdxCaFaire=IdxCaFaire+1 |
| 1049 |
CaFaire(IdxCaFaire)=0 |
| 1050 |
FCaf(Iat)=.TRUE. |
| 1051 |
END IF |
| 1052 |
DejaFait(iat)=.TRUE. |
| 1053 |
END IF |
| 1054 |
END IF |
| 1055 |
DO I=2,LiaisonsBis(n1,0) |
| 1056 |
IAt=LiaisonsBis(n1,I) |
| 1057 |
! PFL 29.Aug.2008 -> |
| 1058 |
! We dissociate the test on 'DejaFait' that indicates that this atom |
| 1059 |
! has already been put in the Zmat |
| 1060 |
! from the test on FCaf that indicates that this atom has been put in the |
| 1061 |
! 'CAFaire' list that deals with identifying its connectivity. |
| 1062 |
! Those two test might differ for a frozen atom linked to non frozen atoms. |
| 1063 |
IF (.NOT.DejaFait(Iat)) THEN |
| 1064 |
izm=izm+1 |
| 1065 |
if (debug) WRITE(*,*) ">1< Adding atom ",Iat,"position izm=",izm |
| 1066 |
! ind_zmat(izm,1)=iat |
| 1067 |
! ind_zmat(izm,2)=n1 |
| 1068 |
! ind_zmat(izm,3)=n2 |
| 1069 |
! ind_zmat(izm,4)=n3 |
| 1070 |
Call add2indzmat(na,izm,iat,n1,n2,n3,ind_zmat,x,y,z) |
| 1071 |
idx_zmat(iat)=izm |
| 1072 |
DejaFait(iat)=.TRUE. |
| 1073 |
END IF |
| 1074 |
IF (.NOT.FCaf(Iat)) THEN |
| 1075 |
CaFaire(IdxCaFaire)=iat |
| 1076 |
IdxCaFaire=IdxCaFaire+1 |
| 1077 |
CaFaire(IdxCaFaire)=0 |
| 1078 |
FCaf(Iat)=.TRUE. |
| 1079 |
END IF |
| 1080 |
! <- PFL 29.Aug.2008 |
| 1081 |
END DO |
| 1082 |
IaFaire=IaFaire+1 |
| 1083 |
END Do ! DO WHILE CaFaire |
| 1084 |
|
| 1085 |
if (debug) THEN |
| 1086 |
WRITE(*,*) 'ind_zmat 2, izm=',izm |
| 1087 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(1,1) |
| 1088 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(2,1), ind_zmat(2,2) |
| 1089 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(3,1), ind_zmat(3,2), ind_zmat(3,3) |
| 1090 |
DO I=4,izm |
| 1091 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(I,1), ind_zmat(I,2), & |
| 1092 |
ind_zmat(I,3), ind_zmat(I,4) |
| 1093 |
END DO |
| 1094 |
END IF |
| 1095 |
|
| 1096 |
! We have finished putting atoms linked to the first one |
| 1097 |
! we will add other frozen atoms of this fragment |
| 1098 |
DO I=1,NbAtFrag(IFrag) |
| 1099 |
Iat=FragAt(IFrag,I) |
| 1100 |
if (debug) WRITE(*,*) "DBG: I,Iat,Frozat,dejafait,frozbloc",I,Iat,FrozAt(Iat), DejaFait(Iat),FrozBlock(Iat,0) |
| 1101 |
IF (FrozAt(Iat).AND.(.NOT.DejaFait(Iat))) THEN |
| 1102 |
! in order to have the zmat as connected as possible, |
| 1103 |
! we look if this atom belongs to a frozblock |
| 1104 |
if (debug) WRITE(*,*) 'Treating atom I,Iat, FrozBlock ',I,Iat, FrozBlock(Iat,0) |
| 1105 |
IF (FrozBlock(Iat,0).EQ.1) THEN |
| 1106 |
! it is a lonely atom :-) |
| 1107 |
d=1e9 |
| 1108 |
DO J=1,izm |
| 1109 |
Call vecteur(iat,ind_zmat(j,1),x,y,z,vx1,vy1,vz1,norm1) |
| 1110 |
if (norm1.le.d) THEN |
| 1111 |
Jat=j |
| 1112 |
d=norm1 |
| 1113 |
END IF |
| 1114 |
END DO |
| 1115 |
n2=ind_zmat(jat,1) |
| 1116 |
SELECT CASE(jat) |
| 1117 |
CASE (1) |
| 1118 |
n3=ind_zmat(2,1) |
| 1119 |
n4=ind_zmat(3,1) |
| 1120 |
CASE (2) |
| 1121 |
n3=ind_zmat(1,1) |
| 1122 |
n4=ind_zmat(3,1) |
| 1123 |
CASE DEFAULT |
| 1124 |
n3=ind_zmat(jAt,2) |
| 1125 |
n4=ind_zmat(jat,3) |
| 1126 |
END SELECT |
| 1127 |
izm=izm+1 |
| 1128 |
! ind_zmat(izm,1)=iat |
| 1129 |
! ind_zmat(izm,2)=n2 |
| 1130 |
! ind_zmat(izm,3)=n3 |
| 1131 |
! ind_zmat(izm,4)=n4 |
| 1132 |
Call add2indzmat(na,izm,iat,n2,n3,n4,ind_zmat,x,y,z) |
| 1133 |
DejaFait(iat)=.TRUE. |
| 1134 |
idx_zmat(iat)=iat |
| 1135 |
ELSE !(FrozBlock(Iat,0).EQ.1) |
| 1136 |
! we have a group of atoms |
| 1137 |
! We search for the atom of the group with the most links |
| 1138 |
ITmp=-1 |
| 1139 |
DO J=1,FrozBlock(Iat,0) |
| 1140 |
Jat=FrozBlock(Iat,J) |
| 1141 |
IF ((.NOT.DejaFait(Jat)).AND. & |
| 1142 |
(LiaisonsBis(Jat,0).GT.ITMP)) THEN |
| 1143 |
JL=Jat |
| 1144 |
ITmp=LiaisonsBis(Jat,0) |
| 1145 |
END IF |
| 1146 |
END DO |
| 1147 |
if (debug) WRITE(*,*) 'JL,ITmp:',JL,ITmp |
| 1148 |
Iat=JL |
| 1149 |
d=1e9 |
| 1150 |
DO J=1,izm |
| 1151 |
Call vecteur(iat,ind_zmat(j,1),x,y,z, vx1,vy1,vz1,norm1) |
| 1152 |
if (norm1.le.d) THEN |
| 1153 |
Jat=j |
| 1154 |
d=norm1 |
| 1155 |
END IF |
| 1156 |
END DO |
| 1157 |
if (debug) WRITE(*,*) 'Jat,d:',Jat,d |
| 1158 |
n2=ind_zmat(jat,1) |
| 1159 |
SELECT CASE(jat) |
| 1160 |
CASE (1) |
| 1161 |
n3=ind_zmat(2,1) |
| 1162 |
n4=ind_zmat(3,1) |
| 1163 |
CASE (2) |
| 1164 |
n3=ind_zmat(1,1) |
| 1165 |
n4=ind_zmat(3,1) |
| 1166 |
CASE DEFAULT |
| 1167 |
n3=ind_zmat(jAt,2) |
| 1168 |
n4=ind_zmat(jat,3) |
| 1169 |
END SELECT |
| 1170 |
izm=izm+1 |
| 1171 |
! ind_zmat(izm,1)=iat |
| 1172 |
! ind_zmat(izm,2)=n2 |
| 1173 |
! ind_zmat(izm,3)=n3 |
| 1174 |
! ind_zmat(izm,4)=n4 |
| 1175 |
Call add2indzmat(na,izm,iat,n2,n3,n4,ind_zmat,x,y,z) |
| 1176 |
idx_zmat(iat)=izm |
| 1177 |
DejaFait(iat)=.TRUE. |
| 1178 |
IdxCaFaire=2 |
| 1179 |
CaFaire(1)=iat |
| 1180 |
CaFaire(2)=0 |
| 1181 |
FCaf(Iat)=.TRUE. |
| 1182 |
|
| 1183 |
if (debug) WRITE(*,*) izm,iat,n2,n3,n4 |
| 1184 |
|
| 1185 |
IaFaire=1 |
| 1186 |
DO WHILE (CaFaire(IaFaire).NE.0) |
| 1187 |
n1=CaFaire(IaFaire) |
| 1188 |
n2=ind_zmat(idx_zmat(N1),2) |
| 1189 |
if (debug) WRITE(*,*) 'DBG Cafaire, Iafaire,n1,n2',Iafaire,n1,n2 |
| 1190 |
if (idx_zmat(N1).EQ.2) THEN |
| 1191 |
! We have a (small) problem: we have to add atoms linked to the 2nd |
| 1192 |
! atom of the zmat. This is a pb because we do not know |
| 1193 |
! which atom to use to define the dihedral angle |
| 1194 |
! we take the third atom of the zmat |
| 1195 |
n3=ind_zmat(3,1) |
| 1196 |
ELSE |
| 1197 |
n3=ind_zmat(idx_zmat(n1),3) |
| 1198 |
END IF |
| 1199 |
if (debug) WRITe(*,*) 'DBG :n3,liaisonBis',n3,LiaisonsBis(n1,0) |
| 1200 |
DO I3=1,LiaisonsBis(n1,0) |
| 1201 |
! PFL 29.Aug.2008 -> |
| 1202 |
! We dissociate the test on 'DejaFait' that indicates that this atom |
| 1203 |
! has already been put in the Zmat |
| 1204 |
! from the test on FCaf that indicates that this atom has been put in the |
| 1205 |
! 'CAFaire' list that deals with identifying its connectivity. |
| 1206 |
! Those two test might differ for a frozen atom linked to non frozen atoms. |
| 1207 |
IAt=LiaisonsBis(n1,I3) |
| 1208 |
if (.NOT.DejaFait(Iat)) THEN |
| 1209 |
izm=izm+1 |
| 1210 |
! ind_zmat(izm,1)=iat |
| 1211 |
! ind_zmat(izm,2)=n1 |
| 1212 |
! ind_zmat(izm,3)=n2 |
| 1213 |
! ind_zmat(izm,4)=n3 |
| 1214 |
Call add2indzmat(na,izm,iat,n1,n2,n3,ind_zmat,x,y,z) |
| 1215 |
idx_zmat(iat)=izm |
| 1216 |
if (I3.EQ.1) n3=ind_zmat(izm,1) |
| 1217 |
DejaFait(Iat)=.TRUE. |
| 1218 |
END IF |
| 1219 |
If (.NOT.FCaf(Iat)) THEN |
| 1220 |
CaFaire(IdxCaFaire)=iat |
| 1221 |
IdxCaFaire=IdxCaFaire+1 |
| 1222 |
CaFaire(IdxCaFaire)=0 |
| 1223 |
FCaf(Iat)=.TRUE. |
| 1224 |
END IF |
| 1225 |
! <- PFL 29.Aug.2008 |
| 1226 |
END DO |
| 1227 |
IaFaire=IaFaire+1 |
| 1228 |
END Do ! DO WHILE CaFaire |
| 1229 |
END IF |
| 1230 |
END IF |
| 1231 |
if (debug) THEN |
| 1232 |
WRITE(*,*) 'ind_zmat 3' |
| 1233 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(1,1) |
| 1234 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(2,1), ind_zmat(2,2) |
| 1235 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(3,1), ind_zmat(3,2), ind_zmat(3,3) |
| 1236 |
DO Ip=4,izm |
| 1237 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(Ip,1), ind_zmat(Ip,2), & |
| 1238 |
ind_zmat(Ip,3), ind_zmat(Ip,4) |
| 1239 |
END DO |
| 1240 |
END IF |
| 1241 |
|
| 1242 |
END DO |
| 1243 |
|
| 1244 |
FrozFrag(IFrag,1)=-1 |
| 1245 |
FrozFrag(IFrag,2)=-1 |
| 1246 |
FrozFrag(IFrag,3)=-1 |
| 1247 |
|
| 1248 |
! we start again with the rest of the molecule... |
| 1249 |
! v 1.01 We add the fragment in the order corresponding to FrozFrag |
| 1250 |
KMax=0 |
| 1251 |
DO I=1,NbFrag |
| 1252 |
IF (FrozFrag(I,1).NE.0) KMax=KMax+1 |
| 1253 |
END DO |
| 1254 |
|
| 1255 |
IF (DEBUG) WRITE(*,*) "Adding the",Kmax,"fragments with frozen atoms" |
| 1256 |
DO K=1, KMax-1 |
| 1257 |
IFrag=0 |
| 1258 |
I0=0 |
| 1259 |
I1=0 |
| 1260 |
DO I=1,NbFrag |
| 1261 |
SELECT CASE(FrozFrag(I,3)-I0) |
| 1262 |
CASE (1:) |
| 1263 |
IFrag=I |
| 1264 |
I0=FrozFrag(I,3) |
| 1265 |
I1=FrozFrag(I,2) |
| 1266 |
CASE (0) |
| 1267 |
if (FrozFrag(I,2).GT.I1) THEN |
| 1268 |
IFrag=I |
| 1269 |
I0=FrozFrag(I,3) |
| 1270 |
I1=FrozFrag(I,2) |
| 1271 |
END IF |
| 1272 |
END SELECT |
| 1273 |
END DO |
| 1274 |
|
| 1275 |
FrozFrag(IFrag,1)=-1 |
| 1276 |
FrozFrag(IFrag,2)=-1 |
| 1277 |
FrozFrag(IFrag,3)=-1 |
| 1278 |
|
| 1279 |
if (debug) WRITE(*,*) "Adding Fragment ",IFrag,K |
| 1280 |
|
| 1281 |
DO I=1,NbAtFrag(IFrag) |
| 1282 |
Iat=FragAt(IFrag,I) |
| 1283 |
IF (FrozAt(Iat).AND.(.NOT.DejaFait(Iat))) THEN |
| 1284 |
! in order to have the zmat as connected as possible, |
| 1285 |
! we look if this atom belongs to a frozblock |
| 1286 |
IF (FrozBlock(Iat,0).EQ.1) THEN |
| 1287 |
! it is a lonely atom :-) |
| 1288 |
if (debug) write(*,*) "DBG 4: Lonely atom",Iat |
| 1289 |
d=1e9 |
| 1290 |
DO J=1,izm |
| 1291 |
Call vecteur(iat,ind_zmat(j,1),x,y,z,vx1,vy1,vz1,norm1) |
| 1292 |
if (norm1.le.d) THEN |
| 1293 |
Jat=j |
| 1294 |
d=norm1 |
| 1295 |
END IF |
| 1296 |
END DO |
| 1297 |
n2=ind_zmat(jat,1) |
| 1298 |
SELECT CASE(jat) |
| 1299 |
CASE (1) |
| 1300 |
n3=ind_zmat(2,1) |
| 1301 |
n4=ind_zmat(3,1) |
| 1302 |
CASE (2) |
| 1303 |
n3=ind_zmat(1,1) |
| 1304 |
n4=ind_zmat(3,1) |
| 1305 |
CASE DEFAULT |
| 1306 |
n3=ind_zmat(jAt,2) |
| 1307 |
n4=ind_zmat(jat,3) |
| 1308 |
END SELECT |
| 1309 |
izm=izm+1 |
| 1310 |
! ind_zmat(izm,1)=iat |
| 1311 |
! ind_zmat(izm,2)=n2 |
| 1312 |
! ind_zmat(izm,3)=n3 |
| 1313 |
! ind_zmat(izm,4)=n4 |
| 1314 |
Call add2indzmat(na,izm,iat,n2,n3,n4,ind_zmat,x,y,z) |
| 1315 |
idx_zmat(iat)=izm |
| 1316 |
DejaFait(iat)=.TRUE. |
| 1317 |
ELSE |
| 1318 |
! we have a group of atoms |
| 1319 |
! We search for the atom of the group with the most links |
| 1320 |
if (debug) write(*,*) "DBG 4b: ",Iat," belong to frozblock",FrozBlock(Iat,0) |
| 1321 |
ITmp=-1 |
| 1322 |
DO J=1,FrozBlock(Iat,0) |
| 1323 |
Jat=FrozBlock(Iat,J) |
| 1324 |
IF ((.NOT.DejaFait(Jat)).AND. & |
| 1325 |
(LiaisonsBis(Jat,0).GT.ITMP)) THEN |
| 1326 |
JL=Jat |
| 1327 |
ITmp=LiaisonsBis(Jat,0) |
| 1328 |
END IF |
| 1329 |
END DO |
| 1330 |
Iat=JL |
| 1331 |
d=1e9 |
| 1332 |
DO J=1,izm |
| 1333 |
Call vecteur(iat,ind_zmat(j,1),x,y,z,vx1,vy1,vz1,norm1) |
| 1334 |
if (norm1.le.d) THEN |
| 1335 |
Jat=j |
| 1336 |
d=norm1 |
| 1337 |
END IF |
| 1338 |
END DO |
| 1339 |
n2=ind_zmat(jat,1) |
| 1340 |
SELECT CASE(jat) |
| 1341 |
CASE (1) |
| 1342 |
n3=ind_zmat(2,1) |
| 1343 |
n4=ind_zmat(3,1) |
| 1344 |
CASE (2) |
| 1345 |
n3=ind_zmat(1,1) |
| 1346 |
n4=ind_zmat(3,1) |
| 1347 |
CASE DEFAULT |
| 1348 |
n3=ind_zmat(jAt,2) |
| 1349 |
n4=ind_zmat(jat,3) |
| 1350 |
END SELECT |
| 1351 |
izm=izm+1 |
| 1352 |
! ind_zmat(izm,1)=iat |
| 1353 |
! ind_zmat(izm,2)=n2 |
| 1354 |
! ind_zmat(izm,3)=n3 |
| 1355 |
! ind_zmat(izm,4)=n4 |
| 1356 |
Call add2indzmat(na,izm,Iat,n2,n3,n4,ind_zmat,x,y,z) |
| 1357 |
idx_zmat(iat)=izm |
| 1358 |
DejaFait(iat)=.TRUE. |
| 1359 |
IdxCaFaire=2 |
| 1360 |
CaFaire(1)=iat |
| 1361 |
CaFaire(2)=0 |
| 1362 |
FCaf(Iat)=.TRUE. |
| 1363 |
IaFaire=1 |
| 1364 |
DO WHILE (CaFaire(IaFaire).NE.0) |
| 1365 |
n1=CaFaire(IaFaire) |
| 1366 |
n2=ind_zmat(idx_zmat(N1),2) |
| 1367 |
if (idx_zmat(N1).EQ.2) THEN |
| 1368 |
! We have a (small) problem: we have to add atoms linked to the 2nd |
| 1369 |
! atom of the zmat. This is a pb because we do not know |
| 1370 |
! which atom to use to define the dihedral angle |
| 1371 |
! we take the third atom of the zmat |
| 1372 |
n3=ind_zmat(3,1) |
| 1373 |
ELSE |
| 1374 |
n3=ind_zmat(idx_zmat(n1),3) |
| 1375 |
END IF |
| 1376 |
DO I3=1,LiaisonsBis(n1,0) |
| 1377 |
IAt=LiaisonsBis(n1,I3) |
| 1378 |
! PFL 29.Aug.2008 -> |
| 1379 |
! We dissociate the test on 'DejaFait' that indicates that this atom |
| 1380 |
! has already been put in the Zmat |
| 1381 |
! from the test on FCaf that indicates that this atom has been put in the |
| 1382 |
! 'CAFaire' list that deals with identifying its connectivity. |
| 1383 |
! Those two test might differ for a frozen atom linked to non frozen atoms. |
| 1384 |
IF (.NOT.DejaFait(Iat)) THEN |
| 1385 |
izm=izm+1 |
| 1386 |
Call add2indzmat(na,izm,Iat,n1,n2,n3,ind_zmat,x,y,z) |
| 1387 |
idx_zmat(iat)=izm |
| 1388 |
n3=iat |
| 1389 |
DejaFait(Iat)=.TRUE. |
| 1390 |
END IF |
| 1391 |
IF (.NOT.FCaf(Iat)) THEN |
| 1392 |
CaFaire(IdxCaFaire)=iat |
| 1393 |
IdxCaFaire=IdxCaFaire+1 |
| 1394 |
CaFaire(IdxCaFaire)=0 |
| 1395 |
FCaf(Iat)=.TRUE. |
| 1396 |
END IF |
| 1397 |
! <- PFL 29.Aug.2008 |
| 1398 |
END DO |
| 1399 |
IaFaire=IaFaire+1 |
| 1400 |
END Do ! DO WHILE CaFaire |
| 1401 |
END IF |
| 1402 |
END IF |
| 1403 |
|
| 1404 |
if (debug) THEN |
| 1405 |
WRITE(*,*) 'ind_zmat 4' |
| 1406 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(1,1) |
| 1407 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(2,1), ind_zmat(2,2) |
| 1408 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(3,1), ind_zmat(3,2), ind_zmat(3,3) |
| 1409 |
DO Ip=4,izm |
| 1410 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(Ip,1), ind_zmat(Ip,2), & |
| 1411 |
ind_zmat(Ip,3), ind_zmat(Ip,4) |
| 1412 |
END DO |
| 1413 |
END IF |
| 1414 |
|
| 1415 |
END DO ! loop on atoms of fragment IFrag |
| 1416 |
END DO ! Loop on all fragments |
| 1417 |
|
| 1418 |
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
| 1419 |
! |
| 1420 |
! General case |
| 1421 |
! |
| 1422 |
! 2 - we have all frozen atoms done... now comes the non frozen atoms |
| 1423 |
! and we should fragment the fragments ! |
| 1424 |
! |
| 1425 |
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
| 1426 |
|
| 1427 |
! First, we get rid of bonds between frozen atoms |
| 1428 |
! the trick is to do this on liaisons while keeping LiaisonsBis ok. |
| 1429 |
|
| 1430 |
if (debug) THEN |
| 1431 |
WRITE(*,*) 'Frozen',NFroz |
| 1432 |
WRITE(*,'(20(1X,I3))') (Frozen(I),I=1,NFroz) |
| 1433 |
END IF |
| 1434 |
|
| 1435 |
DO I=1,na |
| 1436 |
DO J=0,NMAxL |
| 1437 |
LiaisonsIni(I,J)=LiaisonsBis(I,J) |
| 1438 |
END DO |
| 1439 |
! PFL 29.Aug.2008 -> |
| 1440 |
! We re-initialize FCaf in order to add frozen atoms that are connected |
| 1441 |
! to non frozen atoms |
| 1442 |
FCaf(I)=.FALSE. |
| 1443 |
! <- 29.Aug.2008 |
| 1444 |
END DO |
| 1445 |
|
| 1446 |
DO I=1,Na |
| 1447 |
IF (FrozAt(I)) THEN |
| 1448 |
Iat=I |
| 1449 |
if (debug) WRITE(*,'(20(1X,I3))') I,Iat, & |
| 1450 |
(LiaisonsIni(Iat,Itmp),ITmp=0,LiaisonsIni(Iat,0)) |
| 1451 |
DO J=1,LiaisonsIni(Iat,0) |
| 1452 |
Jat=LiaisonsIni(Iat,J) |
| 1453 |
Call Annul(Liaisons,Iat,Jat) |
| 1454 |
Call Annul(Liaisons,Jat,Iat) |
| 1455 |
Call Annul(LiaisonsIni,Jat,Iat) |
| 1456 |
Liaisons(Iat,0)=Liaisons(Iat,0)-1 |
| 1457 |
Liaisons(Jat,0)=Liaisons(Jat,0)-1 |
| 1458 |
LiaisonsIni(Jat,0)=LiaisonsIni(Jat,0)-1 |
| 1459 |
END DO |
| 1460 |
END IF |
| 1461 |
END DO |
| 1462 |
|
| 1463 |
if (debug) THEN |
| 1464 |
WRITE(*,*) "Connections calculees" |
| 1465 |
DO IL=1,na |
| 1466 |
WRITE(IOOUT,1003) Il,(LIAISONS(IL,JL),JL=0,NMaxL) |
| 1467 |
END DO |
| 1468 |
END IF |
| 1469 |
|
| 1470 |
|
| 1471 |
|
| 1472 |
! We re-decompose the system into fragments, but we omit on purpuse |
| 1473 |
! fragments consisting only of frozen atoms |
| 1474 |
! Now, frozblock will contain the frozen atom indices in a given fragment |
| 1475 |
|
| 1476 |
DO I=1,na |
| 1477 |
Fragment(I)=0 |
| 1478 |
NbAtFrag(I)=0 |
| 1479 |
FrozBlock(I,0)=0 |
| 1480 |
END DO |
| 1481 |
IdxFrag=0 |
| 1482 |
NbFrag=0 |
| 1483 |
|
| 1484 |
DO I=1,na |
| 1485 |
IdxCAfaire=1 |
| 1486 |
CaFaire(IdxCaFaire)=0 |
| 1487 |
|
| 1488 |
if (debug) WRITE(*,*) 'Treating atom I, fragment(I)',I,Fragment(I) |
| 1489 |
IF (.NOT.FrozAt(I).OR.(Liaisons(I,0).NE.0)) THEN |
| 1490 |
IF (Fragment(I).EQ.0) THEN |
| 1491 |
IdxFrag=IdxFrag+1 |
| 1492 |
NbFrag=NbFrag+1 |
| 1493 |
IFrag=IdxFrag |
| 1494 |
Fragment(I)=IFrag |
| 1495 |
NbAtFrag(IFrag)=NbAtFrag(IFrag)+1 |
| 1496 |
FragAt(IFrag,NbAtFrag(IFrag))=I |
| 1497 |
ELSE ! fragment(I).EQ.0 |
| 1498 |
IFrag=Fragment(I) |
| 1499 |
END IF ! fragment(I).EQ.0 |
| 1500 |
DO J=1,Liaisons(I,0) |
| 1501 |
Iat=Liaisons(I,J) |
| 1502 |
IF ((Fragment(Iat).NE.0).AND.(Fragment(Iat).NE.IFrag)) THEN |
| 1503 |
WRITE(*,*) 'Error : Atoms ',I,' and ',Iat |
| 1504 |
WRITE(*,*) 'are linked, but belongs to fragments ',IFrag,' and ',Fragment(Iat) |
| 1505 |
STOP |
| 1506 |
END IF |
| 1507 |
IF (Fragment(Iat).EQ.0) THEN |
| 1508 |
IF (.NOT.FCaf(IAt)) THEN |
| 1509 |
CaFaire(IdxCaFaire)=Iat |
| 1510 |
IdxCAfaire=IdxCAFaire+1 |
| 1511 |
FCaf(IAt)=.TRUE. |
| 1512 |
END IF |
| 1513 |
Fragment(Iat)=IFrag |
| 1514 |
NbAtFrag(IFrag)=NbAtFrag(IFrag)+1 |
| 1515 |
FragAt(IFrag,NbAtFrag(IFrag))=Iat |
| 1516 |
END IF |
| 1517 |
END DO |
| 1518 |
CaFaire(IdxCaFaire)=0 |
| 1519 |
|
| 1520 |
If (debug) WRITE(*,'(1X,A,1000I4)') 'Cafaire:',CaFaire(1:IdxCaFaire) |
| 1521 |
If (debug) WRITE(*,*) 'IFrag=',IFrag |
| 1522 |
|
| 1523 |
IAfaire=1 |
| 1524 |
DO WHILE (CaFaire(IAfaire).NE.0) |
| 1525 |
Iat=CaFaire(IaFaire) |
| 1526 |
IF (.NOT.FrozAt(Iat).OR.(Liaisons(Iat,0).NE.0)) THEN |
| 1527 |
if (debug) WRITE(*,*) 'Cafaire treating ',Iat |
| 1528 |
IF (Fragment(Iat).EQ.0) THEN |
| 1529 |
WRITE(*,*) 'Error: Atom ',Iat,' does not belong to any fragment !' |
| 1530 |
STOP |
| 1531 |
END IF |
| 1532 |
|
| 1533 |
DO J=1,Liaisons(Iat,0) |
| 1534 |
Jat=Liaisons(Iat,J) |
| 1535 |
IF ((Fragment(Jat).NE.0).AND.(Fragment(Jat).NE.IFrag)) THEN |
| 1536 |
WRITE(*,*) 'Error: Atoms ',Iat,' and ',Liaisons(Iat,J) |
| 1537 |
WRITE(*,*) 'are linked, but belongs to fragments ',IFrag,' and ',Fragment(Liaisons(Iat,J)) |
| 1538 |
STOP |
| 1539 |
END IF |
| 1540 |
IF (Fragment(Jat).EQ.0) THEN |
| 1541 |
IF (.NOT.FCaf(Liaisons(Iat,J))) THEN |
| 1542 |
CaFaire(IdxCaFaire)=Liaisons(Iat,J) |
| 1543 |
IdxCAfaire=IdxCAFaire+1 |
| 1544 |
FCaf(Liaisons(Iat,J))=.TRUE. |
| 1545 |
END IF |
| 1546 |
Fragment(Jat)=IFrag |
| 1547 |
NbAtFrag(IFrag)=NbAtFrag(IFrag)+1 |
| 1548 |
FragAt(IFrag,NbAtFrag(IFrag))=Jat |
| 1549 |
END IF |
| 1550 |
END DO |
| 1551 |
CaFaire(IdxCaFaire)=0 |
| 1552 |
If (debug) WRITE(*,*) 'IAfaire, IdxCaFaire,Cafaire :',IAfaire,IdxCafaire,' == ',CaFaire(IaFaire+1:IdxCaFaire) |
| 1553 |
IAFaire=IAFaire+1 |
| 1554 |
END IF |
| 1555 |
END DO |
| 1556 |
END IF |
| 1557 |
END DO |
| 1558 |
|
| 1559 |
! We compute FrozBlock now |
| 1560 |
DO IFrag=1,NbFrag |
| 1561 |
DO I=1,NbAtFrag(IFrag) |
| 1562 |
Iat=FragAt(IFrag,I) |
| 1563 |
IF (FrozAt(Iat)) THEN |
| 1564 |
FrozBlock(IFrag,0)=FrozBlock(IFrag,0)+1 |
| 1565 |
FrozBlock(IFrag,FrozBlock(IFrag,0))=IAt |
| 1566 |
END IF |
| 1567 |
END DO |
| 1568 |
END DO |
| 1569 |
|
| 1570 |
|
| 1571 |
if (debug) THEN |
| 1572 |
WRITE(*,*) 'I found ',NbFrag, 'fragments with respectively ' |
| 1573 |
WRITE(*,*) (NbAtFrag(I),I=1,NbFrag), 'atoms' |
| 1574 |
WRITE(*,*) "Fragments atoms are now listed as F in the following" |
| 1575 |
DO I=1,NbFrag |
| 1576 |
WRITE(*,*) Na |
| 1577 |
WRITE(*,*) 'Fragment ', i |
| 1578 |
DO J=1,Na |
| 1579 |
AtName=Nom(Atome(J)) |
| 1580 |
IF (Fragment(J).EQ.I) AtName='F' |
| 1581 |
WRITE(*,'(1X,A5,3(1X,F10.6))') AtName,X(J),Y(J),Z(J) |
| 1582 |
END DO |
| 1583 |
! WRITE(*,*) "FragAt:",(FragAt(I,j),j=1,NbAtFrag(I)) |
| 1584 |
END DO |
| 1585 |
|
| 1586 |
DO I=1,NbFrag |
| 1587 |
WRITE(*,*) 'Fragment ', i |
| 1588 |
WRITE(*,'(A,20(1X,I3))') "FragAt:",(FragAt(I,j),j=1,NbAtFrag(I)) |
| 1589 |
WRITE(*,'(A,20(1X,I3))') "FrozBlock:",(FrozBlock(I,j),j=0,FrozBlock(I,0)) |
| 1590 |
END DO |
| 1591 |
END IF |
| 1592 |
|
| 1593 |
|
| 1594 |
NFroz=0 |
| 1595 |
DO IFrag=1,NbFrag |
| 1596 |
If (FrozBlock(IFrag,0).NE.0) NFroz=NFroz+1 |
| 1597 |
END DO |
| 1598 |
|
| 1599 |
IF (DEBUG) WRITE(*,'(1X,A,I4,A,I4,A)') "Found ",NFroz," fragmenst with frozen atoms, out of",NbFrag," fragments" |
| 1600 |
|
| 1601 |
! We will now add the fragments containing non frozen atoms. |
| 1602 |
! I am not sure that there is a best strategy to add them... |
| 1603 |
! so we add them in the order they were created :-( |
| 1604 |
! First only block with frozen atoms are added |
| 1605 |
izm0=-1 |
| 1606 |
IFrag=1 |
| 1607 |
FCaf=.FALSE. |
| 1608 |
|
| 1609 |
DO IFragFroz=1,NFroz |
| 1610 |
DO WHILE (FrozBlock(IFrag,0).EQ.0) |
| 1611 |
IFrag=IFrag+1 |
| 1612 |
END DO |
| 1613 |
! each atom has at least one frozen atom that will serve as the seed |
| 1614 |
! of this fragment. |
| 1615 |
if (debug) WRITE(*,*) 'Adding fragment :', ifrag,'with',FrozBlock(IFrag,0),' frozen atoms' |
| 1616 |
IF (FrozBlock(IFrag,0).EQ.1) THEN |
| 1617 |
! There is only one frozen atom, easy case ... |
| 1618 |
Iat=FrozBlock(IFrag,1) |
| 1619 |
if (debug) WRITE(*,*) 'Only frozen atom of frag',iat |
| 1620 |
DejaFait(iat)=.TRUE. |
| 1621 |
IdxCaFaire=2 |
| 1622 |
CaFaire(1)=iat |
| 1623 |
CaFaire(2)=0 |
| 1624 |
FCaf(Iat)=.TRUE. |
| 1625 |
IaFaire=1 |
| 1626 |
DO WHILE (CaFaire(IaFaire).NE.0) |
| 1627 |
n1=CaFaire(IaFaire) |
| 1628 |
SELECT CASE(idx_zmat(n1)) |
| 1629 |
CASE (1) |
| 1630 |
n2=ind_zmat(2,1) |
| 1631 |
n3=ind_zmat(3,1) |
| 1632 |
CASE (2) |
| 1633 |
n2=ind_zmat(1,1) |
| 1634 |
n3=ind_zmat(3,1) |
| 1635 |
CASE (3:) |
| 1636 |
n2=ind_zmat(idx_zmat(n1),2) |
| 1637 |
n3=ind_zmat(idx_zmat(n1),3) |
| 1638 |
END SELECT |
| 1639 |
|
| 1640 |
DO I3=1,Liaisons(n1,0) |
| 1641 |
IAt=Liaisons(n1,I3) |
| 1642 |
! PFL 2007.Apr.16 -> |
| 1643 |
! We add ALL atoms linked to n1 to CaFaire |
| 1644 |
! But we delete their link to n1 |
| 1645 |
IF (.NOT.FCaf(Iat)) THEN |
| 1646 |
CaFaire(IdxCaFaire)=Iat |
| 1647 |
IdxCaFaire=IdxCaFaire+1 |
| 1648 |
CaFaire(IdxCaFaire)=0 |
| 1649 |
END IF |
| 1650 |
Call Annul(Liaisons,Iat,n1) |
| 1651 |
Liaisons(iat,0)=Liaisons(Iat,0)-1 |
| 1652 |
! <- PFL 2007.Apr.16 |
| 1653 |
IF (.NOT.DejaFait(Iat)) THEN |
| 1654 |
! we add it to the Zmat |
| 1655 |
izm=izm+1 |
| 1656 |
! ind_zmat(izm,1)=iat |
| 1657 |
! ind_zmat(izm,2)=n1 |
| 1658 |
! ind_zmat(izm,3)=n2 |
| 1659 |
! ind_zmat(izm,4)=n3 |
| 1660 |
Call add2indzmat(na,izm,Iat,n1,n2,n3,ind_zmat,x,y,z) |
| 1661 |
idx_zmat(iat)=izm |
| 1662 |
! Call Annul(Liaisons,n1,iat) |
| 1663 |
n3=iat |
| 1664 |
DejaFait(Iat)=.TRUE. |
| 1665 |
END IF |
| 1666 |
END DO |
| 1667 |
IaFaire=IaFaire+1 |
| 1668 |
|
| 1669 |
if (debug) THEN |
| 1670 |
WRITE(*,*) 'ind_zmat 5' |
| 1671 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(1,1) |
| 1672 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(2,1), ind_zmat(2,2) |
| 1673 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(3,1), ind_zmat(3,2), ind_zmat(3,3) |
| 1674 |
DO Ip=4,izm |
| 1675 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(Ip,1), & |
| 1676 |
ind_zmat(Ip,2),ind_zmat(Ip,3), ind_zmat(Ip,4) |
| 1677 |
END DO |
| 1678 |
END IF |
| 1679 |
|
| 1680 |
END Do ! DO WHILE CaFaire |
| 1681 |
|
| 1682 |
|
| 1683 |
ELSE ! FrozBlock(I,0)==1 |
| 1684 |
if (debug) WRITE(*,*) 'IFrag=',IFrag,'Frozblock(I,0)/=1',Frozblock(IFrag,0) |
| 1685 |
! We have many frozen atoms for one fragment. We will have to choose |
| 1686 |
! the first one, and then to decide when to swich... |
| 1687 |
Iat=0 |
| 1688 |
I0=-1 |
| 1689 |
DO I=1,FrozBlock(IFrag,0) |
| 1690 |
JAt=FrozBlock(IFrag,I) |
| 1691 |
if (debug) WRITE(*,*) Jat, & |
| 1692 |
(LiaisonsBis(Jat,Itmp),Itmp=0,LiaisonsBis(Jat,0)) |
| 1693 |
IF (LiaisonsBis(Jat,0).GT.I0) THEN |
| 1694 |
I0=LiaisonsBis(Jat,0) |
| 1695 |
Iat=Jat |
| 1696 |
END IF |
| 1697 |
END DO |
| 1698 |
! Iat is the starting frozen atom |
| 1699 |
IF (debug) WRITE(*,*) 'Choosing atom ',iat,'as a starting atom for frag',ifrag |
| 1700 |
DejaFait(iat)=.TRUE. |
| 1701 |
IdxCaFaire=2 |
| 1702 |
CaFaire(1)=iat |
| 1703 |
CaFaire(2)=0 |
| 1704 |
IaFaire=1 |
| 1705 |
FCaf(Iat)=.TRUE. |
| 1706 |
DO WHILE (CaFaire(IaFaire).NE.0) |
| 1707 |
n1=CaFaire(IaFaire) |
| 1708 |
if (debug) WRITE(*,*) 'Iafaire,n1,dejafait,idx_zmat', & |
| 1709 |
IaFaire,n1, DejaFait(n1),idx_zmat(n1) |
| 1710 |
if (debug) WRITE(*,*) 'Cafaire', & |
| 1711 |
(CaFaire(J),J=Iafaire,IdxCAfaire) |
| 1712 |
SELECT CASE(idx_zmat(n1)) |
| 1713 |
CASE (1) |
| 1714 |
n2=ind_zmat(2,1) |
| 1715 |
n3=ind_zmat(3,1) |
| 1716 |
CASE (2) |
| 1717 |
n2=ind_zmat(1,1) |
| 1718 |
n3=ind_zmat(3,1) |
| 1719 |
CASE (3:) |
| 1720 |
n2=ind_zmat(idx_zmat(n1),2) |
| 1721 |
n3=ind_zmat(idx_zmat(n1),3) |
| 1722 |
END SELECT |
| 1723 |
|
| 1724 |
if (debug) WRITE(*,*) "DBG n1,Liaisons(n1,0)",n1,Liaisons(n1,0) |
| 1725 |
DO I3=1,Liaisons(n1,0) |
| 1726 |
IAt=Liaisons(n1,I3) |
| 1727 |
if (debug) WRITE(*,*) "DBG I3,Iat",I3,Iat |
| 1728 |
! PFL 2007.Apr.16 -> |
| 1729 |
! We add ALL atoms linked to n1 to CaFaire |
| 1730 |
! But we delete their link to n1 |
| 1731 |
!! PFL 2007.Aug.28 -> |
| 1732 |
! re-add the test on FCaf in order not to put the same atom more than once in |
| 1733 |
! CaFaire array. |
| 1734 |
IF (.NOT.FCaf(Iat)) THEN |
| 1735 |
CaFaire(IdxCaFaire)=Iat |
| 1736 |
IdxCaFaire=IdxCaFaire+1 |
| 1737 |
CaFaire(IdxCaFaire)=0 |
| 1738 |
FCaf(Iat)=.TRUE. |
| 1739 |
if (debug) WRITE(*,*) 'Adding ',iat,' to CaFaire. I3=',I3,'IdxCafaire=',IdxCafaire |
| 1740 |
if (debug) WRITE(*,*) 'Cafaire',(CaFaire(J),J=Iafaire,IdxCAfaire) |
| 1741 |
|
| 1742 |
END IF |
| 1743 |
!! <-- PFL 2007.Aug.28 |
| 1744 |
|
| 1745 |
Call Annul(Liaisons,Iat,n1) |
| 1746 |
Liaisons(iat,0)=Liaisons(Iat,0)-1 |
| 1747 |
! <- PFL 2007.Apr.16 |
| 1748 |
IF (.NOT.DejaFait(Iat)) THEN |
| 1749 |
izm=izm+1 |
| 1750 |
! ind_zmat(izm,1)=iat |
| 1751 |
! ind_zmat(izm,2)=n1 |
| 1752 |
! ind_zmat(izm,3)=n2 |
| 1753 |
! ind_zmat(izm,4)=n3 |
| 1754 |
Call add2indzmat(na,izm,Iat,n1,n2,n3,ind_zmat,x,y,z) |
| 1755 |
idx_zmat(iat)=izm |
| 1756 |
! Call Annul(Liaisons,n1,iat) |
| 1757 |
|
| 1758 |
n3=iat |
| 1759 |
DejaFait(Iat)=.TRUE. |
| 1760 |
END IF |
| 1761 |
END DO |
| 1762 |
|
| 1763 |
if (debug) WRITE(*,*) 'I3,n1,Liaisons(n1,:)', & |
| 1764 |
I3,n1,(Liaisons(n1,J),J=0,Liaisons(n1,0)) |
| 1765 |
|
| 1766 |
|
| 1767 |
if (debug.AND.(izm.GT.izm0)) THEN |
| 1768 |
WRITE(*,*) 'ind_zmat 6, izm=',izm |
| 1769 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(1,1) |
| 1770 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(2,1), ind_zmat(2,2) |
| 1771 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(3,1), ind_zmat(3,2), & |
| 1772 |
ind_zmat(3,3) |
| 1773 |
DO Ip=4,izm |
| 1774 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(Ip,1), & |
| 1775 |
ind_zmat(Ip,2),ind_zmat(Ip,3), ind_zmat(Ip,4) |
| 1776 |
END DO |
| 1777 |
izm0=izm |
| 1778 |
END IF |
| 1779 |
|
| 1780 |
IaFaire=IaFaire+1 |
| 1781 |
|
| 1782 |
|
| 1783 |
END Do ! DO WHILE CaFaire |
| 1784 |
|
| 1785 |
END IF ! FrozBlock(I,0)==1 |
| 1786 |
|
| 1787 |
IFrag=IFrag+1 |
| 1788 |
END DO ! Loop on all fragments |
| 1789 |
|
| 1790 |
|
| 1791 |
DO IFrag=1,NbFrag |
| 1792 |
IF (FrozBlock(IFrag,0).EQ.0) THEN |
| 1793 |
if (debug) WRITE(*,*) 'Adding fragment :', ifrag,'with no frozen atoms' |
| 1794 |
! We have no frozen atoms for this fragment. We will have to choose |
| 1795 |
! the first atom to put. |
| 1796 |
! For now, we do not care of the 'central' atom (ie the one with |
| 1797 |
! no CP atoms...) |
| 1798 |
! We just take the atom that is the closest to the already placed |
| 1799 |
! atoms ! |
| 1800 |
|
| 1801 |
|
| 1802 |
I0=0 |
| 1803 |
I1=0 |
| 1804 |
d=1e9 |
| 1805 |
DO J=1,izm |
| 1806 |
Jat=ind_zmat(J,1) |
| 1807 |
DO I=1,NbAtfrag(IFrag) |
| 1808 |
IAt=FragAt(IFrag,I) |
| 1809 |
IF (.NOT.DejaFait(Iat)) THEN |
| 1810 |
Call vecteur(Iat,Jat,x,y,z,vx1,vy1,vz1,norm1) |
| 1811 |
IF (norm1.LT.d) THEN |
| 1812 |
I1=Jat |
| 1813 |
I0=Iat |
| 1814 |
d=Norm1 |
| 1815 |
END IF |
| 1816 |
END IF |
| 1817 |
END DO |
| 1818 |
END DO |
| 1819 |
|
| 1820 |
Iat=I0 |
| 1821 |
n1=I1 |
| 1822 |
|
| 1823 |
IF (debug) WRITE(*,*) Iat,' starting atom for frag',ifrag |
| 1824 |
|
| 1825 |
|
| 1826 |
SELECT CASE(idx_zmat(n1)) |
| 1827 |
CASE (1) |
| 1828 |
n2=ind_zmat(2,1) |
| 1829 |
n3=ind_zmat(3,1) |
| 1830 |
CASE (2) |
| 1831 |
n2=ind_zmat(1,1) |
| 1832 |
n3=ind_zmat(3,1) |
| 1833 |
CASE (3:) |
| 1834 |
n2=ind_zmat(idx_zmat(n1),2) |
| 1835 |
n3=ind_zmat(idx_zmat(n1),3) |
| 1836 |
END SELECT |
| 1837 |
|
| 1838 |
izm=izm+1 |
| 1839 |
! ind_zmat(izm,1)=iat |
| 1840 |
! ind_zmat(izm,2)=n1 |
| 1841 |
! ind_zmat(izm,3)=n2 |
| 1842 |
! ind_zmat(izm,4)=n3 |
| 1843 |
Call add2indzmat(na,izm,Iat,n1,n2,n3,ind_zmat,x,y,z) |
| 1844 |
idx_zmat(iat)=izm |
| 1845 |
|
| 1846 |
|
| 1847 |
DejaFait(iat)=.TRUE. |
| 1848 |
IdxCaFaire=2 |
| 1849 |
CaFaire(1)=iat |
| 1850 |
CaFaire(2)=0 |
| 1851 |
IaFaire=1 |
| 1852 |
FCaf(Iat)=.TRUE. |
| 1853 |
DO WHILE (CaFaire(IaFaire).NE.0) |
| 1854 |
n1=CaFaire(IaFaire) |
| 1855 |
if (debug) WRITE(*,*) 'Iafaire,n1',IaFaire,n1, & |
| 1856 |
DejaFait(n1),idx_zmat(n1) |
| 1857 |
if (debug) WRITE(*,*) 'Cafaire', & |
| 1858 |
(CaFaire(J),J=Iafaire,IdxCAfaire) |
| 1859 |
SELECT CASE(idx_zmat(n1)) |
| 1860 |
CASE (1) |
| 1861 |
n2=ind_zmat(2,1) |
| 1862 |
n3=ind_zmat(3,1) |
| 1863 |
CASE (2) |
| 1864 |
n2=ind_zmat(1,1) |
| 1865 |
n3=ind_zmat(3,1) |
| 1866 |
CASE (3:) |
| 1867 |
n2=ind_zmat(idx_zmat(n1),2) |
| 1868 |
n3=ind_zmat(idx_zmat(n1),3) |
| 1869 |
END SELECT |
| 1870 |
|
| 1871 |
|
| 1872 |
DO I3=1,Liaisons(n1,0) |
| 1873 |
IAt=Liaisons(n1,I3) |
| 1874 |
! PFL 2007.Apr.16 -> |
| 1875 |
! We add ALL atoms linked to n1 to CaFaire |
| 1876 |
! But we delete their link to n1 |
| 1877 |
!! PFL 2007.Aug.28 -> |
| 1878 |
! re-add the test on FCaf in order not to put the same atom more than once in |
| 1879 |
! CaFaire array. |
| 1880 |
IF (.NOT.FCaf(Iat)) THEN |
| 1881 |
CaFaire(IdxCaFaire)=Iat |
| 1882 |
IdxCaFaire=IdxCaFaire+1 |
| 1883 |
CaFaire(IdxCaFaire)=0 |
| 1884 |
FCaf(Iat)=.TRUE. |
| 1885 |
END IF |
| 1886 |
!! <-- PFL 2007.Aug.28 |
| 1887 |
|
| 1888 |
Call Annul(Liaisons,Iat,n1) |
| 1889 |
Liaisons(iat,0)=Liaisons(Iat,0)-1 |
| 1890 |
if (debug) WRITE(*,*) 'Adding ',iat,' to CaFaire. I3=',I3 |
| 1891 |
if (debug) WRITE(*,*) 'Cafaire',(CaFaire(J),J=Iafaire,IdxCAfaire) |
| 1892 |
|
| 1893 |
! <- PFL 2007.Apr.16 |
| 1894 |
IF (.NOT.DejaFait(Liaisons(n1,i3))) THEN |
| 1895 |
IAt=Liaisons(n1,I3) |
| 1896 |
izm=izm+1 |
| 1897 |
! ind_zmat(izm,1)=iat |
| 1898 |
! ind_zmat(izm,2)=n1 |
| 1899 |
! ind_zmat(izm,3)=n2 |
| 1900 |
! ind_zmat(izm,4)=n3 |
| 1901 |
Call add2indzmat(na,izm,Iat,n1,n2,n3,ind_zmat,x,y,z) |
| 1902 |
idx_zmat(iat)=izm |
| 1903 |
|
| 1904 |
n3=iat |
| 1905 |
DejaFait(Iat)=.TRUE. |
| 1906 |
END IF |
| 1907 |
|
| 1908 |
if (debug) WRITE(*,*) 'I3,n1,Liaisons(n1,:)', & |
| 1909 |
I3,n1,(Liaisons(n1,J),J=0,Liaisons(n1,0)) |
| 1910 |
END DO |
| 1911 |
IaFaire=IaFaire+1 |
| 1912 |
|
| 1913 |
if (debug) THEN |
| 1914 |
WRITE(*,*) 'ind_zmat 7', izm |
| 1915 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(1,1) |
| 1916 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(2,1), ind_zmat(2,2) |
| 1917 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(3,1), ind_zmat(3,2),ind_zmat(3,3) |
| 1918 |
DO Ip=4,izm |
| 1919 |
WRITE(*,'(1X,4(1X,I5))') ind_zmat(Ip,1), & |
| 1920 |
ind_zmat(Ip,2), & |
| 1921 |
ind_zmat(Ip,3), ind_zmat(Ip,4) |
| 1922 |
END DO |
| 1923 |
END IF |
| 1924 |
|
| 1925 |
END Do ! DO WHILE CaFaire |
| 1926 |
END IF ! FrozBlock(IFrag,0).EQ.0 |
| 1927 |
|
| 1928 |
END DO ! Loop on all fragments without frozen atoms |
| 1929 |
|
| 1930 |
if (debug) THEN |
| 1931 |
WRITE(*,*) Na+Izm |
| 1932 |
WRITE(*,*) 'Done... ', izm |
| 1933 |
DO J=1,Na |
| 1934 |
WRITE(*,'(1X,A5,3(1X,F10.6))') Nom(Atome(J)),X(J),Y(J),Z(J) |
| 1935 |
END DO |
| 1936 |
DO I=1,Izm |
| 1937 |
J=ind_zmat(I,1) |
| 1938 |
WRITE(*,'(1X,A5,3(1X,F10.6))') 'X ',X(J),Y(J),Z(J) |
| 1939 |
END DO |
| 1940 |
IF (izm.NE.Na) THEN |
| 1941 |
WRITE(*,*) "Atoms not done:" |
| 1942 |
DO I=1,Na |
| 1943 |
IF (.NOT.DejaFait(I)) WRITE(*,'(I5)',ADVANCE='NO') I |
| 1944 |
END DO |
| 1945 |
END IF |
| 1946 |
END IF |
| 1947 |
|
| 1948 |
|
| 1949 |
! We have ind_zmat. We calculate val_zmat :-) |
| 1950 |
if (debug) WRITE(*,*) "Calculating val_zmat" |
| 1951 |
|
| 1952 |
val_zmat(1,1)=0.d0 |
| 1953 |
val_zmat(1,2)=0.d0 |
| 1954 |
val_zmat(1,3)=0.d0 |
| 1955 |
val_zmat(2,2)=0.d0 |
| 1956 |
val_zmat(2,3)=0.d0 |
| 1957 |
val_zmat(3,3)=0.d0 |
| 1958 |
|
| 1959 |
n1=ind_zmat(2,1) |
| 1960 |
n2=ind_zmat(2,2) |
| 1961 |
|
| 1962 |
CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
| 1963 |
|
| 1964 |
val_zmat(2,1)=norm1 |
| 1965 |
|
| 1966 |
|
| 1967 |
n1=ind_zmat(3,1) |
| 1968 |
n2=ind_zmat(3,2) |
| 1969 |
n3=ind_zmat(3,3) |
| 1970 |
|
| 1971 |
CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
| 1972 |
|
| 1973 |
val_zmat(3,1)=norm1 |
| 1974 |
|
| 1975 |
CALL vecteur(n2,n3,x,y,z,vx2,vy2,vz2,norm2) |
| 1976 |
val=angle(vx1,vy1,vz1,norm1,vx2,vy2,vz2,norm2) |
| 1977 |
|
| 1978 |
val_zmat(3,2)=val |
| 1979 |
|
| 1980 |
DO i=4,na |
| 1981 |
|
| 1982 |
n1=ind_zmat(i,1) |
| 1983 |
n2=ind_zmat(i,2) |
| 1984 |
n3=ind_zmat(i,3) |
| 1985 |
n4=ind_zmat(i,4) |
| 1986 |
|
| 1987 |
if (debug) WRITE(*,*) "Doing i,n1,n2,n3,n4",i,n1,n2,n3,n4 |
| 1988 |
CALL vecteur(n2,n1,x,y,z,vx1,vy1,vz1,norm1) |
| 1989 |
|
| 1990 |
CALL vecteur(n2,n3,x,y,z,vx2,vy2,vz2,norm2) |
| 1991 |
val=angle(vx1,vy1,vz1,norm1,vx2,vy2,vz2,norm2) |
| 1992 |
|
| 1993 |
CALL vecteur(n3,n4,x,y,z,vx3,vy3,vz3,norm3) |
| 1994 |
CALL produit_vect(vx1,vy1,vz1,vx2,vy2,vz2, & |
| 1995 |
vx4,vy4,vz4,norm4) |
| 1996 |
CALL produit_vect(vx3,vy3,vz3,vx2,vy2,vz2, & |
| 1997 |
vx5,vy5,vz5,norm5) |
| 1998 |
|
| 1999 |
val_d=angle_d(vx4,vy4,vz4,norm4, vx5,vy5,vz5,norm5, & |
| 2000 |
vx2,vy2,vz2,norm2) |
| 2001 |
|
| 2002 |
! write(*,11) n1,n2,norm1,n3,val,n4,val_d |
| 2003 |
!11 format (2(1x,i3),1x,f8.4,2(1x,i3,1x,f8.3)) |
| 2004 |
|
| 2005 |
val_zmat(i,1)=norm1 |
| 2006 |
val_zmat(i,2)=val |
| 2007 |
val_zmat(i,3)=val_d |
| 2008 |
|
| 2009 |
END DO |
| 2010 |
|
| 2011 |
if (debug) THEN |
| 2012 |
WRITE(*,*) 'DBG Cre_Zmat_Constr: ind_zmat' |
| 2013 |
DO I=1,na |
| 2014 |
WRITE(*,'(1X,5I5)') (ind_zmat(i,j),j=1,5) |
| 2015 |
END DO |
| 2016 |
|
| 2017 |
WRITE(*,*) 'DBG Cre_Zmat_Constr: Full zmat' |
| 2018 |
DO I=1,na |
| 2019 |
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) |
| 2020 |
END DO |
| 2021 |
|
| 2022 |
END IF |
| 2023 |
|
| 2024 |
if (debug) WRITE(*,*) "Deallocate (FrozDist,Fragment, NbAtFrag,FragAt)" |
| 2025 |
DEALLOCATE(FrozDist,Fragment, NbAtFrag,FragAt) |
| 2026 |
if (debug) WRITE(*,*) "Deallocate FrozFrag, IdxFragAt, FrozBlock" |
| 2027 |
! DEALLOCATE(FrozFrag, IdxFragAt, FrozBlock) |
| 2028 |
DEALLOCATE(FrozFrag,FrozBlock) |
| 2029 |
if (debug) WRITE(*,*) "Deallocate (DistFroz,Liaisons)" |
| 2030 |
DEALLOCATE(DistFroz,Liaisons) |
| 2031 |
if (debug) WRITE(*,*) "Deallocate (LiaisonsIni)" |
| 2032 |
DEALLOCATE(LiaisonsIni) |
| 2033 |
if (debug) WRITE(*,*) "Deallocate(CaFaire,DejaFait,FrozAt)" |
| 2034 |
DEALLOCATE(CaFaire,DejaFait,FrozAt) |
| 2035 |
if (debug) WRITE(*,*) "Deallocate (LiaisonsBis" |
| 2036 |
DEALLOCATE(LiaisonsBis) |
| 2037 |
|
| 2038 |
if (debugGaussian) THEN |
| 2039 |
WRITE(*,*) 'DBG Cre_Zmat_Constr_Frag: Gaussian Zmat - START' |
| 2040 |
Call WriteMixed_Gaussian(na,atome,LocalNCart,ind_zmat,val_zmat) |
| 2041 |
WRITE(*,*) 'DBG Cre_Zmat_Constr_Frag: Gaussian Zmat - END' |
| 2042 |
END IF |
| 2043 |
|
| 2044 |
|
| 2045 |
|
| 2046 |
if (debug) WRITE(*,*) "=============================== Exiting Calc_zmat_contr_frag ========================" |
| 2047 |
|
| 2048 |
END SUBROUTINE Calc_Zmat_const_frag |
| 2049 |
|
| 2050 |
|