From: Adam Sieradzan <adasko@piasek4.chem.univ.gda.pl>
Date: Wed, 23 Sep 2015 17:31:51 +0000 (+0200)
Subject: bug fix in extconf
X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=commitdiff_plain;h=481eb42509493d4d1e082eb01a7479377c6db79c

bug fix in extconf
---

diff --git a/source/unres/src_MD-M/chainbuild.F b/source/unres/src_MD-M/chainbuild.F
index 157baa9..a0fe42c 100644
--- a/source/unres/src_MD-M/chainbuild.F
+++ b/source/unres/src_MD-M/chainbuild.F
@@ -22,120 +22,27 @@ C Set lprn=.true. for debugging
       call chainbuild_cart
       return
       end
-#ifdef DEBUG
-      if (perbox) then
-      cost=dcos(theta(3))
-      sint=dsin(theta(3))
-      print *,'before refsys'
-      call refsys(2,3,4,e1,e2,e3,fail)
-      print *,'after refsys'
-          if (fail) then
-            e2(1)=0.0d0
-            e2(2)=1.0d0
-            e2(3)=0.0d0
-          endif
-      dc(1,0)=c(1,1)
-      dc(2,0)=c(2,1)
-      dc(3,0)=c(3,1)
-      print *,'dc',dc(1,0),dc(2,0),dc(3,0)
-      dc(1,1)=c(1,2)-c(1,1)
-      dc(2,1)=c(2,2)-c(2,1)
-      dc(3,1)=c(3,2)-c(3,1)
-      dc(1,2)=c(1,3)-c(1,2)
-      dc(2,2)=c(2,3)-c(2,2)
-      dc(3,2)=c(3,3)-c(3,2)
-      t(1,1,1)=e1(1)
-      t(1,2,1)=e1(2)
-      t(1,3,1)=e1(3)
-      t(2,1,1)=e2(1)
-      t(2,2,1)=e2(2)
-      t(2,3,1)=e2(3)
-      t(3,1,1)=e3(1)
-      t(3,2,1)=e3(2)
-      t(3,3,1)=e3(3)
-      veclen=0.0d0
-      do i=1,3
-       veclen=veclen+(c(i,2)-c(i,1))**2
-      enddo
-      veclen=sqrt(veclen)
-      r(1,1,1)= 1.0D0
-      r(1,2,1)= 0.0D0
-      r(1,3,1)= 0.0D0
-      r(2,1,1)= 0.0D0
-      r(2,2,1)= 1.0D0
-      r(2,3,1)= 0.0D0
-      r(3,1,1)= 0.0D0
-      r(3,2,1)= 0.0D0
-      r(3,3,1)= 1.0D0
-      do i=1,3
-        do j=1,3
-          rt(i,j,1)=t(i,j,1)
-        enddo
-      enddo
-      do i=1,3
-        do j=1,3
-          prod(i,j,1)=0.0D0
-          prod(i,j,2)=t(i,j,1)
-        enddo
-        prod(i,i,1)=1.0D0
-      enddo
-        call locate_side_chain(2)
-      do i=4,nres
-#ifdef OSF
-      theti=theta(i)
-      if (theti.ne.theti) theti=100.0
-      phii=phi(i)
-      if (phii.ne.phii) phii=180.0
-#else
-      theti=theta(i)
-      phii=phi(i)
-#endif
-      cost=dcos(theti)
-      sint=dsin(theti)
-      cosphi=dcos(phii)
-      sinphi=dsin(phii)
-* Define the matrices of the rotation about the virtual-bond valence angles
-* theta, T(i,j,k), virtual-bond dihedral angles gamma (miscalled PHI in this
-* program), R(i,j,k), and, the cumulative matrices of rotation RT
-      t(1,1,i-2)=-cost
-      t(1,2,i-2)=-sint
-      t(1,3,i-2)= 0.0D0
-      t(2,1,i-2)=-sint
-      t(2,2,i-2)= cost
-      t(2,3,i-2)= 0.0D0
-      t(3,1,i-2)= 0.0D0
-      t(3,2,i-2)= 0.0D0
-      t(3,3,i-2)= 1.0D0
-      r(1,1,i-2)= 1.0D0
-      r(1,2,i-2)= 0.0D0
-      r(1,3,i-2)= 0.0D0
-      r(2,1,i-2)= 0.0D0
-      r(2,2,i-2)=-cosphi
-      r(2,3,i-2)= sinphi
-      r(3,1,i-2)= 0.0D0
-      r(3,2,i-2)= sinphi
-      r(3,3,i-2)= cosphi
-      rt(1,1,i-2)=-cost
-      rt(1,2,i-2)=-sint
-      rt(1,3,i-2)=0.0D0
-      rt(2,1,i-2)=sint*cosphi
-      rt(2,2,i-2)=-cost*cosphi
-      rt(2,3,i-2)=sinphi
-      rt(3,1,i-2)=-sint*sinphi
-      rt(3,2,i-2)=cost*sinphi
-      rt(3,3,i-2)=cosphi
-        call matmult(prod(1,1,i-2),rt(1,1,i-2),prod(1,1,i-1))
-      do j=1,3
-        dc_norm(j,i-1)=prod(j,1,i-1)
-        dc(j,i-1)=vbld(i)*prod(j,1,i-1)
-      enddo
-        call locate_side_chain(i-1)
-       enddo
-      else
-C
-C Define the origin and orientation of the coordinate system and locate the
+C#ifdef DEBUG
+C      if (perbox) then
 C first three CA's and SC(2).
 C
+      subroutine chainbuild_extconf
+C 
+C Build the virtual polypeptide chain. Side-chain centroids are moveable.
+C As of 2/17/95.
+C
+      implicit real*8 (a-h,o-z)
+      include 'DIMENSIONS'
+      include 'COMMON.CHAIN'
+      include 'COMMON.LOCAL'
+      include 'COMMON.GEO'
+      include 'COMMON.VAR'
+      include 'COMMON.IOUNITS'
+      include 'COMMON.NAMES'
+      include 'COMMON.INTERACT'
+      double precision e1(3),e2(3),e3(3)
+      logical lprn,perbox,fail
+
       call orig_frame
 *
 * Build the alpha-carbon chain.
@@ -175,11 +82,11 @@ C
       enddo   
  1212 format (a3,'(',i3,')',2(f10.5,2f10.2))
 
-      endif
+C      endif
       endif
       return
       end
-#endif
+C#endif
 c-------------------------------------------------------------------------
       subroutine orig_frame
 C
diff --git a/source/unres/src_MD-M/fitsq.f b/source/unres/src_MD-M/fitsq.f
index 1c97e6d..2040074 100644
--- a/source/unres/src_MD-M/fitsq.f
+++ b/source/unres/src_MD-M/fitsq.f
@@ -44,11 +44,11 @@ c
         enddo
       enddo
       rms=dabs(rms/fn)
-
+      
 c      write(iout,*)'xav = ',(xav(j),j=1,3)                                    
 c      write(iout,*)'yav = ',(yav(j),j=1,3)                                    
 c      write(iout,*)'t   = ',(t(j),j=1,3)
-c      write(iout,*)'rms=',rms
+      write(iout,*)'rms=',rms
       if (rms.lt.small) return
                                                                         
                                                                         
diff --git a/source/unres/src_MD-M/readrtns_CSA.F b/source/unres/src_MD-M/readrtns_CSA.F
index bdc7c9d..d25c4eb 100644
--- a/source/unres/src_MD-M/readrtns_CSA.F
+++ b/source/unres/src_MD-M/readrtns_CSA.F
@@ -1132,6 +1132,7 @@ C initial geometry.
           omeg(i)=-120d0*deg2rad
           if (itype(i).le.0) omeg(i)=-omeg(i)
          enddo
+        call chainbuild_extconf
         else
           if(me.eq.king.or..not.out1file)
      &     write (iout,'(a)') 'Random-generated initial geometry.'
diff --git a/source/unres/src_MD-M/rmsd.F b/source/unres/src_MD-M/rmsd.F
index 82749b4..58c4a1b 100644
--- a/source/unres/src_MD-M/rmsd.F
+++ b/source/unres/src_MD-M/rmsd.F
@@ -43,6 +43,7 @@ c---------------------------------------------------------------------------
       rminroz=100d2
 c      print *,"nz_start",nz_start," nz_end",nz_end
 c      if (symetr.le.1) then
+       print *,nperm,"nperm"
       do kkk=1,nperm
 c      do i=nz_start,nz_end
 c        iatom=iatom+1
@@ -81,14 +82,14 @@ c      enddo
 c      endif
       
 c ----- diagnostics
-c         do kkk=1,nperm
-c          write (iout,*) 'Ccopy and CREFcopy'
-c          print '(i5,3f10.5,5x,3f10.5)',(k,(ccopy(j,k),j=1,3),
-c     &           (crefcopy(j,k),j=1,3),k=1,iatom)
-c          write (iout,'(i5,3f10.5,5x,3f10.5)') (k,(ccopy(j,k),j=1,3),
-c     &           (crefcopy(j,k),j=1,3),k=1,iatom)
-c         enddo
-c ----- end diagnostics
+C         do kkk=1,nperm
+          write (iout,*) 'Ccopy and CREFcopy adasko',iatom
+          print '(i5,3f10.5,5x,3f10.5)',(k,(ccopy(j,k),j=1,3),
+     &           (crefcopy(j,k),j=1,3),k=1,iatom)
+          write (iout,'(i5,3f10.5,5x,3f10.5)') (k,(ccopy(j,k),j=1,3),
+     &           (crefcopy(j,k),j=1,3),k=1,iatom)
+C         enddo
+Cc ----- end diagnostics
 c      do kkk=1,nperm
       call fitsq(roznica,ccopy(1,1),crefcopy(1,1),iatom,
      &                                      przes,obrot,non_conv) 
@@ -108,7 +109,7 @@ c          call mpi_abort(mpi_comm_world,ierror,ierrcode)
           stop
 #endif
        endif
-c       write (iout,*) "roznica", roznica,kkk
+       write (iout,*) "roznica", roznica,kkk
        if (roznica.le.rminroz) rminroz=roznica
        enddo
        drms=dsqrt(dabs(rminroz))
diff --git a/source/unres/src_MD/readrtns.F b/source/unres/src_MD/readrtns.F
index af416e8..0493d41 100644
--- a/source/unres/src_MD/readrtns.F
+++ b/source/unres/src_MD/readrtns.F
@@ -1188,6 +1188,7 @@ C initial geometry.
          do i=2,nres-1
           omeg(i)=-120d0*deg2rad
          enddo
+        call chainbuild
         else
           if(me.eq.king.or..not.out1file)
      &     write (iout,'(a)') 'Random-generated initial geometry.'