modyfication for tube

[unres.git] / source / unres / src_MD-M / MD_A-MTS.F

diff --git a/source/unres/src_MD-M/MD_A-MTS.F b/source/unres/src_MD-M/MD_A-MTS.F
index d3c3cb0..3a45231 100644 (file)
--- a/source/unres/src_MD-M/MD_A-MTS.F
+++ b/source/unres/src_MD-M/MD_A-MTS.F
@@ -196,7 +196,11 @@ c Variable time step algorithm.
 #endif
         endif
         if (ntwe.ne.0) then
-         if (mod(itime,ntwe).eq.0) call statout(itime)
+         if (mod(itime,ntwe).eq.0) then
+           call statout(itime)
+C           call enerprint(potEcomp)
+C           print *,itime,'AFM',Eafmforc,etot
+         endif
 #ifdef VOUT
         do j=1,3
           v_work(j)=d_t(j,0)
@@ -209,7 +213,7 @@ c Variable time step algorithm.
           enddo
         enddo
         do i=nnt,nct
-          if (itype(i).ne.10 .and. itype(i).ne.21) then
+          if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
             do j=1,3
               ind=ind+1
               v_work(ind)=d_t(j,i+nres)
@@ -230,6 +234,9 @@ c Variable time step algorithm.
 #endif
         endif
         if (mod(itime,ntwx).eq.0) then
+          write(iout,*) 'time=',itime
+C          call check_ecartint
+          call returnbox
           write (tytul,'("time",f8.2)') totT
           if(mdpdb) then
              call hairpin(.true.,nharp,iharp)
@@ -513,6 +520,8 @@ c Second step of the velocity Verlet algorithm
           endif                    
           if (rattle) call rattle2
           totT=totT+d_time
+          totTafm=totT
+C          print *,totTafm,"TU?"
           if (d_time.ne.d_time0) then
             d_time=d_time0
 #ifndef   LANG0
@@ -910,6 +919,7 @@ c Compute the complete potential energy
       potE=potEcomp(0)-potEcomp(20)
 c      potE=energia_short(0)+energia_long(0)
       totT=totT+d_time
+      totTafm=totT
 c Calculate the kinetic and the total energy and the kinetic temperature
       call kinetic(EK)
       totE=EK+potE
@@ -955,7 +965,7 @@ c  forces).
         enddo
       enddo
       do i=nnt,nct
-        if (itype(i).ne.10 .and. itype(i).ne.21) then
+        if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
           inres=i+nres
           do j=1,3
             d_t(j,inres)=d_t(j,inres)+0.5d0*d_a(j,inres)*d_time
@@ -996,6 +1006,8 @@ c Applying velocity Verlet algorithm - step 1 to coordinates
         d_t(j,0)=d_t_old(j,0)+adt
       enddo
       do i=nnt,nct-1   
+C      SPYTAC ADAMA
+C       do i=0,nres
         do j=1,3    
           adt=d_a_old(j,i)*d_time
           adt2=0.5d0*adt
@@ -1005,7 +1017,8 @@ c Applying velocity Verlet algorithm - step 1 to coordinates
         enddo
       enddo
       do i=nnt,nct
-        if (itype(i).ne.10 .and. itype(i).ne.21) then
+C        do i=0,nres
+        if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
           inres=i+nres
           do j=1,3    
             adt=d_a_old(j,inres)*d_time
@@ -1049,7 +1062,7 @@ c  Step 2 of the velocity Verlet algorithm: update velocities
         enddo
       enddo
       do i=nnt,nct
-        if (itype(i).ne.10 .and. itype(i).ne.21) then
+        if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
           inres=i+nres
           do j=1,3
             d_t(j,inres)=d_t_new(j,inres)+0.5d0*d_a(j,inres)*d_time
@@ -1087,12 +1100,25 @@ c Applying velocity Verlet algorithm - step 1 to coordinates
 c
 c Compute friction and stochastic forces
 c
+#ifdef MPI
       time00=MPI_Wtime()
+#else
+      time00=tcpu()
+#endif
       call friction_force
+#ifdef MPI
       time_fric=time_fric+MPI_Wtime()-time00
       time00=MPI_Wtime()
+#else
+      time_fric=time_fric+tcpu()-time00
+      time00=tcpu()
+#endif
       call stochastic_force(stochforcvec) 
+#ifdef MPI
       time_stoch=time_stoch+MPI_Wtime()-time00
+#else
+      time_stoch=time_stoch+tcpu()-time00
+#endif
 c
 c Compute the acceleration due to friction forces (d_af_work) and stochastic
 c forces (d_as_work)
@@ -1148,7 +1174,7 @@ c
         ind=ind+3
       enddo
       do i=nnt,nct
-        if (itype(i).ne.10 .and. itype(i).ne.21) then
+        if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
           inres=i+nres
           do j=1,3    
             adt=(d_a_old(j,inres)+d_af_work(ind+j))*d_time
@@ -1213,7 +1239,7 @@ c
         ind=ind+3
       enddo
       do i=nnt,nct
-        if (itype(i).ne.10 .and. itype(i).ne.21) then
+        if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
           inres=i+nres
           do j=1,3
             d_t(j,inres)=d_t_new(j,inres)+(0.5d0*(d_a(j,inres)
@@ -1260,6 +1286,7 @@ c            accel(j)=aux(j)+0.5d0*(d_a(j,i)-d_a_old(j,i))
 c            if (dabs(accel(j)).gt.amax) amax=dabs(accel(j))
             if (dabs(accel(j)).gt.dabs(accel_old(j))) then
               dacc=dabs(accel(j)-accel_old(j))
+c              write (iout,*) i,dacc
               if (dacc.gt.amax) amax=dacc
             endif
           enddo
@@ -1278,7 +1305,7 @@ c        accel(j)=aux(j)
         enddo
       endif
       do i=nnt,nct
-        if (itype(i).ne.10 .and. itype(i).ne.21) then
+        if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
           do j=1,3 
 c            accel(j)=accel(j)+d_a(j,i+nres)-d_a_old(j,i+nres)
             accel_old(j)=accel_old(j)+d_a_old(j,i+nres)
@@ -1289,6 +1316,7 @@ c            accel(j)=accel(j)+d_a(j,i+nres)-d_a_old(j,i+nres)
 c          if (dabs(accel(j)).gt.amax) amax=dabs(accel(j))
           if (dabs(accel(j)).gt.dabs(accel_old(j))) then
             dacc=dabs(accel(j)-accel_old(j))
+c            write (iout,*) "side-chain",i,dacc
             if (dacc.gt.amax) amax=dacc
           endif
         enddo
@@ -1331,7 +1359,7 @@ c            write (iout,*) "back",i,j,epdriftij
           enddo
         endif
 c Side chains
-        if (itype(i).ne.10 .and. itype(i).ne.21) then
+        if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
           do j=1,3 
             epdriftij=
      &       dabs((d_a(j,i+nres)-d_a_old(j,i+nres))*gxcart(j,i))
@@ -1378,7 +1406,7 @@ c      write(iout,*) "fact", fact
         enddo
       enddo
       do i=nnt,nct
-        if (itype(i).ne.10 .and. itype(i).ne.21) then
+        if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
           inres=i+nres
           do j=1,3
             d_t(j,inres)=fact*d_t(j,inres)
@@ -1433,7 +1461,8 @@ c if the friction coefficients do not depend on surface area
           stdforcp(i)=stdfp*dsqrt(gamp)
         enddo
         do i=nnt,nct
-          stdforcsc(i)=stdfsc(itype(i))*dsqrt(gamsc(itype(i)))
+          stdforcsc(i)=stdfsc(iabs(itype(i)))
+     &                *dsqrt(gamsc(iabs(itype(i))))
         enddo
       endif
 c Open the pdb file for snapshotshots
@@ -1507,11 +1536,13 @@ c        statname=statname(:ilen(statname)-5)//qstr(:ipos-1)//'.stat'
        if (restart1file) then
          if (me.eq.king)
      &     inquire(file=mremd_rst_name,exist=file_exist)
+#ifdef MPI
            write (*,*) me," Before broadcast: file_exist",file_exist
          call MPI_Bcast(file_exist,1,MPI_LOGICAL,king,CG_COMM,
      &          IERR)
          write (*,*) me," After broadcast: file_exist",file_exist
 c        inquire(file=mremd_rst_name,exist=file_exist)
+#endif
         if(me.eq.king.or..not.out1file)
      &   write(iout,*) "Initial state read by master and distributed"
        else
@@ -1541,6 +1572,7 @@ c        inquire(file=mremd_rst_name,exist=file_exist)
         endif
         call random_vel
         totT=0.0d0
+        totTafm=totT
        endif
       else
 c Generate initial velocities
@@ -1548,6 +1580,8 @@ c Generate initial velocities
      &   write(iout,*) "Initial velocities randomly generated"
         call random_vel
         totT=0.0d0
+CtotTafm is the variable for AFM time which eclipsed during  
+        totTafm=totT
       endif
 c      rest2name = prefix(:ilen(prefix))//'.rst'
       if(me.eq.king.or..not.out1file)then
@@ -1619,6 +1653,7 @@ c Removing the velocity of the center of mass
 #endif
       call zerograd
       call etotal(potEcomp)
+      call enerprint(potEcomp)
       if (large) call enerprint(potEcomp)
 #ifdef TIMING_ENE
 #ifdef MPI
@@ -1637,11 +1672,11 @@ c Removing the velocity of the center of mass
      &   "Time step reduced to",d_time,
      &   " because of too large initial acceleration."
       endif
-      if(me.eq.king.or..not.out1file)then 
-       write(iout,*) "Potential energy and its components"
-       call enerprint(potEcomp)
+C      if(me.eq.king.or..not.out1file)then 
+C       write(iout,*) "Potential energy and its components"
+C       call enerprint(potEcomp)
 c       write(iout,*) (potEcomp(i),i=0,n_ene)
-      endif
+C      endif
       potE=potEcomp(0)-potEcomp(20)
       totE=EK+potE
       itime=0
@@ -1770,7 +1805,7 @@ c-----------------------------------------------------------
       include 'COMMON.IOUNITS'
       include 'COMMON.NAMES'
       include 'COMMON.TIME1'
-      double precision xv,sigv,lowb,highb
+      double precision xv,sigv,lowb,highb,vec_afm(3)
 c Generate random velocities from Gaussian distribution of mean 0 and std of KT/m 
 c First generate velocities in the eigenspace of the G matrix
 c      write (iout,*) "Calling random_vel dimen dimen3",dimen,dimen3
@@ -1784,10 +1819,27 @@ c      call flush(iout)
           lowb=-5*sigv
           highb=5*sigv
           d_t_work_new(ii)=anorm_distr(xv,sigv,lowb,highb)
+
 c          write (iout,*) "i",i," ii",ii," geigen",geigen(i),
 c     &      " d_t_work_new",d_t_work_new(ii)
         enddo
       enddo
+C       if (SELFGUIDE.gt.0) then
+C       distance=0.0
+C       do j=1,3
+C       vec_afm(j)=c(j,afmend)-c(j,afmbeg)  
+C       distance=distance+vec_afm(j)**2
+C       enddo
+C       distance=dsqrt(distance)
+C       do j=1,3
+C         d_t_work_new(j+(afmbeg-1)*3)=-velAFMconst*vec_afm(j)/distance
+C         d_t_work_new(j+(afmend-1)*3)=velAFMconst*vec_afm(j)/distance
+C         write(iout,*) "myvel",d_t_work_new(j+(afmbeg-1)*3),
+C     &    d_t_work_new(j+(afmend-1)*3)
+C       enddo
+
+C       endif
+
 c diagnostics
 c      Ek1=0.0d0
 c      ii=0
@@ -1824,7 +1876,7 @@ c Transfer to the d_t vector
         enddo
       enddo
       do i=nnt,nct
-        if (itype(i).ne.10 .and. itype(i).ne.21) then
+        if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
           do j=1,3
             ind=ind+1
             d_t(j,i+nres)=d_t_work(ind)
@@ -2053,7 +2105,7 @@ c      enddo
         ind=ind+3
       enddo
       do i=nnt,nct
-        if (itype(i).ne.10 .and. itype(i).ne.21) then
+        if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
           do j=1,3
             dc_work(ind+j)=dc_old(j,i+nres)
             d_t_work(ind+j)=d_t_old(j,i+nres)
@@ -2162,7 +2214,7 @@ c
         ind=ind+3
       enddo
       do i=nnt,nct
-        if (itype(i).ne.10 .and. itype(i).ne.21) then
+        if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
           inres=i+nres
           do j=1,3
             d_t(j,inres)=d_t_work(ind+j)
@@ -2319,7 +2371,7 @@ c      enddo
         ind=ind+3
       enddo
       do i=nnt,nct
-        if (itype(i).ne.10 .and. itype(i).ne.21) then
+        if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
           do j=1,3
             dc_work(ind+j)=dc_old(j,i+nres)
             d_t_work(ind+j)=d_t_old(j,i+nres)
@@ -2368,7 +2420,7 @@ c      enddo
         ind=ind+3
       enddo
       do i=nnt,nct
-        if (itype(i).ne.10 .and. itype(i).ne.21) then
+        if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
           inres=i+nres
           do j=1,3
             dc(j,inres)=dc_work(ind+j)
@@ -2429,7 +2481,7 @@ c          ddt2=ddt2+vrand_mat2(i,j)*stochforcvecV(j)
         ind=ind+3
       enddo
       do i=nnt,nct
-        if (itype(i).ne.10 .and. itype(i).ne.21) then
+        if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
           inres=i+nres
           do j=1,3
             d_t(j,inres)=d_t_work(ind+j)