X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD-M%2FMD_A-MTS.F;h=070476d62d0e50fbc6c5b682beceecd69c36c530;hb=148ec6f6cb1015ce2b9e36ebcb0a6d346b390a5f;hp=6c6fb143c6ddb18cdde3ba4dac20bbcbc9411f9a;hpb=478a9d9a1c99eb3f4bc4ca676ff3162bdd01d633;p=unres.git diff --git a/source/unres/src_MD-M/MD_A-MTS.F b/source/unres/src_MD-M/MD_A-MTS.F index 6c6fb14..070476d 100644 --- 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 @@ -1575,10 +1609,35 @@ c Removing the velocity of the center of mass write (iout,*) (vcm(j),j=1,3) endif if (.not.rest) then - call chainbuild - if(iranconf.ne.0) then + if (start_from_model) then + i_model=iran_num(1,constr_homology) + write (iout,*) 'starting from model ',i_model + do i=1,2*nres + do j=1,3 + c(j,i)=chomo(j,i,i_model) + enddo + enddo + + call int_from_cart(.true.,.false.) + call sc_loc_geom(.false.) + do i=1,nres-1 + do j=1,3 + dc(j,i)=c(j,i+1)-c(j,i) + dc_norm(j,i)=dc(j,i)*vbld_inv(i+1) + enddo + enddo + do i=2,nres-1 + do j=1,3 + dc(j,i+nres)=c(j,i+nres)-c(j,i) + dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres) + enddo + enddo + endif +c call chainbuild_cart + write (iout,*) "PREMINIM ",preminim + if(iranconf.eq.0 .and. preminim) then if (overlapsc) then - print *, 'Calling OVERLAP_SC' + write (iout,*) 'Calling OVERLAP_SC' call overlap_sc(fail) endif @@ -1598,14 +1657,93 @@ c Removing the velocity of the center of mass call minimize(etot,varia,iretcode,nfun) call var_to_geom(nvar,varia) endif + if(me.eq.king.or..not.out1file) then + write(iout,*) "Minimized energy is",etot + write(iout,*) 'SUMSL return code is',iretcode,' eval ',nfun + call etotal(potEcomp) + call enerprint(potEcomp) + endif + endif + if(iranconf.ne.0) then +c 8/22/17 AL Loop to produce a low-energy random conformation + DO iranmin=1,10 + if (overlapsc) then + if(me.eq.king.or..not.out1file) + & write (iout,*) 'Calling OVERLAP_SC' + call overlap_sc(fail) + endif + + if (searchsc) then + call sc_move(2,nres-1,10,1d10,nft_sc,etot) + print *,'SC_move',nft_sc,etot + if(me.eq.king.or..not.out1file) + & write(iout,*) 'SC_move',nft_sc,etot + endif + + if(dccart)then + print *, 'Calling MINIM_DC' + call minim_dc(etot,iretcode,nfun) + else + call geom_to_var(nvar,varia) + print *,'Calling MINIMIZE.' + call minimize(etot,varia,iretcode,nfun) + call var_to_geom(nvar,varia) + endif if(me.eq.king.or..not.out1file) & write(iout,*) 'SUMSL return code is',iretcode,' eval ',nfun + + if (isnan(etot) .or. etot.gt.1.0d4) then + write (iout,*) "Energy too large",etot, + & " trying another random conformation" + do itrial=1,100 + itmp=1 + call gen_rand_conf(itmp,*30) + goto 40 + 30 write (iout,*) 'Failed to generate random conformation', + & ', itrial=',itrial + write (*,*) 'Processor:',me, + & ' Failed to generate random conformation', + & ' itrial=',itrial + call intout +#ifdef AIX + call flush_(iout) +#else + call flush(iout) +#endif + enddo + write (iout,'(a,i3,a)') 'Processor:',me, + & ' error in generating random conformation.' + write (*,'(a,i3,a)') 'Processor:',me, + & ' error in generating random conformation.' + call flush(iout) +#ifdef MPI + call MPI_Abort(mpi_comm_world,error_msg,ierrcode) +#else + stop +#endif + 40 continue + else + goto 44 + endif + ENDDO + + write (iout,'(a,i3,a)') 'Processor:',me, + & ' failed to generate a low-energy random conformation.' + write (*,'(a,i3,a)') 'Processor:',me, + & ' failed to generate a low-energy random conformation.' + call flush(iout) +#ifdef MPI + call MPI_Abort(mpi_comm_world,error_msg,ierrcode) +#else + stop +#endif + 44 continue endif endif call chainbuild_cart call kinetic(EK) if (tbf) then - call verlet_bath(EK) + call verlet_bath endif kinetic_T=2.0d0/(dimen3*Rb)*EK if(me.eq.king.or..not.out1file)then @@ -1770,7 +1908,7 @@ 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 +1922,27 @@ 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 +1979,7 @@ 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 +2208,7 @@ 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 +2317,7 @@ 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 +2474,7 @@ 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 +2523,7 @@ 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 +2584,7 @@ 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)