From: Adam Liwo Date: Sun, 10 May 2015 02:34:55 +0000 (+0200) Subject: Fixed geomout.F X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=commitdiff_plain;h=0b9ce12f1a05d752c261b28ea7dbc3eb7dbda58f Fixed geomout.F --- diff --git a/bin/cluster/unres_clustMD-mult_gfort_MPICH_E0LL2Y.exe b/bin/cluster/unres_clustMD-mult_gfort_MPICH_E0LL2Y.exe new file mode 100755 index 0000000..8ab987d Binary files /dev/null and b/bin/cluster/unres_clustMD-mult_gfort_MPICH_E0LL2Y.exe differ diff --git a/bin/cluster/unres_clustMD-mult_gfort_MPICH_GAB.exe b/bin/cluster/unres_clustMD-mult_gfort_MPICH_GAB.exe new file mode 100755 index 0000000..ccbddd9 Binary files /dev/null and b/bin/cluster/unres_clustMD-mult_gfort_MPICH_GAB.exe differ diff --git a/bin/cluster/unres_clustMD-mult_ifort_MPICH_GAB.exe b/bin/cluster/unres_clustMD-mult_ifort_MPICH_GAB.exe new file mode 100755 index 0000000..998f129 Binary files /dev/null and b/bin/cluster/unres_clustMD-mult_ifort_MPICH_GAB.exe differ diff --git a/source/unres/src_MD/intcartderiv.F.org b/source/unres/src_MD/intcartderiv.F.org new file mode 100644 index 0000000..33c23a0 --- /dev/null +++ b/source/unres/src_MD/intcartderiv.F.org @@ -0,0 +1,728 @@ + subroutine intcartderiv + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' +#ifdef MPI + include 'mpif.h' +#endif + include 'COMMON.SETUP' + include 'COMMON.CHAIN' + include 'COMMON.VAR' + include 'COMMON.GEO' + include 'COMMON.INTERACT' + include 'COMMON.DERIV' + include 'COMMON.IOUNITS' + include 'COMMON.LOCAL' + include 'COMMON.SCCOR' + double precision dcostheta(3,2,maxres), + & dcosphi(3,3,maxres),dsinphi(3,3,maxres), + & dcosalpha(3,3,maxres),dcosomega(3,3,maxres), + & dsinomega(3,3,maxres),vo1(3),vo2(3),vo3(3), + & dummy(3),vp1(3),vp2(3),vp3(3),vpp1(3),n(3) + +#if defined(MPI) && defined(PARINTDER) + if (nfgtasks.gt.1 .and. me.eq.king) + & call MPI_Bcast(8,1,MPI_INTEGER,king,FG_COMM,IERROR) +#endif + pi4 = 0.5d0*pipol + pi34 = 3*pi4 + +c write (iout,*) "iphi1_start",iphi1_start," iphi1_end",iphi1_end +c Derivatives of theta's +#if defined(MPI) && defined(PARINTDER) +c We need dtheta(:,:,i-1) to compute dphi(:,:,i) + do i=max0(ithet_start-1,3),ithet_end +#else + do i=3,nres +#endif + cost=dcos(theta(i)) + sint=sqrt(1-cost*cost) + do j=1,3 + dcostheta(j,1,i)=-(dc_norm(j,i-1)+cost*dc_norm(j,i-2))/ + & vbld(i-1) + dtheta(j,1,i)=-1/sint*dcostheta(j,1,i) + dcostheta(j,2,i)=-(dc_norm(j,i-2)+cost*dc_norm(j,i-1))/ + & vbld(i) + dtheta(j,2,i)=-1/sint*dcostheta(j,2,i) + enddo + enddo + +#if defined(MPI) && defined(PARINTDER) +c We need dtheta(:,:,i-1) to compute dphi(:,:,i) + do i=max0(ithet_start-1,3),ithet_end +#else + do i=3,nres +#endif + if ((itype(i-1).ne.10).and.(itype(i-1).ne.21)) then + cost1=dcos(omicron(1,i)) + sint1=sqrt(1-cost1*cost1) + cost2=dcos(omicron(2,i)) + sint2=sqrt(1-cost2*cost2) + do j=1,3 +CC Calculate derivative over first omicron (Cai-2,Cai-1,SCi-1) + dcosomicron(j,1,1,i)=-(dc_norm(j,i-1+nres)+ + & cost1*dc_norm(j,i-2))/ + & vbld(i-1) + domicron(j,1,1,i)=-1/sint1*dcosomicron(j,1,1,i) + dcosomicron(j,1,2,i)=-(dc_norm(j,i-2) + & +cost1*(dc_norm(j,i-1+nres)))/ + & vbld(i-1+nres) + domicron(j,1,2,i)=-1/sint1*dcosomicron(j,1,2,i) +CC Calculate derivative over second omicron Sci-1,Cai-1 Cai +CC Looks messy but better than if in loop + dcosomicron(j,2,1,i)=-(-dc_norm(j,i-1+nres) + & +cost2*dc_norm(j,i-1))/ + & vbld(i) + domicron(j,2,1,i)=-1/sint2*dcosomicron(j,2,1,i) + dcosomicron(j,2,2,i)=-(dc_norm(j,i-1) + & +cost2*(-dc_norm(j,i-1+nres)))/ + & vbld(i-1+nres) +c write(iout,*) "vbld", i,itype(i),vbld(i-1+nres) + domicron(j,2,2,i)=-1/sint2*dcosomicron(j,2,2,i) + enddo + endif + enddo + + + +c Derivatives of phi: +c If phi is 0 or 180 degrees, then the formulas +c have to be derived by power series expansion of the +c conventional formulas around 0 and 180. +#ifdef PARINTDER + do i=iphi1_start,iphi1_end +#else + do i=4,nres +#endif +c the conventional case + sint=dsin(theta(i)) + sint1=dsin(theta(i-1)) + sing=dsin(phi(i)) + cost=dcos(theta(i)) + cost1=dcos(theta(i-1)) + cosg=dcos(phi(i)) + scalp=scalar(dc_norm(1,i-3),dc_norm(1,i-1)) + fac0=1.0d0/(sint1*sint) + fac1=cost*fac0 + fac2=cost1*fac0 + fac3=cosg*cost1/(sint1*sint1) + fac4=cosg*cost/(sint*sint) +c Obtaining the gamma derivatives from sine derivative + if (phi(i).gt.-pi4.and.phi(i).le.pi4.or. + & phi(i).gt.pi34.and.phi(i).le.pi.or. + & phi(i).gt.-pi.and.phi(i).le.-pi34) then + call vecpr(dc_norm(1,i-1),dc_norm(1,i-2),vp1) + call vecpr(dc_norm(1,i-3),dc_norm(1,i-1),vp2) + call vecpr(dc_norm(1,i-3),dc_norm(1,i-2),vp3) + do j=1,3 + ctgt=cost/sint + ctgt1=cost1/sint1 + cosg_inv=1.0d0/cosg + dsinphi(j,1,i)=-sing*ctgt1*dtheta(j,1,i-1) + & -(fac0*vp1(j)+sing*dc_norm(j,i-3))*vbld_inv(i-2) + dphi(j,1,i)=cosg_inv*dsinphi(j,1,i) + dsinphi(j,2,i)= + & -sing*(ctgt1*dtheta(j,2,i-1)+ctgt*dtheta(j,1,i)) + & -(fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1) + dphi(j,2,i)=cosg_inv*dsinphi(j,2,i) +c Bug fixed 3/24/05 (AL) + dsinphi(j,3,i)=-sing*ctgt*dtheta(j,2,i) + & +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i) +c & +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i-1) + dphi(j,3,i)=cosg_inv*dsinphi(j,3,i) + enddo +c Obtaining the gamma derivatives from cosine derivative + else + do j=1,3 + dcosphi(j,1,i)=fac1*dcostheta(j,1,i-1)+fac3* + & dcostheta(j,1,i-1)-fac0*(dc_norm(j,i-1)-scalp* + & dc_norm(j,i-3))/vbld(i-2) + dphi(j,1,i)=-1/sing*dcosphi(j,1,i) + dcosphi(j,2,i)=fac1*dcostheta(j,2,i-1)+fac2* + & dcostheta(j,1,i)+fac3*dcostheta(j,2,i-1)+fac4* + & dcostheta(j,1,i) + dphi(j,2,i)=-1/sing*dcosphi(j,2,i) + dcosphi(j,3,i)=fac2*dcostheta(j,2,i)+fac4* + & dcostheta(j,2,i)-fac0*(dc_norm(j,i-3)-scalp* + & dc_norm(j,i-1))/vbld(i) + dphi(j,3,i)=-1/sing*dcosphi(j,3,i) + enddo + endif + enddo + + do i=1,nres-1 + do j=1,3 + dc_norm2(j,i-2+nres)=-dc_norm(j,i-2+nres) +cc write(iout,*) dc_norm2(j,i-2+nres),"dcnorm" + enddo + enddo +Calculate derivative of Tauangle +#ifdef PARINTDER + do i=itau_start,itau_end +#else + do i=3,nres +#endif + if ((itype(i-2).eq.21).or.(itype(i-2).eq.10)) cycle +cc dtauangle(j,intertyp,dervityp,residue number) +cc INTERTYP=1 SC...Ca...Ca..Ca +c the conventional case + sint=dsin(theta(i)) + sint1=dsin(omicron(2,i-1)) + sing=dsin(tauangle(1,i)) + cost=dcos(theta(i)) + cost1=dcos(omicron(2,i-1)) + cosg=dcos(tauangle(1,i)) + scalp=scalar(dc_norm2(1,i-2+nres),dc_norm(1,i-1)) + fac0=1.0d0/(sint1*sint) + fac1=cost*fac0 + fac2=cost1*fac0 + fac3=cosg*cost1/(sint1*sint1) + fac4=cosg*cost/(sint*sint) +cc write(iout,*) "faki",fac0,fac1,fac2,fac3,fac4 +c Obtaining the gamma derivatives from sine derivative + if (tauangle(1,i).gt.-pi4.and.tauangle(1,i).le.pi4.or. + & tauangle(1,i).gt.pi34.and.tauangle(1,i).le.pi.or. + & tauangle(1,i).gt.-pi.and.tauangle(1,i).le.-pi34) then + call vecpr(dc_norm(1,i-1),dc_norm(1,i-2),vp1) + call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-1),vp2) + call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-2),vp3) + do j=1,3 + ctgt=cost/sint + ctgt1=cost1/sint1 + cosg_inv=1.0d0/cosg + dsintau(j,1,1,i)=-sing*ctgt1*domicron(j,2,2,i-1) + &-(fac0*vp1(j)+sing*(dc_norm2(j,i-2+nres))) + & *vbld_inv(i-2+nres) + dtauangle(j,1,1,i)=cosg_inv*dsintau(j,1,1,i) + dsintau(j,1,2,i)= + & -sing*(ctgt1*domicron(j,2,1,i-1)+ctgt*dtheta(j,1,i)) + & -(fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1) +c write(iout,*) "dsintau", dsintau(j,1,2,i) + dtauangle(j,1,2,i)=cosg_inv*dsintau(j,1,2,i) +c Bug fixed 3/24/05 (AL) + dsintau(j,1,3,i)=-sing*ctgt*dtheta(j,2,i) + & +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i) +c & +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i-1) + dtauangle(j,1,3,i)=cosg_inv*dsintau(j,1,3,i) + enddo +c Obtaining the gamma derivatives from cosine derivative + else + do j=1,3 + dcostau(j,1,1,i)=fac1*dcosomicron(j,2,2,i-1)+fac3* + & dcosomicron(j,2,2,i-1)-fac0*(dc_norm(j,i-1)-scalp* + & (dc_norm2(j,i-2+nres)))/vbld(i-2+nres) + dtauangle(j,1,1,i)=-1/sing*dcostau(j,1,1,i) + dcostau(j,1,2,i)=fac1*dcosomicron(j,2,1,i-1)+fac2* + & dcostheta(j,1,i)+fac3*dcosomicron(j,2,1,i-1)+fac4* + & dcostheta(j,1,i) + dtauangle(j,1,2,i)=-1/sing*dcostau(j,1,2,i) + dcostau(j,1,3,i)=fac2*dcostheta(j,2,i)+fac4* + & dcostheta(j,2,i)-fac0*(-dc_norm(j,i-2+nres)-scalp* + & dc_norm(j,i-1))/vbld(i) + dtauangle(j,1,3,i)=-1/sing*dcostau(j,1,3,i) +c write (iout,*) "else",i + enddo + endif +c do k=1,3 +c write(iout,*) "tu",i,k,(dtauangle(j,1,k,i),j=1,3) +c enddo + enddo +CC Second case Ca...Ca...Ca...SC +#ifdef PARINTDER + do i=itau_start,itau_end +#else + do i=4,nres +#endif + if ((itype(i-1).eq.21).or.(itype(i-1).eq.10)) cycle +c the conventional case + sint=dsin(omicron(1,i)) + sint1=dsin(theta(i-1)) + sing=dsin(tauangle(2,i)) + cost=dcos(omicron(1,i)) + cost1=dcos(theta(i-1)) + cosg=dcos(tauangle(2,i)) +c do j=1,3 +c dc_norm2(j,i-1+nres)=-dc_norm(j,i-1+nres) +c enddo + scalp=scalar(dc_norm(1,i-3),dc_norm(1,i-1+nres)) + fac0=1.0d0/(sint1*sint) + fac1=cost*fac0 + fac2=cost1*fac0 + fac3=cosg*cost1/(sint1*sint1) + fac4=cosg*cost/(sint*sint) +c Obtaining the gamma derivatives from sine derivative +c write (iout,*) "i",i," tauangle2",tauangle(2,i) + if (tauangle(2,i).gt.-pi4.and.tauangle(2,i).le.pi4.or. + & tauangle(2,i).gt.pi34.and.tauangle(2,i).le.pi.or. + & tauangle(2,i).gt.-pi.and.tauangle(2,i).le.-pi34) then + call vecpr(dc_norm2(1,i-1+nres),dc_norm(1,i-2),vp1) + call vecpr(dc_norm(1,i-3),dc_norm(1,i-1+nres),vp2) + call vecpr(dc_norm(1,i-3),dc_norm(1,i-2),vp3) + do j=1,3 + ctgt=cost/sint + ctgt1=cost1/sint1 + cosg_inv=1.0d0/cosg + dsintau(j,2,1,i)=-sing*ctgt1*dtheta(j,1,i-1) + & +(fac0*vp1(j)-sing*dc_norm(j,i-3))*vbld_inv(i-2) +c write(iout,*) i,j,dsintau(j,2,1,i),sing*ctgt1*dtheta(j,1,i-1), +c &fac0*vp1(j),sing*dc_norm(j,i-3),vbld_inv(i-2),"dsintau(2,1)" + dtauangle(j,2,1,i)=cosg_inv*dsintau(j,2,1,i) + dsintau(j,2,2,i)= + & -sing*(ctgt1*dtheta(j,2,i-1)+ctgt*domicron(j,1,1,i)) + & -(fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1) +c write(iout,*) "sprawdzenie",i,j,sing*ctgt1*dtheta(j,2,i-1), +c & sing*ctgt*domicron(j,1,2,i), +c & (fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1) + dtauangle(j,2,2,i)=cosg_inv*dsintau(j,2,2,i) +c Bug fixed 3/24/05 (AL) + dsintau(j,2,3,i)=-sing*ctgt*domicron(j,1,2,i) + & +(fac0*vp3(j)-sing*dc_norm(j,i-1+nres))*vbld_inv(i-1+nres) +c & +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i-1) + dtauangle(j,2,3,i)=cosg_inv*dsintau(j,2,3,i) + enddo +c Obtaining the gamma derivatives from cosine derivative + else + do j=1,3 + dcostau(j,2,1,i)=fac1*dcostheta(j,1,i-1)+fac3* + & dcostheta(j,1,i-1)-fac0*(dc_norm(j,i-1+nres)-scalp* + & dc_norm(j,i-3))/vbld(i-2) + dtauangle(j,2,1,i)=-1/sing*dcostau(j,2,1,i) + dcostau(j,2,2,i)=fac1*dcostheta(j,2,i-1)+fac2* + & dcosomicron(j,1,1,i)+fac3*dcostheta(j,2,i-1)+fac4* + & dcosomicron(j,1,1,i) + dtauangle(j,2,2,i)=-1/sing*dcostau(j,2,2,i) + dcostau(j,2,3,i)=fac2*dcosomicron(j,1,2,i)+fac4* + & dcosomicron(j,1,2,i)-fac0*(dc_norm(j,i-3)-scalp* + & dc_norm(j,i-1+nres))/vbld(i-1+nres) + dtauangle(j,2,3,i)=-1/sing*dcostau(j,2,3,i) +c write(iout,*) i,j,"else", dtauangle(j,2,3,i) + enddo + endif + enddo + + +CCC third case SC...Ca...Ca...SC +#ifdef PARINTDER + + do i=itau_start,itau_end +#else + do i=3,nres +#endif +c the conventional case + if ((itype(i-1).eq.21).or.(itype(i-1).eq.10).or. + &(itype(i-2).eq.21).or.(itype(i-2).eq.10)) cycle + sint=dsin(omicron(1,i)) + sint1=dsin(omicron(2,i-1)) + sing=dsin(tauangle(3,i)) + cost=dcos(omicron(1,i)) + cost1=dcos(omicron(2,i-1)) + cosg=dcos(tauangle(3,i)) + do j=1,3 + dc_norm2(j,i-2+nres)=-dc_norm(j,i-2+nres) +c dc_norm2(j,i-1+nres)=-dc_norm(j,i-1+nres) + enddo + scalp=scalar(dc_norm2(1,i-2+nres),dc_norm(1,i-1+nres)) + fac0=1.0d0/(sint1*sint) + fac1=cost*fac0 + fac2=cost1*fac0 + fac3=cosg*cost1/(sint1*sint1) + fac4=cosg*cost/(sint*sint) +c Obtaining the gamma derivatives from sine derivative + if (tauangle(3,i).gt.-pi4.and.tauangle(3,i).le.pi4.or. + & tauangle(3,i).gt.pi34.and.tauangle(3,i).le.pi.or. + & tauangle(3,i).gt.-pi.and.tauangle(3,i).le.-pi34) then + call vecpr(dc_norm(1,i-1+nres),dc_norm(1,i-2),vp1) + call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-1+nres),vp2) + call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-2),vp3) + do j=1,3 + ctgt=cost/sint + ctgt1=cost1/sint1 + cosg_inv=1.0d0/cosg + dsintau(j,3,1,i)=-sing*ctgt1*domicron(j,2,2,i-1) + & -(fac0*vp1(j)-sing*dc_norm(j,i-2+nres)) + & *vbld_inv(i-2+nres) + dtauangle(j,3,1,i)=cosg_inv*dsintau(j,3,1,i) + dsintau(j,3,2,i)= + & -sing*(ctgt1*domicron(j,2,1,i-1)+ctgt*domicron(j,1,1,i)) + & -(fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1) + dtauangle(j,3,2,i)=cosg_inv*dsintau(j,3,2,i) +c Bug fixed 3/24/05 (AL) + dsintau(j,3,3,i)=-sing*ctgt*domicron(j,1,2,i) + & +(fac0*vp3(j)-sing*dc_norm(j,i-1+nres)) + & *vbld_inv(i-1+nres) +c & +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i-1) + dtauangle(j,3,3,i)=cosg_inv*dsintau(j,3,3,i) + enddo +c Obtaining the gamma derivatives from cosine derivative + else + do j=1,3 + dcostau(j,3,1,i)=fac1*dcosomicron(j,2,2,i-1)+fac3* + & dcosomicron(j,2,2,i-1)-fac0*(dc_norm(j,i-1+nres)-scalp* + & dc_norm2(j,i-2+nres))/vbld(i-2+nres) + dtauangle(j,3,1,i)=-1/sing*dcostau(j,3,1,i) + dcostau(j,3,2,i)=fac1*dcosomicron(j,2,1,i-1)+fac2* + & dcosomicron(j,1,1,i)+fac3*dcosomicron(j,2,1,i-1)+fac4* + & dcosomicron(j,1,1,i) + dtauangle(j,3,2,i)=-1/sing*dcostau(j,3,2,i) + dcostau(j,3,3,i)=fac2*dcosomicron(j,1,2,i)+fac4* + & dcosomicron(j,1,2,i)-fac0*(dc_norm2(j,i-2+nres)-scalp* + & dc_norm(j,i-1+nres))/vbld(i-1+nres) + dtauangle(j,3,3,i)=-1/sing*dcostau(j,3,3,i) +c write(iout,*) "else",i + enddo + endif + enddo +#ifdef CRYST_SC +c Derivatives of side-chain angles alpha and omega +#if defined(MPI) && defined(PARINTDER) + do i=ibond_start,ibond_end +#else + do i=2,nres-1 +#endif + if(itype(i).ne.10) then + fac5=1.0d0/dsqrt(2*(1+dcos(theta(i+1)))) + fac6=fac5/vbld(i) + fac7=fac5*fac5 + fac8=fac5/vbld(i+1) + fac9=fac5/vbld(i+nres) + scala1=scalar(dc_norm(1,i-1),dc_norm(1,i+nres)) + scala2=scalar(dc_norm(1,i),dc_norm(1,i+nres)) + cosa=dsqrt(0.5d0/(1.0d0+dcos(theta(i+1))))*( + & scalar(dC_norm(1,i),dC_norm(1,i+nres)) + & -scalar(dC_norm(1,i-1),dC_norm(1,i+nres))) + sina=sqrt(1-cosa*cosa) + sino=dsin(omeg(i)) + do j=1,3 + dcosalpha(j,1,i)=fac6*(scala1*dc_norm(j,i-1)- + & dc_norm(j,i+nres))-cosa*fac7*dcostheta(j,1,i+1) + dalpha(j,1,i)=-1/sina*dcosalpha(j,1,i) + dcosalpha(j,2,i)=fac8*(dc_norm(j,i+nres)- + & scala2*dc_norm(j,i))-cosa*fac7*dcostheta(j,2,i+1) + dalpha(j,2,i)=-1/sina*dcosalpha(j,2,i) + dcosalpha(j,3,i)=(fac9*(dc_norm(j,i)- + & dc_norm(j,i-1))-(cosa*dc_norm(j,i+nres))/ + & vbld(i+nres)) + dalpha(j,3,i)=-1/sina*dcosalpha(j,3,i) + enddo +c obtaining the derivatives of omega from sines + if(omeg(i).gt.-pi4.and.omeg(i).le.pi4.or. + & omeg(i).gt.pi34.and.omeg(i).le.pi.or. + & omeg(i).gt.-pi.and.omeg(i).le.-pi34) then + fac15=dcos(theta(i+1))/(dsin(theta(i+1))* + & dsin(theta(i+1))) + fac16=dcos(alph(i))/(dsin(alph(i))*dsin(alph(i))) + fac17=1.0d0/(dsin(theta(i+1))*dsin(alph(i))) + call vecpr(dc_norm(1,i+nres),dc_norm(1,i),vo1) + call vecpr(dc_norm(1,i+nres),dc_norm(1,i-1),vo2) + call vecpr(dc_norm(1,i),dc_norm(1,i-1),vo3) + coso_inv=1.0d0/dcos(omeg(i)) + do j=1,3 + dsinomega(j,1,i)=sino*(fac15*dcostheta(j,1,i+1) + & +fac16*dcosalpha(j,1,i))-fac17/vbld(i)*vo1(j)-( + & sino*dc_norm(j,i-1))/vbld(i) + domega(j,1,i)=coso_inv*dsinomega(j,1,i) + dsinomega(j,2,i)=sino*(fac15*dcostheta(j,2,i+1) + & +fac16*dcosalpha(j,2,i))+fac17/vbld(i+1)*vo2(j) + & -sino*dc_norm(j,i)/vbld(i+1) + domega(j,2,i)=coso_inv*dsinomega(j,2,i) + dsinomega(j,3,i)=sino*fac16*dcosalpha(j,3,i)- + & fac17/vbld(i+nres)*vo3(j)-sino*dc_norm(j,i+nres)/ + & vbld(i+nres) + domega(j,3,i)=coso_inv*dsinomega(j,3,i) + enddo + else +c obtaining the derivatives of omega from cosines + fac10=sqrt(0.5d0*(1-dcos(theta(i+1)))) + fac11=sqrt(0.5d0*(1+dcos(theta(i+1)))) + fac12=fac10*sina + fac13=fac12*fac12 + fac14=sina*sina + do j=1,3 + dcosomega(j,1,i)=(-(0.25d0*cosa/fac11* + & dcostheta(j,1,i+1)+fac11*dcosalpha(j,1,i))*fac12+ + & (0.25d0/fac10*sina*dcostheta(j,1,i+1)+cosa/sina* + & fac10*dcosalpha(j,1,i))*(scala2-fac11*cosa))/fac13 + domega(j,1,i)=-1/sino*dcosomega(j,1,i) + dcosomega(j,2,i)=(((dc_norm(j,i+nres)-scala2* + & dc_norm(j,i))/vbld(i+1)-0.25d0*cosa/fac11* + & dcostheta(j,2,i+1)-fac11*dcosalpha(j,2,i))*fac12+ + & (scala2-fac11*cosa)*(0.25d0*sina/fac10* + & dcostheta(j,2,i+1)+fac10*cosa/sina*dcosalpha(j,2,i) + & ))/fac13 + domega(j,2,i)=-1/sino*dcosomega(j,2,i) + dcosomega(j,3,i)=1/fac10*((1/vbld(i+nres)*(dc_norm(j,i)- + & scala2*dc_norm(j,i+nres))-fac11*dcosalpha(j,3,i))*sina+ + & (scala2-fac11*cosa)*(cosa/sina*dcosalpha(j,3,i)))/fac14 + domega(j,3,i)=-1/sino*dcosomega(j,3,i) + enddo + endif + endif + enddo +#endif +#if defined(MPI) && defined(PARINTDER) + if (nfgtasks.gt.1) then +#ifdef DEBUG + write (iout,*) "Gather dtheta" +cd call flush(iout) +c write (iout,*) "dtheta before gather" +c do i=1,nres +c write (iout,'(i3,3(3f8.5,3x))') i,((dtheta(j,k,i),k=1,3),j=1,2) +c enddo +#endif + call MPI_Gatherv(dtheta(1,1,ithet_start),ithet_count(fg_rank), + & MPI_THET,dtheta(1,1,1),ithet_count(0),ithet_displ(0),MPI_THET, + & king,FG_COMM,IERROR) +#ifdef DEBUG +cd write (iout,*) "Gather dphi" +cd call flush(iout) + write (iout,*) "dphi before gather" + do i=1,nres + write (iout,'(i3,3(3f8.5,3x))') i,((dphi(j,k,i),k=1,3),j=1,3) + enddo +#endif + call MPI_Gatherv(dphi(1,1,iphi1_start),iphi1_count(fg_rank), + & MPI_GAM,dphi(1,1,1),iphi1_count(0),iphi1_displ(0),MPI_GAM, + & king,FG_COMM,IERROR) +cd write (iout,*) "Gather dalpha" +cd call flush(iout) +#ifdef CRYST_SC + call MPI_Gatherv(dalpha(1,1,ibond_start),ibond_count(fg_rank), + & MPI_GAM,dalpha(1,1,1),ibond_count(0),ibond_displ(0),MPI_GAM, + & king,FG_COMM,IERROR) +cd write (iout,*) "Gather domega" +cd call flush(iout) + call MPI_Gatherv(domega(1,1,ibond_start),ibond_count(fg_rank), + & MPI_GAM,domega(1,1,1),ibond_count(0),ibond_displ(0),MPI_GAM, + & king,FG_COMM,IERROR) +#endif + endif +#endif +#ifdef DEBUG + write (iout,*) "dtheta after gather" + do i=1,nres + write (iout,'(i3,3(3f8.5,3x))') i,((dtheta(j,k,i),j=1,3),j=1,2) + enddo + write (iout,*) "dphi after gather" + do i=1,nres + write (iout,'(i3,3(3f8.5,3x))') i,((dphi(j,k,i),j=1,3),k=1,3) + enddo +#endif + return + end + + subroutine checkintcartgrad + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' +#ifdef MPI + include 'mpif.h' +#endif + include 'COMMON.CHAIN' + include 'COMMON.VAR' + include 'COMMON.GEO' + include 'COMMON.INTERACT' + include 'COMMON.DERIV' + include 'COMMON.IOUNITS' + include 'COMMON.SETUP' + double precision dthetanum(3,2,maxres),dphinum(3,3,maxres) + & ,dalphanum(3,3,maxres), domeganum(3,3,maxres) + double precision theta_s(maxres),phi_s(maxres),alph_s(maxres), + & omeg_s(maxres),dc_norm_s(3) + double precision aincr /1.0d-5/ + + do i=1,nres + phi_s(i)=phi(i) + theta_s(i)=theta(i) + alph_s(i)=alph(i) + omeg_s(i)=omeg(i) + enddo +c Check theta gradient + write (iout,*) + & "Analytical (upper) and numerical (lower) gradient of theta" + write (iout,*) + do i=3,nres + do j=1,3 + dcji=dc(j,i-2) + dc(j,i-2)=dcji+aincr + call chainbuild_cart + call int_from_cart1(.false.) + dthetanum(j,1,i)=(theta(i)-theta_s(i))/aincr + dc(j,i-2)=dcji + dcji=dc(j,i-1) + dc(j,i-1)=dc(j,i-1)+aincr + call chainbuild_cart + dthetanum(j,2,i)=(theta(i)-theta_s(i))/aincr + dc(j,i-1)=dcji + enddo + write (iout,'(i5,3f10.5,5x,3f10.5)') i,(dtheta(j,1,i),j=1,3), + & (dtheta(j,2,i),j=1,3) + write (iout,'(5x,3f10.5,5x,3f10.5)') (dthetanum(j,1,i),j=1,3), + & (dthetanum(j,2,i),j=1,3) + write (iout,'(5x,3f10.5,5x,3f10.5)') + & (dthetanum(j,1,i)/dtheta(j,1,i),j=1,3), + & (dthetanum(j,2,i)/dtheta(j,2,i),j=1,3) + write (iout,*) + enddo +c Check gamma gradient + write (iout,*) + & "Analytical (upper) and numerical (lower) gradient of gamma" + do i=4,nres + do j=1,3 + dcji=dc(j,i-3) + dc(j,i-3)=dcji+aincr + call chainbuild_cart + dphinum(j,1,i)=(phi(i)-phi_s(i))/aincr + dc(j,i-3)=dcji + dcji=dc(j,i-2) + dc(j,i-2)=dcji+aincr + call chainbuild_cart + dphinum(j,2,i)=(phi(i)-phi_s(i))/aincr + dc(j,i-2)=dcji + dcji=dc(j,i-1) + dc(j,i-1)=dc(j,i-1)+aincr + call chainbuild_cart + dphinum(j,3,i)=(phi(i)-phi_s(i))/aincr + dc(j,i-1)=dcji + enddo + write (iout,'(i5,3(3f10.5,5x))') i,(dphi(j,1,i),j=1,3), + & (dphi(j,2,i),j=1,3),(dphi(j,3,i),j=1,3) + write (iout,'(5x,3(3f10.5,5x))') (dphinum(j,1,i),j=1,3), + & (dphinum(j,2,i),j=1,3),(dphinum(j,3,i),j=1,3) + write (iout,'(5x,3(3f10.5,5x))') + & (dphinum(j,1,i)/dphi(j,1,i),j=1,3), + & (dphinum(j,2,i)/dphi(j,2,i),j=1,3), + & (dphinum(j,3,i)/dphi(j,3,i),j=1,3) + write (iout,*) + enddo +c Check alpha gradient + write (iout,*) + & "Analytical (upper) and numerical (lower) gradient of alpha" + do i=2,nres-1 + if(itype(i).ne.10) then + do j=1,3 + dcji=dc(j,i-1) + dc(j,i-1)=dcji+aincr + call chainbuild_cart + dalphanum(j,1,i)=(alph(i)-alph_s(i)) + & /aincr + dc(j,i-1)=dcji + dcji=dc(j,i) + dc(j,i)=dcji+aincr + call chainbuild_cart + dalphanum(j,2,i)=(alph(i)-alph_s(i)) + & /aincr + dc(j,i)=dcji + dcji=dc(j,i+nres) + dc(j,i+nres)=dc(j,i+nres)+aincr + call chainbuild_cart + dalphanum(j,3,i)=(alph(i)-alph_s(i)) + & /aincr + dc(j,i+nres)=dcji + enddo + endif + write (iout,'(i5,3(3f10.5,5x))') i,(dalpha(j,1,i),j=1,3), + & (dalpha(j,2,i),j=1,3),(dalpha(j,3,i),j=1,3) + write (iout,'(5x,3(3f10.5,5x))') (dalphanum(j,1,i),j=1,3), + & (dalphanum(j,2,i),j=1,3),(dalphanum(j,3,i),j=1,3) + write (iout,'(5x,3(3f10.5,5x))') + & (dalphanum(j,1,i)/dalpha(j,1,i),j=1,3), + & (dalphanum(j,2,i)/dalpha(j,2,i),j=1,3), + & (dalphanum(j,3,i)/dalpha(j,3,i),j=1,3) + write (iout,*) + enddo +c Check omega gradient + write (iout,*) + & "Analytical (upper) and numerical (lower) gradient of omega" + do i=2,nres-1 + if(itype(i).ne.10) then + do j=1,3 + dcji=dc(j,i-1) + dc(j,i-1)=dcji+aincr + call chainbuild_cart + domeganum(j,1,i)=(omeg(i)-omeg_s(i)) + & /aincr + dc(j,i-1)=dcji + dcji=dc(j,i) + dc(j,i)=dcji+aincr + call chainbuild_cart + domeganum(j,2,i)=(omeg(i)-omeg_s(i)) + & /aincr + dc(j,i)=dcji + dcji=dc(j,i+nres) + dc(j,i+nres)=dc(j,i+nres)+aincr + call chainbuild_cart + domeganum(j,3,i)=(omeg(i)-omeg_s(i)) + & /aincr + dc(j,i+nres)=dcji + enddo + endif + write (iout,'(i5,3(3f10.5,5x))') i,(domega(j,1,i),j=1,3), + & (domega(j,2,i),j=1,3),(domega(j,3,i),j=1,3) + write (iout,'(5x,3(3f10.5,5x))') (domeganum(j,1,i),j=1,3), + & (domeganum(j,2,i),j=1,3),(domeganum(j,3,i),j=1,3) + write (iout,'(5x,3(3f10.5,5x))') + & (domeganum(j,1,i)/domega(j,1,i),j=1,3), + & (domeganum(j,2,i)/domega(j,2,i),j=1,3), + & (domeganum(j,3,i)/domega(j,3,i),j=1,3) + write (iout,*) + enddo + return + end + + subroutine chainbuild_cart + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' +#ifdef MPI + include 'mpif.h' +#endif + include 'COMMON.SETUP' + include 'COMMON.CHAIN' + include 'COMMON.LOCAL' + include 'COMMON.TIME1' + include 'COMMON.IOUNITS' + +#ifdef MPI + if (nfgtasks.gt.1) then +c write (iout,*) "BCAST in chainbuild_cart" +c call flush(iout) +c Broadcast the order to build the chain and compute internal coordinates +c to the slaves. The slaves receive the order in ERGASTULUM. + time00=MPI_Wtime() +c write (iout,*) "CHAINBUILD_CART: DC before BCAST" +c do i=0,nres +c write (iout,'(i3,3f10.5,5x,3f10.5)') i,(dc(j,i),j=1,3), +c & (dc(j,i+nres),j=1,3) +c enddo + if (fg_rank.eq.0) + & call MPI_Bcast(7,1,MPI_INTEGER,king,FG_COMM,IERROR) + time_bcast7=time_bcast7+MPI_Wtime()-time00 + time01=MPI_Wtime() + call MPI_Bcast(dc(1,0),6*(nres+1),MPI_DOUBLE_PRECISION, + & king,FG_COMM,IERR) +c write (iout,*) "CHAINBUILD_CART: DC after BCAST" +c do i=0,nres +c write (iout,'(i3,3f10.5,5x,3f10.5)') i,(dc(j,i),j=1,3), +c & (dc(j,i+nres),j=1,3) +c enddo +c write (iout,*) "End BCAST in chainbuild_cart" +c call flush(iout) + time_bcast=time_bcast+MPI_Wtime()-time00 + time_bcastc=time_bcastc+MPI_Wtime()-time01 + endif +#endif + do j=1,3 + c(j,1)=dc(j,0) + enddo + do i=2,nres + do j=1,3 + c(j,i)=c(j,i-1)+dc(j,i-1) + enddo + enddo + do i=1,nres + do j=1,3 + c(j,i+nres)=c(j,i)+dc(j,i+nres) + enddo + enddo +c write (iout,*) "CHAINBUILD_CART" +c call cartprint + call int_from_cart1(.false.) + return + end