| 1 | ! **************************************************************
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| 2 | !
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| 3 | ! This file contains the subroutines: enyshe
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| 4 | !
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| 5 | ! Copyright 2003-2005 Frank Eisenmenger, U.H.E. Hansmann,
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| 6 | ! Shura Hayryan, Chin-Ku
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| 7 | ! Copyright 2007 Frank Eisenmenger, U.H.E. Hansmann,
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| 8 | ! Jan H. Meinke, Sandipan Mohanty
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| 9 | !
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| 10 | ! **************************************************************
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| 11 |
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| 12 |
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| 13 | real*8 function enyshe(nml)
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| 14 |
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| 15 | !> PURPOSE: Calculate internal energy of molecule 'nml' with ECEPP parameters
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| 16 | !!
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| 17 | !! CALLS: none
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| 18 | !!
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| 19 | !! The function loops over all moving sets within the molecule. Within
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| 20 | !! this loop it loops over the van-der-Waals domains of each atom in the
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| 21 | !! moving set and finally over the atoms that belong to the 1-4 interaction
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| 22 | !! set.
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| 23 | !< ............................................................................
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| 24 |
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| 25 | include 'INCL.H'
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| 26 | include 'mpif.h'
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| 27 | ! include 'VT.inc'
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| 28 |
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| 29 |
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| 30 | ! If nml == 0 calculate the interaction between all pairs.
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| 31 | double precision eysmsum, teysm, teyel, teyvw, teyhb, teyvr
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| 32 | double precision startwtime, e0, vr, cqi, xi, yi, zi, xij, yij
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| 33 | double precision zij, rij2, rij4, rij6, rij, sr, ep, endwtime
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| 34 |
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| 35 | integer nml, ntlvr, ifivr, i1s, iend, istart, loopcounter, io, iv
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| 36 | integer ia, it, ic, i2s, ims, i1, i2, i, ity, ivw, j, jty, i14
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| 37 | integer ierror
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| 38 |
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| 39 | if (nml.eq.0) then
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| 40 | ntlvr = nvr
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| 41 | else
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| 42 | ntlvr=nvrml(nml)
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| 43 | endif
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| 44 |
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| 45 | if (ntlvr.eq.0) then
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| 46 | write (logString, '(a,i4)')
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| 47 | & ' enyshe> No variables defined in molecule #',nml
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| 48 | return
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| 49 | endif
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| 50 |
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| 51 | ! call mpi_comm_size(my_mpi_comm,no,ierr)
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| 52 |
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| 53 | eysmsum = 0.0
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| 54 | enyshe=0.0
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| 55 | teysm = 0.0
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| 56 | teyel=0.0
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| 57 | teyvw=0.0
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| 58 | teyhb=0.0
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| 59 | teyvr=0.0
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| 60 |
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| 61 | if (nml.eq.0) then
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| 62 | ifivr = ivrml1(1)
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| 63 | i1s = imsml1(ntlml) + nmsml(ntlml)
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| 64 | else
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| 65 | ! Index of first variable in molecule.
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| 66 | ifivr=ivrml1(nml)
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| 67 | ! Index of last moving set in molecule
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| 68 | i1s=imsml1(nml)+nmsml(nml)
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| 69 | endif
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| 70 | ! Loop over variables in reverse order
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| 71 | ! This is the first loop to parallize. We'll just split the moving sets
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| 72 | ! over the number of available processors and sum the energy up in the end.
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| 73 |
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| 74 | ! Number of moving sets per processor
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| 75 | iend = ifivr
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| 76 | istart = ifivr + ntlvr - 1
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| 77 |
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| 78 | startwtime = MPI_Wtime()
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| 79 | loopcounter = 0
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| 80 | ! do io=ifivr+ntlvr-1,ifivr,-1
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| 81 | do io = workPerProcessor(nml, myrank) - 1,
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| 82 | & workPerProcessor(nml, myrank+1), -1
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| 83 | if (io.lt.istart) then
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| 84 | i1s = imsvr1(iorvr(io + 1))
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| 85 | endif
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| 86 | ! The array iorvr contains the variables in an "apropriate" order.
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| 87 | iv=iorvr(io)
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| 88 | ! Index of the primary moving atom for the variable with index iv
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| 89 | ia=iatvr(iv)
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| 90 | ! Get the type of variable iv (valence length, valence angle, dihedral angle)
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| 91 | it=ityvr(iv)
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| 92 | ! Class of variable iv's potential (Q: What are they)
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| 93 | ic=iclvr(iv)
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| 94 | ! If iv is a dihedral angle ...
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| 95 | if (it.eq.3) then
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| 96 | ! Barrier height * 1/2 of the potential of iv.
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| 97 | e0=e0to(ic)
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| 98 | ! Calculate the periodic potential term. sgto is the sign of the barrier, rnto is
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| 99 | ! the periodicity and toat is torsion angle(?) associate with atom ia.
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| 100 | if (e0.ne.0.)
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| 101 | & teyvr=teyvr+e0*(1.0+sgto(ic)*cos(toat(ia)*rnto(ic)))
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| 102 | ! else if iv is a valence angle ...
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| 103 | elseif (it.eq.2) then
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| 104 | ! vr is the valence angle of ia
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| 105 | vr=baat(ia)
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| 106 | ! else if iv is a valence length...
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| 107 | elseif (it.eq.1) then
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| 108 | ! vr is the length of the valence bond
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| 109 | vr=blat(ia)
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| 110 | endif
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| 111 |
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| 112 | ! ============================================ Energies & Atomic forces
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| 113 | ! index of next to last moving set
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| 114 | i2s=i1s-1
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| 115 | ! index of first moving set associated with iv
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| 116 | i1s=imsvr1(iv)
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| 117 | ! Loop over all moving sets starting from the one associated with vr to the end.
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| 118 | do ims=i1s,i2s
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| 119 | ! First atom of the current moving set
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| 120 | i1=latms1(ims)
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| 121 | ! Last atom of the current moving set
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| 122 | i2=latms2(ims)
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| 123 | ! Loop over all atoms of the current moving set.
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| 124 | do i=i1,i2
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| 125 | ! Atom class of current atom
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| 126 | ity=ityat(i)
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| 127 | ! Point charge at current atom
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| 128 | cqi=conv*cgat(i)
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| 129 | ! Cartesian coordinates of current atom
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| 130 | xi=xat(i)
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| 131 | yi=yat(i)
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| 132 | zi=zat(i)
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| 133 | ! Loop over the atoms of the van der Waals domain belonging to atom i
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| 134 | do ivw=ivwat1(i),ivwat2(i)
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| 135 | ! Loop over the atoms of the van der Waals domain of the atoms of the
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| 136 | ! van der Waals domain of atom i
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| 137 | ! Q: Which atoms are in these domains?
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| 138 | do j=lvwat1(ivw),lvwat2(ivw)
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| 139 |
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| 140 | loopcounter = loopcounter + 1
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| 141 | ! Atom type of partner
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| 142 | jty=ityat(j)
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| 143 | ! Differences in cartesian coordinates
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| 144 | xij=xat(j)-xi
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| 145 | yij=yat(j)-yi
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| 146 | zij=zat(j)-zi
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| 147 | ! Cartesian distance and higher powers
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| 148 | rij2=xij*xij+yij*yij+zij*zij
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| 149 | rij4=rij2*rij2
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| 150 | rij6=rij4*rij2
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| 151 | rij=sqrt(rij2)
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| 152 | ! Are we using a distance dependent dielectric constant?
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| 153 | if(epsd) then
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| 154 | sr=slp*rij
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| 155 | ep=plt-(sr*sr+2.0*sr+2.0)*(plt-1.0)*exp(-sr)/2.0
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| 156 | else
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| 157 | ep = 1.0d0
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| 158 | end if
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| 159 | ! Coulomb interaction
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| 160 | teyel=teyel+cqi*cgat(j)/(rij*ep)
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| 161 | ! If the two atoms cannot form a hydrogen bond use 6-12 Lennard-Jones potential
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| 162 | if (ihbty(ity,jty).eq.0) then
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| 163 | teyvw=teyvw+aij(ity,jty)/(rij6*rij6)
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| 164 | & -cij(ity,jty)/rij6
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| 165 | else
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| 166 | ! For hydrogen bonding use 10-12 Lennard-Jones potential
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| 167 | teyhb=teyhb+ahb(ity,jty)/(rij6*rij6)
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| 168 | & -chb(ity,jty)/(rij6*rij4)
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| 169 | endif
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| 170 |
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| 171 | enddo
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| 172 | enddo
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| 173 |
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| 174 | ! Loop over 1-4 interaction partners
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| 175 | ! The interactions between atoms that are three bonds apart in the protein are
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| 176 | ! dominated by quantum mechanical effects. They are treated separately.
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| 177 | do i14=i14at1(i),i14at2(i)
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| 178 | loopcounter = loopcounter + 1
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| 179 | j=l14at(i14)
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| 180 |
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| 181 | jty=ityat(j)
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| 182 |
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| 183 | xij=xat(j)-xi
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| 184 | yij=yat(j)-yi
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| 185 | zij=zat(j)-zi
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| 186 | rij2=xij*xij+yij*yij+zij*zij
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| 187 | rij4=rij2*rij2
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| 188 | rij6=rij4*rij2
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| 189 | rij = sqrt(rij2)
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| 190 | ! Are we using a distance dependent dielectric constant?
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| 191 | if(epsd) then
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| 192 | sr=slp*rij
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| 193 | ep=plt-(sr*sr+2.0*sr+2.0)*(plt-1.0)*exp(-sr)/2.0
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| 194 | else
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| 195 | ep=1.0d0
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| 196 | end if
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| 197 |
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| 198 | teyel=teyel+cqi*cgat(j)/(rij*ep)
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| 199 | ! If hydrogen bonding is not possible use 6-12 Lennard-Jones potential.
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| 200 | if (ihbty(ity,jty).eq.0) then
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| 201 | teyvw=teyvw+a14(ity,jty)/(rij6*rij6)
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| 202 | & -cij(ity,jty)/rij6
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| 203 | else
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| 204 | ! Use 10-12 Lennard-Jones potential for hydrogen bonds.
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| 205 | teyhb=teyhb+ahb(ity,jty)/(rij6*rij6)
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| 206 | & -chb(ity,jty)/(rij6*rij4)
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| 207 | endif
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| 208 | enddo ! ... 1-4-partners of i
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| 209 | enddo ! ... atoms i
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| 210 | enddo ! ... m.s.
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| 211 | enddo ! ... variables
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| 212 |
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| 213 | teysm = teyel + teyvw + teyhb + teyvr
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| 214 |
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| 215 | endwtime = MPI_Wtime()
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| 216 |
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| 217 | ! Collect energies from all nodes and sum them up
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| 218 | call MPI_ALLREDUCE(teysm, eysmsum, 1, MPI_DOUBLE_PRECISION,
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| 219 | & MPI_SUM, my_mpi_comm, ierror)
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| 220 | call MPI_ALLREDUCE(teyel, eyel, 1, MPI_DOUBLE_PRECISION, MPI_SUM,
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| 221 | & my_mpi_comm, ierror)
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| 222 | call MPI_ALLREDUCE(teyvw, eyvw, 1, MPI_DOUBLE_PRECISION, MPI_SUM,
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| 223 | & my_mpi_comm, ierror)
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| 224 | call MPI_ALLREDUCE(teyhb, eyhb, 1, MPI_DOUBLE_PRECISION, MPI_SUM,
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| 225 | & my_mpi_comm, ierror)
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| 226 | call MPI_ALLREDUCE(teyvr, eyvr, 1, MPI_DOUBLE_PRECISION, MPI_SUM,
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| 227 | & my_mpi_comm, ierror)
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| 228 |
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| 229 | enyshe=eysmsum
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| 230 | ! call VTEnd(101, ierr)
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| 231 | return
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| 232 | end
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| 233 |
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