Changeset 38d77eb
- Timestamp:
- 11/19/09 11:29:48 (14 years ago)
- Branches:
- master
- Children:
- 7137e5d
- Parents:
- 32289cd
- Files:
-
- 49 edited
Legend:
- Unmodified
- Added
- Removed
-
INCL.H
r32289cd r38d77eb 2 2 3 3 character*255 version 4 character*255 logString 4 5 5 6 integer MAX_REPLICA, MAX_PROC, mxml, mxrs, mxat, mxbd, mxath -
INCP.H
r32289cd r38d77eb 44 44 ! ir=0 45 45 ! do i=1,nchp 46 ! write (*,*) ' ===== chain |',chnp(i),'|'46 ! write (logString, *) ' ===== chain |',chnp(i),'|' 47 47 ! do j=1,nchrsp(i) 48 48 ! ir=ir+1 49 ! write (*,*) ' ----- ',rsidp(ir),' ',rsnmp(ir),' ',nrsatp(ir)49 ! write (logString, *) ' ----- ',rsidp(ir),' ',rsnmp(ir),' ',nrsatp(ir) 50 50 ! k1=irsatp(ir) 51 51 ! k2=k1+nrsatp(ir)-1 52 52 ! do k=k1,k2 53 ! write (*,*) ' ',noatp(k),' ',atnmp(k),' ',(xyzp(l,k),l=1,3)53 ! write (logString, *) ' ',noatp(k),' ',atnmp(k),' ',(xyzp(l,k),l=1,3) 54 54 ! enddo 55 55 ! enddo -
addend.f
r32289cd r38d77eb 42 42 &.or.grn(:3).eq.'nme'.or.grc(:3).eq.'nme') then 43 43 44 write(*,'(2a)') ' addend> N-Acetyl (ace) or N-Methylamide (nme)' 45 & ,' should be put in SEQUENCE file, not added as end groups' 44 write (logString, '(2a)') 45 & ' addend> N-Acetyl (ace) or N-Methylamide (nme)', 46 & ' should be put in SEQUENCE file, not added as end groups' 46 47 47 48 stop … … 59 60 sbrs='nh2+' 60 61 else 61 write ( *,'(2a)') ' addend> ',62 write (logString, '(2a)') ' addend> ', 62 63 & ' No N-terminal Hyp possible with ECEPP/3 dataset' 63 64 stop … … 87 88 else 88 89 89 write (*,'(2a)') ' addend> Can add only ',90 write (logString, '(2a)') ' addend> Can add only ', 90 91 & 'nh2 or nh3+ to N-terminus' 91 92 stop … … 98 99 else ! ace 99 100 100 write (*,'(2a)') ' addend> Acetyl group',101 write (logString, '(2a)') ' addend> Acetyl group', 101 102 & ' at N-terminus not modified' 102 103 endif … … 128 129 else 129 130 130 write (*,'(2a)') ' addend> Can add only ',131 write (logString, '(2a)') ' addend> Can add only ', 131 132 & 'cooh or coo- to C-terminus' 132 133 stop … … 139 140 else ! N'-methylamide 140 141 141 write (*,'(2a)') ' addend> N-Methylamide',142 write (logString, '(2a)') ' addend> N-Methylamide', 142 143 & ' at C-terminus not modified' 143 144 … … 149 150 cg = cg + cgat(i) 150 151 enddo 151 if (abs(cg).gt.1.d-5) write(*,'(a,i2,a,f7.3,/)') 152 & ' addend> Net charge of molecule #' 152 if (abs(cg).gt.1.d-5) then 153 write (logString, '(a,i2,a,f7.3)') 154 & ' addend> Net charge of molecule #' 153 155 & ,nml,': ',cg 156 endif 154 157 155 158 return … … 204 207 endif 205 208 enddo 206 write (*,'(4a,i4,a,i4)') ' rplgrp> cannot find atom >',rpat, 207 &'< to be replaced in residue ',seq(nrs),nrs,' of molecule ',nml 209 write (logString, '(4a,i4,a,i4)') ' rplgrp> cannot find atom >', 210 & rpat, 211 & '< to be replaced in residue ',seq(nrs),nrs,' of molecule ',nml 208 212 stop 209 213 … … 234 238 if (iowat(ibd(i)).ne.nfirp) then 235 239 if (ibdrg.ne.0) then 236 write ( *,'(2a,i3)')240 write (logString, '(2a,i3)') 237 241 & ' rplgrp> Can handle only simple ring at 1st', 238 242 & ' atom of molecule #',nml … … 261 265 goto 11 262 266 else 263 write ( *,'(4a,i4,a,i4)')267 write (logString, '(4a,i4,a,i4)') 264 268 & ' rplgrp> Cannot replace BACKBONE atom ',rpat, 265 269 & ' of residue ',seq(nrs),nrs,' in molecule #',nml … … 275 279 ! _______________________________ get data for substituent atoms 276 280 3 if (iopfil(lunlib,reslib,'old','formatted').le.izero) then 277 write ( *,'(a,/,a,i3,2a)')281 write (logString, '(a,/,a,i3,2a)') 278 282 & ' rplgrp> ERROR opening library of residues:', 279 283 & ' LUN=',lunlib,' FILE=',reslib(1:iendst(reslib)) … … 289 293 endif 290 294 enddo 291 write ( *,'(4a)') ' rplgrp> Cannot find atom >',rpat,295 write (logString, '(4a)') ' rplgrp> Cannot find atom >',rpat, 292 296 &'< in substituent residue ',sbrs 293 297 stop … … 372 376 else ! more atoms 373 377 if ((ilaat+nsh).gt.mxat) then 374 write (*,'(a,i5)') ' rplgrp> number of atoms > ',mxat 378 write (logString, '(a,i5)') ' rplgrp> number of atoms > ', 379 & mxat 375 380 stop 376 381 endif … … 466 471 nb=nb+1 467 472 if (nb.gt.mxbd) then 468 write ( *,'(6a,/,2a,3(i4,a))')473 write (logString, '(6a,/,2a,3(i4,a))') 469 474 & ' rplgrp> Cannot add atoms following ',rpat, 470 475 & ' from group ',sbrs,' to atom ',rpat, … … 593 598 else 594 599 if ((ilavr+jsh).gt.mxvr) then 595 write (*,'(a,i5)') ' rplgrp> number of variables > ',mxvr 600 write (logString, '(a,i5)') 601 & ' rplgrp> number of variables > ',mxvr 596 602 stop 597 603 endif … … 628 634 return 629 635 ! __________________________________________ Errors 630 10 write ( *,'(3a,/,2a,i4,a,i4,/,2a)')636 10 write (logString, '(3a,/,2a,i4,a,i4,/,2a)') 631 637 & ' rplgrp> Cannot replace atom(s) following ',rpat, 632 638 & ' from INSIDE a ring',' in residue: ',seq(nrs),nrs, 633 639 & ' in molecule #',nml,' or in substitute: ',sbrs 634 640 stop 635 11 write ( *,'(4a,i4,a,i4,/,a)')641 11 write (logString, '(4a,i4,a,i4,/,a)') 636 642 & ' rplgrp> Cannot replace atom(s) following ',rpat, 637 643 & ' of residue ',seq(nrs),nrs,' in molecule #',nml, … … 686 692 endif 687 693 else 688 write (*,*) ' redchg> dont know which end goup is present' 694 write(logString,*) 695 & ' redchg> dont know which end goup is present' 689 696 stop 690 697 endif … … 698 705 699 706 if (iopfil(lunchg,chgfil,'old','formatted').le.izero) then 700 write ( *,'(a,/,a,i3,2a)')707 write (logString, '(a,/,a,i3,2a)') 701 708 & ' redchg> ERROR opening library of charges:', 702 709 & ' LUN=',lunchg,' FILE=',chgfil(1:iendst(chgfil)) … … 722 729 endif 723 730 enddo 724 write (*,'(6a)') ' redchg> Cannot find atom: ',atnm, 731 write (logString, '(6a)') ' redchg> Cannot find atom: ', 732 & atnm, 725 733 & ' for entry: ',cgty,' in library: ', 726 734 & chgfil(1:iendst(chgfil)) … … 729 737 return 730 738 else 731 write ( *,'(4a)')739 write (logString, '(4a)') 732 740 & ' redchg> must increase MXATH to read data for entry: ', 733 741 & cgty,' in library: ',chgfil(1:iendst(chgfil)) … … 737 745 endif 738 746 goto 1 739 3 write ( *,'(4a)')747 3 write (logString, '(4a)') 740 748 & ' redchg> Cannot find entry: ',cgty,' in library: ', 741 749 & chgfil(1:iendst(chgfil)) … … 746 754 747 755 if (iopfil(lunlib,reslib,'old','formatted').le.izero) then 748 write ( *,'(a,/,a,i3,2a)')756 write (logString, '(a,/,a,i3,2a)') 749 757 & ' redchg> ERROR opening library of residues:', 750 758 & ' LUN=',lunlib,' FILE=',reslib(1:iendst(reslib)) … … 769 777 endif 770 778 enddo 771 write (*,'(6a)') ' redchg> Cannot find atom: ',atnm, 779 write (logString, '(6a)') ' redchg> Cannot find atom: ', 780 & atnm, 772 781 & ' for entry: ',cgty,' in library: ', 773 782 & reslib(1:iendst(reslib)) … … 776 785 return 777 786 else 778 write ( *,'(4a)')787 write (logString, '(4a)') 779 788 & ' redchg> must increase MXATH to read data for entry: ', 780 789 & cgty,' in library: ',reslib(1:iendst(reslib)) … … 784 793 endif 785 794 goto 4 786 6 write ( *,'(4a)')795 6 write (logString, '(4a)') 787 796 & ' redchg> Cannot find entry: ',cgty,' in library: ', 788 797 & reslib(1:iendst(reslib)) … … 792 801 endif 793 802 794 10 write ( *,'(4a)')803 10 write (logString, '(4a)') 795 804 & ' redchg> Do not have charges for N/C-terminal residue ', 796 805 & res,' modified with group :',sbrs -
anneal.f
r32289cd r38d77eb 84 84 85 85 eol=energy() 86 write (*,'(a,e12.5,/)') 'energy of start configuration: ',eol 86 write (logString, '(a,e12.5,/)') 87 & 'energy of start configuration: ',eol 87 88 88 89 ! Write start configuration in pdb-format into file … … 94 95 call metropolis(eol,acz,can_weight) 95 96 end do 96 write(*,*) 'Energy after equilibration:',eol 97 write (logString, *) 98 & 'Energy after equilibration:', eol 97 99 98 100 !======================Simulation by simulated annealing … … 131 133 132 134 acz = acz/dble(nsw*nvr) 133 write (*,*) 'acceptance rate:',acz134 write (*,*)135 write (logString, *) 'acceptance rate:',acz 136 write (logString, *) 135 137 ! ------------ Output Dihedreals of final configuration 136 write (*,*) 'last energy',eol138 write (logString, *) 'last energy',eol 137 139 call outvar(0,' ') 138 140 ! Output final conformation as pdb-file 139 141 call outpdb(0,"final.pdb") 140 write (*,*)142 write (logString, *) 141 143 142 144 ! ------------ Output Dihedreals of conformation with lowest energy 143 write (*,*) 'lowest energy ever found:',nemin,ymin145 write (logString, *) 'lowest energy ever found:',nemin,ymin 144 146 close(14) 145 147 ! ===================== -
bgs.f
r32289cd r38d77eb 327 327 ! enw=energy() 328 328 ! if (abs(enw-eol1).gt.0.000001) then 329 ! write (*,*) 'rejected bgs move: energy change :',eol1,enw329 ! write (logString, *) 'rejected bgs move: energy change :',eol1,enw 330 330 ! endif 331 ! write (*,*) 'rejected bgs move: ',eol1,enw,wfw,wbw,rd331 ! write (logString, *) 'rejected bgs move: ',eol1,enw,wfw,wbw,rd 332 332 bgs=0 333 333 endif -
bldmol.f
r32289cd r38d77eb 134 134 135 135 if (ix.ne.0) then 136 write ( *,'(2a,i3)')136 write (logString, '(2a,i3)') 137 137 & ' fnd3ba> Can handle only simple ring at 1st', 138 138 & ' atom of molecule #',nml … … 166 166 endif 167 167 168 write ( *,'(4a,i4,a,i4)')168 write (logString, '(4a,i4,a,i4)') 169 169 & ' fnd3ba> Cannot find backbone atom following ',nmat(i2), 170 170 & ' of residue ',seq(irs),irs,' in molecule #',nml -
canon.f
r32289cd r38d77eb 69 69 eol = energy() 70 70 e_min = eol 71 write ( *,'(a,e12.5,/)') 'energy of start configuration:',eol71 write (logString, '(a,e12.5,/)') 'energy of start configuration:',eol 72 72 73 73 ! Write start configuration in pdb-format into file … … 79 79 call metropolis(eol,acz,can_weight) 80 80 end do 81 write (*,*) 'Energy after equilibration:',eol81 write (logString, *) 'Energy after equilibration:',eol 82 82 83 83 !======================Simulation in canonical ensemble … … 86 86 call metropolis(eol,acz,can_weight) 87 87 if (eol.lt.e_min) then 88 write ( *,*) "New minimum energy:", eol, "t=", nsw89 write ( *,*) eyel,eyhb,eyvr,eysl88 write (logString, *) "New minimum energy:", eol, "t=", nsw 89 write (logString, *) eyel,eyhb,eyvr,eysl 90 90 e_min = eol 91 91 call outpdb(0, "minen.pdb") … … 116 116 117 117 acz = acz/dble(nsw*nvr) 118 write (*,*) 'acceptance rate:',acz119 write (*,*)118 write (logString, *) 'acceptance rate:',acz 119 write (logString, *) 120 120 ! ------------ Output Dihedreals of final configuration 121 write (*,*) 'last energy',eol121 write (logString, *) 'last energy',eol 122 122 call outvar(0,'lastconf.var') 123 123 ! Output final conformation as pdb-file -
cnteny.f
r32289cd r38d77eb 37 37 38 38 if (ntlvr.eq.0) then 39 write ( *,'(a,i4)')39 write (logString, '(a,i4)') 40 40 & ' cnteny> No variables defined in molecule #',nml 41 41 return … … 184 184 nbc=nbc+1 185 185 ir=nursat(i) 186 write (*,'(1x,i4,1x,a4,1x,a4,a2,e11.4)') ir,seq(ir),nmat(i),187 & 186 write (logString, '(1x,i4,1x,a4,1x,a4,a2,e11.4)') ir,seq(ir), 187 & nmat(i), ': ',ey 188 188 endif 189 189 enddo -
contacts.f
r32289cd r38d77eb 161 161 do nr_j=nr_i+3,irsml2(nmol) ! Over res. j 162 162 163 ! write (*,'(2i3)'),nr_i,nr_j163 ! write (logString, '(2i3)'),nr_i,nr_j 164 164 165 165 ic=0 … … 173 173 if(sqrt(rij2).lt.rcut) ic=1 174 174 175 ! write (*,'(2i3)'),nr_i,nr_j175 ! write (logString, '(2i3)'),nr_i,nr_j 176 176 177 177 ijcont(nr_i,nr_j)=ic -
dihedr.f
r32289cd r38d77eb 57 57 return 58 58 else 59 write (*,'(a,4i5)')' dihedr> Error in coordinates of atoms #: ' 59 write (logString, '(a,4i5)') 60 & ' dihedr> Error in coordinates of atoms #: ' 60 61 & ,i1,i2,i3,i4 61 62 62 write ( *,*) 'stored coordinates are xvals :',63 write (logString, *) 'stored coordinates are xvals :', 63 64 & xat(i1),xat(i2),xat(i3),xat(i4) 64 write ( *,*) 'yvals:', yat(i1),yat(i2),yat(i3),yat(i4)65 write ( *,*) 'zvals:', zat(i1),zat(i2),zat(i3),zat(i4)65 write (logString, *) 'yvals:', yat(i1),yat(i2),yat(i3),yat(i4) 66 write (logString, *) 'zvals:', zat(i1),zat(i2),zat(i3),zat(i4) 66 67 call outvar(0,'crash.var') 67 68 stop … … 110 111 111 112 else 112 write (*,'(a,3i5)')' valang> Error in coordinates of atoms #: ' 113 write (logString, '(a,3i5)') 114 & ' valang> Error in coordinates of atoms #: ' 113 115 & ,i1,i2,i3 114 write ( *,*) 'stored coordinates are xvals :',116 write (logString, *) 'stored coordinates are xvals :', 115 117 & xat(i1),xat(i2),xat(i3) 116 write ( *,*) 'yvals:', yat(i1),yat(i2),yat(i3)117 write ( *,*) 'zvals:', zat(i1),zat(i2),zat(i3)118 write (logString, *) 'yvals:', yat(i1),yat(i2),yat(i3) 119 write (logString, *) 'zvals:', zat(i1),zat(i2),zat(i3) 118 120 call outvar(0,'crash.var') 119 121 stop -
enyflx.f
r32289cd r38d77eb 33 33 ntlvr=nvrml(nml) 34 34 if (ntlvr.eq.0) then 35 write ( *,'(a,i4)')35 write (logString, '(a,i4)') 36 36 & ' enyflx> No variables defined in molecule #',nml 37 37 return -
enyshe.f
r32289cd r38d77eb 41 41 42 42 if (ntlvr.eq.0) then 43 write ( *,'(a,i4)')43 write (logString, '(a,i4)') 44 44 & ' enyshe> No variables defined in molecule #',nml 45 45 return -
enyshe_p.f
r32289cd r38d77eb 46 46 47 47 if (ntlvr.eq.0) then 48 write ( *,'(a,i4)')48 write (logString, '(a,i4)') 49 49 & ' enyshe> No variables defined in molecule #',nml 50 50 return -
enysol.f
r32289cd r38d77eb 30 30 ! functions 31 31 integer nursat 32 32 33 33 34 integer numbox, inbox, indsort, look, i, ii, ia, ib, ibox, icount … … 157 158 numbox(j)=nboxj 158 159 if (nboxj.gt.mxbox) then 159 write(*,'(a)') 'enysol> bad mxboxe-2' 160 write(*,*) 'diagnostics ...' 161 write(*,*) 'atom ',j 162 write(*,*) 'position ',xat(j),yat(j),zat(j) 163 write(*,*) 'box indices ',mx,my,mz 164 write(*,*) 'resulting boxindex and limit ',nboxj,mxbox 160 write (logString, '(a)') 'enysol> bad mxboxe-2' 161 write (logString, *) 'diagnostics ...' 162 write (logString, *) 'atom ',j 163 write (logString, *) 'position ',xat(j),yat(j),zat(j) 164 write (logString, *) 'box indices ',mx,my,mz 165 write (logString, *) 'resulting boxindex and limit ', 166 & nboxj,mxbox 165 167 166 168 stop … … 350 352 351 353 read(lin(1:5),'(i5)') npnt 352 ! write (*,'(a,i5)') 'the number of points---->',npnt354 ! write (logString, '(a,i5)') 'the number of points---->',npnt 353 355 354 356 ! Read the surface points -
enysol_p.f
r32289cd r38d77eb 159 159 numbox(j)=nboxj 160 160 if (nboxj.gt.mxbox) then 161 write(*,'(a)') 'enysol> bad mxboxe-2' 162 write(*,*) 'diagnostics ...' 163 write(*,*) 'atom ',j 164 write(*,*) 'position ',xat(j),yat(j),zat(j) 165 write(*,*) 'box indices ',mx,my,mz 166 write(*,*) 'resulting boxindex and limit ',nboxj,mxbox 161 write (logString, '(a)') 'enysol> bad mxboxe-2' 162 write (logString, *) 'diagnostics ...' 163 write (logString, *) 'atom ',j 164 write (logString, *) 'position ',xat(j),yat(j),zat(j) 165 write (logString, *) 'box indices ',mx,my,mz 166 write (logString, *) 'resulting boxindex and limit ',nboxj, 167 & mxbox 167 168 168 169 stop … … 195 196 if (myrank.eq.(no - 1)) iboxmax = ncbox 196 197 if (myrank.eq.-1) then 197 write ( *,*) 'enysol> Summary:', enysolct, ncbox, boxpp,198 & ndx, ndy, ndz198 write (logString, *) 'enysol> Summary:', enysolct, ncbox, 199 & boxpp, ndx, ndy, ndz 199 200 endif 200 201 do ibox = iboxmin + 1, iboxmax + 1 … … 333 334 call MPI_ALLREDUCE(eysl, eyslsum, 1, MPI_DOUBLE_PRECISION, 334 335 & MPI_SUM,my_mpi_comm, ierror) 335 ! write (*,*) 'enysol>', myrank, eysl, eyslsum336 ! write (logString, *) 'enysol>', myrank, eysl, eyslsum 336 337 tsurfres = surfres 337 338 call MPI_ALLREDUCE(tsurfres, surfres, mxrs, MPI_DOUBLE_PRECISION, … … 341 342 endwtime = MPI_Wtime() 342 343 if (myrank.le.-1) then 343 write ( *,*) 'enysol>',myrank,enysolct,344 write (logString, *) 'enysol>',myrank,enysolct, 344 345 & iboxmin + 1, iboxmax + 1, 345 346 & endwtime - startwtime, "s" … … 376 377 377 378 read(lin(1:5),'(i5)') npnt 378 ! write (*,'(a,i5)') 'the number of points---->',npnt379 ! write (logString, '(a,i5)') 'the number of points---->',npnt 379 380 380 381 ! Read the surface points -
esolan.f
r32289cd r38d77eb 130 130 & +(zold(j)-zold(i))**2! Distance between atom i and j 131 131 if(ddp.lt.1e-10) then 132 write(*,*)'ERROR in data: centres of two atoms coincide!' 133 write(*,*)i,j,xold(i),yold(i),zold(i),rvdw(i), 132 write (logString, *) 133 & 'ERROR in data: centres of two atoms coincide!' 134 write (logString, *)i,j,xold(i),yold(i),zold(i),rvdw(i), 134 135 & xold(j),yold(j),zold(j),rvdw(j) 135 136 stop 'Centres of atoms coincide!' -
getmol.f
r32289cd r38d77eb 49 49 50 50 if (iopfil(lunlib,reslib,'old','formatted').le.izero) then 51 write ( *,'(a,/,a,i3,2a)')51 write (logString, '(a,/,a,i3,2a)') 52 52 & ' getmol> ERROR opening library of residues:', 53 53 & ' LUN=',lunlib,' FILE=',reslib(1:iendst(reslib)) … … 74 74 75 75 if (res(:3).eq.'nme'.and.nrs.ne.ilars) then 76 write ( *,'(3a)') ' getmol> residue >',res,76 write (logString, '(3a)') ' getmol> residue >',res, 77 77 & '< allowed at C-terminus only !' 78 78 close(lunlib) 79 79 stop 80 80 elseif (res(:3).eq.'ace'.and.nrs.ne.ifirs) then 81 write ( *,'(3a)') ' getmol> residue >',res,81 write (logString, '(3a)') ' getmol> residue >',res, 82 82 & '< allowed at N-terminus only !' 83 83 close(lunlib) … … 88 88 89 89 if ((nat+ntlat).gt.mxat) then 90 write ( *,'(a,i5)') ' getmol> number of atoms > ',mxat90 write (logString, '(a,i5)') ' getmol> number of atoms > ',mxat 91 91 close(lunlib) 92 92 stop 93 93 endif 94 94 if ((nvr+ntlvr).gt.mxvr) then 95 write (*,'(a,i5)') ' getmol> number of variables > ',mxvr 95 write (logString, '(a,i5)') ' getmol> number of variables > ' 96 & ,mxvr 96 97 close(lunlib) 97 98 stop … … 139 140 nbd=nbdat(nh) 140 141 if (nbd.eq.mxbd) then 141 write (*,'(a,i2,a,i4,2a,i4,a)')142 write (logString, '(a,i2,a,i4,2a,i4,a)') 142 143 & ' getmol> need ',(mxbd+2), 143 144 & 'th bond to connect residues ', … … 154 155 155 156 if (t.eq.0.0) then 156 write ( *,'(3a,/,2a)')157 write (logString, '(3a,/,2a)') 157 158 & ' getmol> DIHEDRAL for atom ',nmat(nj), 158 159 & ' should be PHASE angle with respect to atom ', … … 312 313 313 314 if (nat.gt.mxath) then 314 write ( *,'(a,i5)') ' redres> number of atoms > ',mxath315 write (logString, '(a,i5)') ' redres> number of atoms > ',mxath 315 316 close(lunlib) 316 317 stop … … 340 341 if (iexcp.eq.0.and.i.le.jow) then 341 342 if (i.eq.jow) then 342 write (*,'(5a)') ' redres> atom ',nmath(i),' of ',343 write(logString,'(5a)') ' redres> atom ',nmath(i),' of ', 343 344 & resl,' cannot preceed itself ' 344 345 else 345 write (*,'(5a,i4)') ' redres> atom ',nmath(i),' of ', 346 write (logString, '(5a,i4)') 347 & ' redres> atom ',nmath(i),' of ', 346 348 & resl,' should be placed AFTER atom #',jow 347 349 endif … … 394 396 395 397 if (nvrr.gt.mxvrh) then 396 write (*,'(a,i5)') ' redres> number of variables > ', 398 write (logString, '(a,i5)') 399 & ' redres> number of variables > ', 397 400 & mxvrh 398 401 close(lunlib) … … 423 426 424 427 ! ____________________________________________________________ ERRORS 425 2 write (*,'(4a)') ' redres> residue >',resl,'< NOT FOUND in ', 428 2 write (logString, '(4a)') ' redres> residue >',resl, 429 & '< NOT FOUND in ', 426 430 &reslib(1:iendst(reslib)) 427 431 close(lunlib) 428 432 stop 429 433 430 3 write (*,'(a,i4,2a)') ' redres> ERROR reading line No. ',nln, 431 &' in ',reslib(1:iendst(reslib)) 434 3 write (logString, '(a,i4,2a)') ' redres> ERROR reading line No. ', 435 & nln, 436 & ' in ',reslib(1:iendst(reslib)) 432 437 close(lunlib) 433 438 stop 434 439 435 4 write (*,'(4a)') ' redres> Incorrect order of bonds for atom ', 440 4 write (logString, '(4a)') 441 & ' redres> Incorrect order of bonds for atom ', 436 442 & nmath(i),' of ',resl 437 443 438 5 write ( *,'(8x,2a)') '... must correct ',444 5 write (logString, '(8x,2a)') '... must correct ', 439 445 & reslib(1:iendst(reslib)) 440 446 close(lunlib) 441 447 stop 442 448 443 6 write ( *,'(a,i2,4a)') ' redres> unknown type :',ity,449 6 write (logString, '(a,i2,4a)') ' redres> unknown type :',ity, 444 450 & ': for atom ',nmath(i),' in residue ',resl 445 451 close(lunlib) 446 452 stop 447 453 448 7 write ( *,'(a,i2,4a)') ' redres> unknown class :',ic,454 7 write (logString, '(a,i2,4a)') ' redres> unknown class :',ic, 449 455 & ': for variable ',nm(j),' in residue ',resl 450 456 close(lunlib) -
gradient.f
r32289cd r38d77eb 57 57 else 58 58 59 write (*,*) 'gradient> Set itysol < 0'59 write (logString, *) 'gradient> Set itysol < 0' 60 60 stop 61 61 endif -
hbond.f
r32289cd r38d77eb 59 59 ntlvr=nvrml(nml) 60 60 if (ntlvr.eq.0) then 61 write ( *,'(a,i4)')61 write (logString, '(a,i4)') 62 62 & ' hbond> No variables defined in molecule #',nml 63 63 return … … 108 108 ixtyhb(ntyhb)=ixhb 109 109 else 110 write(*,*) ' hbond> increase parameter MXTYHB' 110 write (logString, *) 111 & ' hbond> increase parameter MXTYHB' 111 112 stop 112 113 endif … … 139 140 ixtyhb(ntyhb)=ixhb 140 141 else 141 write(*,*) ' hbond> increase parameter MXTYHB' 142 write (logString, *) 143 & ' hbond> increase parameter MXTYHB' 142 144 stop 143 145 endif … … 158 160 ! enddo 159 161 160 if (ipr.gt.0) write(*,'(1x,a,/)') ' hbond> Hydrogen Bonds:' 162 if (ipr.gt.0) write (logString, '(1x,a,/)') 163 & ' hbond> Hydrogen Bonds:' 161 164 162 165 if (ntyhb.gt.0) then … … 287 290 adab=valang(id,ia,ib)*crd 288 291 289 write (*,*) ' '290 write (*,*) ' Dah: ',dah,' Dad: ',dad291 write (*,*) ' Adha: ',adha,' Ahab: ',adha,' Adab: ',adab292 write (*,*) ' '292 write (logString, *) ' ' 293 write (logString, *) ' Dah: ',dah,' Dad: ',dad 294 write (logString, *) ' Adha: ',adha,' Ahab: ',adha,' Adab: ',adab 295 write (logString, *) ' ' 293 296 294 297 return -
init_energy.f
r32289cd r38d77eb 66 66 67 67 !----Initialize solvation part if necessary 68 write ( *,*) 'init_energy: itysol = ',itysol69 write (*,*) 'init_energy: esol_scaling = ',isolscl68 write (logString, *) 'init_energy: itysol = ',itysol 69 write (logString, *) 'init_energy: esol_scaling = ',isolscl 70 70 71 71 its = iabs(itysol) … … 82 82 83 83 if (itysol.ne.0) then 84 write(*,'(a)') ' init_energy> undefined solvent type !' 84 write (logString, '(a)') 85 & ' init_energy> undefined solvent type !' 85 86 stop 86 87 endif … … 96 97 return 97 98 98 10 write (*, '(a)') 'Cannot open the file with surface points' 99 10 write (logString, '(a)') 100 & 'Cannot open the file with surface points' 99 101 stop 100 102 -
main.f
r32289cd r38d77eb 81 81 82 82 ntlml = 0 83 write ( *,*) 'Solvent: ', itysol83 write (logString, *) 'Solvent: ', itysol 84 84 ! Initialize random number generator. 85 85 call sgrnd(31433) … … 118 118 lrand = .true. 119 119 E = energy() 120 write (*,*) E, eyel,eyvw,eyhb,eyvr120 write (logString, *) E, eyel,eyvw,eyhb,eyvr 121 121 call outpdb(1, "polyA.pdb") 122 122 ! Canonical Monte Carlo 123 !call canon(nequi, nsweep, nmes, temp, lrand)123 call canon(nequi, nsweep, nmes, temp, lrand) 124 124 125 125 ! For simulated annealing uncomment the lines below -
main_bgl_p.f
r32289cd r38d77eb 57 57 call mpi_init(ierr) 58 58 ! call pmi_cart_comm_create(comm_cart,ierr) 59 write (*,*) "Initialized MPI. Now setting up communicators."59 write (logString, *) "Initialized MPI. Now setting up communicators." 60 60 call flush(6) 61 61 ndims = 4 … … 81 81 call MPI_Cart_GET(comm_cart, ndims, dims, periods, coords, ierr) 82 82 83 write (*,*) ndims, dims, periods, coords83 write (logString, *) ndims, dims, periods, coords 84 84 call flush(6) 85 85 ! call VTSetup() … … 192 192 & + (coords(3)/ldims(3))*nblock(1)*nblock(2) 193 193 194 write (*,*) myrank, color, ldims, nblock194 write (logString, *) myrank, color, ldims, nblock 195 195 196 196 call mpi_comm_split(comm_cart,color,myrank,local_comm,ierr) … … 216 216 ! call mpi_group_range_incl(group_world, 1, proc_range, group(i) 217 217 ! & ,error) 218 ! write ( *,*) "Assigning rank ", j, proc_range,218 ! write (logString, *) "Assigning rank ", j, proc_range, 219 219 ! & "to group", group(i) 220 220 ! call flush(6) … … 227 227 ! my_mpi_comm = comm(i) 228 228 ! rep_id = i - 1 229 ! write ( *,*) rep_id, "has comm", my_mpi_comm229 ! write (logString, *) rep_id, "has comm", my_mpi_comm 230 230 ! call flush(6) 231 231 ! endif … … 233 233 ! 234 234 ! c Setup the communicator used for parallel tempering 235 ! write ( *,*) "PTGroup=", ranks(:num_replica)235 ! write (logString, *) "PTGroup=", ranks(:num_replica) 236 236 ! call flush(6) 237 237 ! call mpi_group_incl(group_world, num_replica, ranks, group_partem, … … 241 241 ! 242 242 ! if (partem_comm.ne.MPI_COMM_NULL) then 243 ! write ( *,*) partem_comm,myrank, "is master for ", rep_id, "."243 ! write (logString, *) partem_comm,myrank, "is master for ", rep_id, "." 244 244 ! endif 245 245 … … 247 247 call mpi_comm_size(my_mpi_comm,no,ierr) 248 248 rep_id = color 249 write ( *,*) "My new rank is ", myrank, "of", no249 write (logString, *) "My new rank is ", myrank, "of", no 250 250 call flush(6) 251 251 if (myrank.eq.0) then 252 252 color = 1 253 write ( *,*) 'My rank and color:', myrank, color253 write (logString, *) 'My rank and color:', myrank, color 254 254 call flush(6) 255 255 else … … 258 258 call mpi_comm_split(comm_cart,color,0,partem_comm,ierr) 259 259 260 ! write (*,*) "Finalizing MPI."260 ! write (logString, *) "Finalizing MPI." 261 261 ! call flush(6) 262 262 ! CALL mpi_finalize(ierr) … … 295 295 296 296 ! ======================================== start of parallel tempering run 297 write ( *,*) "There are ", no,297 write (logString, *) "There are ", no, 298 298 & " processors available for ",rep_id 299 299 call flush(6) … … 309 309 310 310 if(my_pt_rank.eq.0) then 311 write (*,*) "time for simulation using ", num_proc,311 write (logString, *) "time for simulation using ", num_proc, 312 312 & " processors =", endwtime - startwtime, " seconds" 313 313 call flush(6) -
main_p.f
r32289cd r38d77eb 151 151 call mpi_group_range_incl(group_world, 1, proc_range, group(i) 152 152 & ,error) 153 write ( *,*) "Assigning rank ", j, proc_range,153 write (logString, *) "Assigning rank ", j, proc_range, 154 154 & "to group", group(i) 155 155 call flush(6) … … 162 162 my_mpi_comm = comm(i) 163 163 rep_id = i - 1 164 write ( *,*) rep_id, "has comm", my_mpi_comm164 write (logString, *) rep_id, "has comm", my_mpi_comm 165 165 call flush(6) 166 166 endif … … 168 168 169 169 ! Setup the communicator used for parallel tempering 170 write ( *,*) "PTGroup=", ranks(:num_replica)170 write (logString, *) "PTGroup=", ranks(:num_replica) 171 171 call flush(6) 172 172 call mpi_group_incl(group_world, num_replica, ranks, group_partem, … … 176 176 177 177 if (partem_comm.ne.MPI_COMM_NULL) then 178 write (*,*) partem_comm,myrank, "is master for ", rep_id, "." 178 write (logString, *) partem_comm,myrank, "is master for ", 179 & rep_id, "." 179 180 endif 180 181 … … 182 183 call mpi_comm_size(my_mpi_comm,no,ierr) 183 184 184 write ( *,*) "My new rank is ", myrank, "of", no185 write (logString, *) "My new rank is ", myrank, "of", no 185 186 call flush(6) 186 187 ! = Done setting up communicators ===================================== … … 220 221 221 222 ! ======================================== start of parallel tempering run 222 write ( *,*) "There are ", no,223 write (logString, *) "There are ", no, 223 224 & " processors available for ",rep_id 224 225 call flush(6) … … 234 235 235 236 if(my_pt_rank.eq.0) then 236 write (*,*) "time for simulation using ", num_proc,237 write (logString, *) "time for simulation using ", num_proc, 237 238 & " processors =", endwtime - startwtime, " seconds" 238 239 call flush(6) -
metropolis.f
r32289cd r38d77eb 172 172 enw = energy() 173 173 if(abs(eol-enw).gt.0.000001) then 174 write(*,*) 'metropolis: eol,enw,difference:', eol, enw, eol-enw 174 write (logString, *) 'metropolis: eol,enw,difference:', eol, 175 & enw, eol-enw 175 176 if (eol.lt.100000) then 176 177 stop 'metropolis: eol and enw difference unacceptable' -
mincjg.f
r32289cd r38d77eb 57 57 & d(mxn),xa(mxn),ga(mxn),dt(mxn),yt(mxn),gt(mxn) 58 58 59 59 character(255) logString 60 60 61 ier = 0 61 62 iter = 0 … … 93 94 94 95 if ( gdit .ge. 0.d0 ) then 95 write (*,*) ' mincjg> search direction is uphill'96 write (logString, *) ' mincjg> search direction is uphill' 96 97 ier = 3 97 98 goto 6 … … 162 163 163 164 ier=2 164 write(*,*) ' mincjg> too small step in search direction' 165 write (logString, *) 166 & ' mincjg> too small step in search direction' 165 167 endif 166 168 … … 230 232 if ( iter .ge. (iterfm + MXFCON) ) then 231 233 ier = 4 232 write(*,*) ' mincjg> line search failed to reduce function' 234 write (logString, *) 235 & ' mincjg> line search failed to reduce function' 233 236 return 234 237 endif … … 304 307 call move(nfun,n,f,x,g) 305 308 306 write (*,*) ' mincjg> ier = ',ier309 write (logString, *) ' mincjg> ier = ',ier 307 310 308 311 return -
minim.f
r32289cd r38d77eb 58 58 59 59 if (msv.gt.msvmx) then 60 write ( *,'(a,i5)') ' minreg> parameter MSV > ',msvmx60 write (logString, '(a,i5)') ' minreg> parameter MSV > ',msvmx 61 61 stop 62 62 endif … … 66 66 call gradient() 67 67 68 write (*,'(/,a,/)') ' Energy BEFORE minimization:'68 write (logString, '(/,a,/)') ' Energy BEFORE minimization:' 69 69 70 70 if (ireg.eq.0) then 71 71 72 write ( *,'(a,e12.5,/,3(a,e11.4),/,2(a,e11.4),/)') ' Total: ',73 & eysm,72 write (logString, '(a,e12.5,/,3(a,e11.4),/,2(a,e11.4),/)') 73 & ' Total: ', eysm, 74 74 & ' Coulomb: ',eyel,' Lennard-Jones: ',eyvw,' HB: ',eyhb, 75 75 & ' Variables: ',eyvr,' Solvatation: ',eysl … … 78 78 79 79 80 write ( *,'(a,e12.5,/,3(a,e11.4),/,3(a,e11.4),/)') ' Total: ',81 & wtey*eysm + wtrg*eyrg,80 write (logString, '(a,e12.5,/,3(a,e11.4),/,3(a,e11.4),/)') 81 & ' Total: ', wtey*eysm + wtrg*eyrg, 82 82 & ' Coulomb: ',eyel,' Lennard-Jones: ',eyvw,' HB: ',eyhb, 83 83 & ' Variables: ',eyvr,' Solvatation: ',eysl, … … 148 148 ! gdrg2 = max(acc,gdrg2) 149 149 ! wtrg = wtrg * sqrt(gdey2/gdrg2) 150 ! write (*,*) ' --> Wt_energy = ',wtey,' Wt_regul. = ',wtrg151 ! write (*,*) ' '150 ! write (logString, *) ' --> Wt_energy = ',wtey,' Wt_regul. = ',wtrg 151 ! write (logString, *) ' ' 152 152 ! endif 153 153 … … 184 184 185 185 if (nop.lt.mxop) then 186 write ( *,'(a)') ' ---- CONVERGENCE ----'186 write (logString, '(a)') ' ---- CONVERGENCE ----' 187 187 else 188 write ( *,'(a)') '---- STEP LIMIT ----'189 endif 190 191 192 write ( *,'(/,2a,/)') ' Final energies ',188 write (logString, '(a)') '---- STEP LIMIT ----' 189 endif 190 191 192 write (logString, '(/,2a,/)') ' Final energies ', 193 193 & '__________________________________________________' 194 194 … … 197 197 if (ireg.eq.0) then 198 198 199 write ( *,'(a,e12.5,/,3(a,e11.4),/,2(a,e11.4))') ' Total: ',eysm,200 & ' Coulomb: ',eyel,' Lennard-Jones: ',eyvw,' HB: ',eyhb,201 & ' Variables: ',eyvr,' Solvatation: ',eysl199 write (logString, '(a,e12.5,/,3(a,e11.4),/,2(a,e11.4))') 200 & ' Total: ',eysm,' Coulomb: ',eyel,' Lennard-Jones: ',eyvw, 201 & ' HB: ',eyhb, ' Variables: ',eyvr,' Solvatation: ',eysl 202 202 203 203 else 204 204 205 write ( *,'(a,e12.5,/,3(a,e11.4),/,3(a,e11.4))') ' Total: ',206 & 205 write (logString, '(a,e12.5,/,3(a,e11.4),/,3(a,e11.4))') 206 & ' Total: ', wtey*eysm + wtrg*eyrg, 207 207 & ' Coulomb: ',eyel,' Lennard-Jones: ',eyvw,' HB: ',eyhb, 208 208 & ' Variables: ',eyvr,' Solvatation: ',eysl, … … 211 211 endif 212 212 213 write ( *,'(/,a,/)') ' Variables _________________'213 write (logString, '(/,a,/)') ' Variables _________________' 214 214 215 215 nv = 0 … … 221 221 if (abs(vr).gt.pi) vr=vr-sign(pi2,vr) 222 222 223 write ( *,'(1x,a,1x,i4,f8.1,a,f5.1,a)') nmvr(i),nursvr(i),224 & vr*crd,' (',abs(difang(vr,vlvro(i)))*crd,')'223 write (logString, '(1x,a,1x,i4,f8.1,a,f5.1,a)') nmvr(i), 224 & nursvr(i), vr*crd,' (',abs(difang(vr,vlvro(i)))*crd,')' 225 225 226 226 vlvr(i) = vr … … 231 231 if (ireg.ne.0) then 232 232 233 write ( *,'(/,a,/)') ' Global Variables ___________'233 write (logString,'(/,a,/)') ' Global Variables ___________' 234 234 235 235 do i=1,ntlml 236 write (*,*) ' Molecule #',i,' old new'236 write (logString, *) ' Molecule #',i,' old new' 237 237 do j=1,3 238 write (*,*) gbpro(j,i),' ',gbpr(j,i)238 write (logString, *) gbpro(j,i),' ',gbpr(j,i) 239 239 enddo 240 240 do j=4,6 241 write (*,*) gbpro(j,i)*crd,' ',gbpr(j,i)*crd241 write (logString, *) gbpro(j,i)*crd,' ',gbpr(j,i)*crd 242 242 enddo 243 243 enddo … … 245 245 endif 246 246 247 write ( *,'(/,2a)') ' Gradient ',247 write (logString,'(/,2a)') ' Gradient ', 248 248 & '______________________________________________________________' 249 249 250 write ( *,'(8(1x,f8.3))') (gdvr(i),i=1,nv)250 write (logString,'(8(1x,f8.3))') (gdvr(i),i=1,nv) 251 251 252 252 if (ireg.ne.0) then 253 253 254 write (*,*) ' -------------- global variables ------------' 255 write (*,'(6(1x,f8.3))') (gdvr(i+nv),i=1,ngbvr) 254 write (logString, *) 255 & ' -------------- global variables ------------' 256 write (logString, '(6(1x,f8.3))') (gdvr(i+nv),i=1,ngbvr) 256 257 257 258 endif … … 336 337 esm=eysm 337 338 338 write ( *,'(a,i5,a,2(e13.6,a))') ' Step ',nop,': energy ',esm339 & ,' (',gdsmey,' )'339 write (logString, '(a,i5,a,2(e13.6,a))') ' Step ',nop, 340 & ': energy ', esm, ' (',gdsmey,' )' 340 341 341 342 else … … 355 356 esm=wtey*eysm+wtrg*eyrg 356 357 357 write ( *,'(a,i5,a,3(e13.6,a))') ' Step ',nop,': energy ',esm358 & 358 write (logString, '(a,i5,a,3(e13.6,a))') ' Step ',nop, 359 & ': energy ',esm,' (',gdsmey,',',gdsmrg,' )' 359 360 360 361 endif -
minqsn.f
r32289cd r38d77eb 66 66 integer ir 67 67 68 68 character(255) logString 69 69 70 parameter ( eps1=0.1d0, 70 71 & eps2=0.7d0, … … 142 143 143 144 3 if (nfun.ge.maxfun) then 144 !c write ( *,*) ' minfor> exceeded max. number of function calls'145 !c write (logString, *) ' minfor> exceeded max. number of function calls' 145 146 return 146 147 endif … … 224 225 goto 2 225 226 else ! rank of new matrix is deficient 226 write (*,*) ' minfor> rank of hessian < number of variables' 227 write (logString, *) 228 & ' minfor> rank of hessian < number of variables' 227 229 return 228 230 endif -
mklist.f
r32289cd r38d77eb 45 45 ntlms=nmsml(nml) 46 46 if (ntlms.eq.0) then 47 write ( *,'(a,i4)')47 write (logString, '(a,i4)') 48 48 & ' mklist> No mov. sets defined in molecule #',nml 49 49 nvwml(nml)=0 … … 107 107 n2i=n2i+1 108 108 if (n2i.gt.mx2) then 109 write (*,'(a,i3,2a)') ' mklist> Molecule # ',nml, 109 write(logString, '(a,i3,2a)') ' mklist> Molecule # ', 110 & nml, 110 111 & ': too many atoms bound to ',nmat(iob) 111 112 stop … … 125 126 n2i=n2i+1 126 127 if (n2i.gt.mx2) then 127 write (*,'(a,i3,a)') ' mklist> Molecule # ' 128 write (logString, '(a,i3,a)') 129 & ' mklist> Molecule # ' 128 130 & ,nml,': too many atoms in list L2I' 129 131 stop … … 141 143 n2i=n2i+1 142 144 if (n2i.gt.mx2) then 143 write ( *,'(a,i3,2a)') ' mklist> Molecule # '145 write (logString, '(a,i3,2a)') ' mklist> Molecule # ' 144 146 & ,nml,': too many atoms bound to ',nmat(iob) 145 147 stop … … 165 167 n1i=n1i+1 166 168 if (n1i.gt.mxbd) then 167 write (*,'(a,i3,2a)') ' mklist> Molecule # ',nml, 169 write (logString, '(a,i3,2a)') ' mklist> Molecule # ', 170 & nml, 168 171 & ': too many atoms bound to ',nmat(ib) 169 172 stop … … 177 180 n2i=n2i+1 178 181 if (n2i.gt.mx2) then 179 write (*,'(a,i3,2a)') ' mklist> Molecule # ',nml, 180 & ': too many atoms bound to branches of ',nmat(ib) 182 write (logString, '(a,i3,2a)') 183 & ' mklist> Molecule # ',nml, 184 & ': too many atoms bound to branches of ',nmat(ib) 181 185 stop 182 186 endif … … 194 198 n2i=n2i+1 195 199 if (n2i.gt.mx2) then 196 write (*,'(a,i3,a)') ' mklist> Molecule # ',nml, 197 & ': too many atoms n list L2I ' 200 write (logString, '(a,i3,a)') ' mklist> Molecule # ', 201 & nml, 202 & ': too many atoms n list L2I ' 198 203 stop 199 204 endif … … 207 212 ! ________________________________________ Current 2ND list -> VdW-interact. 208 213 if ((nvw+n2nd).gt.mxvw) then 209 write (*,'(a,i4,a,i5)') ' mklist> Molecule # ',nml, 214 write (logString, '(a,i4,a,i5)') ' mklist> Molecule # ', 215 & nml, 210 216 & ': Number of vdw-domains > ',mxvw 211 217 stop … … 273 279 ! ____________________________________________ Summary 274 280 ! do i=ifiat,ilaat 275 ! write ( *,'(3a,i5,a)') ' ######## atom ',nmat(i),'(',i,')'281 ! write (logString, '(3a,i5,a)') ' ######## atom ',nmat(i),'(',i,')' 276 282 ! iv1=ivwat1(i) 277 283 ! iv2=ivwat2(i) 278 284 ! if (iv1.le.iv2) then 279 ! write (*,'(a)') ' ---> vdW :'285 ! write (logString, '(a)') ' ---> vdW :' 280 286 ! do j=iv1,iv2 281 ! write ( *,'(i5,a,i5)') lvwat1(j),'-',lvwat2(j)287 ! write (logString, '(i5,a,i5)') lvwat1(j),'-',lvwat2(j) 282 288 ! enddo 283 289 ! endif … … 285 291 ! i42=i14at2(i) 286 292 ! if (i41.le.i42) then 287 ! write (*,'(a)') ' ---> 1-4 :'288 ! write (*,'(10i5)') (l14at(j),j=i41,i42)293 ! write (logString, '(a)') ' ---> 1-4 :' 294 ! write (logString, '(10i5)') (l14at(j),j=i41,i42) 289 295 ! endif 290 296 ! enddo … … 292 298 return 293 299 294 1 write ( *,'(a,i4,a,i5)') ' mklist> Molecule # ',nml,300 1 write (logString, '(a,i4,a,i5)') ' mklist> Molecule # ',nml, 295 301 & ': Number of 1-4 interactions > ',mx14 296 302 stop … … 312 318 implicit none 313 319 integer mx, j, n, j1, l1, j2, l2, i1, i2, ja, k 314 320 character(255) logString 315 321 dimension l1(mx),l2(mx) 316 322 … … 334 340 n=n+1 335 341 if (n.gt.mx) then 336 write ( *,'(a)') ' quench> too many sets'342 write (logString, '(a)') ' quench> too many sets' 337 343 stop 338 344 endif -
mulcan_par.f
r32289cd r38d77eb 83 83 ! 84 84 eol = energy() 85 write ( *,'(a,e12.5,/)') 'Energy of start configuration: ',eol86 write (*,*)85 write (logString, '(a,e12.5,/)') 'Energy of start configuration: ',eol 86 write (logString, *) 87 87 88 88 call outpdb(1, 'start.pdb') … … 100 100 muold = int(min(xmax,max(xmin,eol/ebin+sign(0.5d0,eol)))) 101 101 ihist(muold) = ihist(muold) + 1 102 write ( *,*) nsw, eol, acz102 write (logString, *) nsw, eol, acz 103 103 ! 104 104 ! ITERATE MULTICANONICAL WEIGHTS EVERY NUP SWEEPS … … 143 143 ! FINAL OUTPUT: 144 144 acz = acz/dble(nsw*nvr) 145 write (*,*) 'last energy',eol146 write (*,*) 'aczeptance rate:',acz145 write (logString, *) 'last energy',eol 146 write (logString, *) 'aczeptance rate:',acz 147 147 ! 148 148 ! OUTPUT OF FINAL HISTOGRAM 149 149 ! 150 write (*,*) 'Histogram:'150 write (logString, *) 'Histogram:' 151 151 do i=kmin,kmax 152 152 if(xhist(i).gt.0.0d0) then 153 write (*,*) i,xhist(i)153 write (logString, *) i,xhist(i) 154 154 end if 155 155 end do -
mulcan_par_mod.f90
r32289cd r38d77eb 103 103 104 104 eol = energy() 105 write ( *,'(a,e12.5,/)') 'Energy of start configuration: ',eol106 write (*,*)105 write (logString, '(a,e12.5,/)') 'Energy of start configuration: ',eol 106 write (logString, *) 107 107 108 108 call outpdb(1, 'start.pdb') … … 158 158 ! Final output 159 159 acz = acz/dble(nsw*nvr) 160 write (*,*) 'last energy',eol161 write (*,*) 'acceptance rate:',acz162 163 write (*,*) 'Histogram:'160 write (logString, *) 'last energy',eol 161 write (logString, *) 'acceptance rate:',acz 162 163 write (logString, *) 'Histogram:' 164 164 do i=kmin,kmax 165 165 if(xhist(i).gt.0.0d0) then 166 write (*,*) i,xhist(i)166 write (logString, *) i,xhist(i) 167 167 end if 168 168 end do … … 266 266 end do 267 267 end do 268 write (*,*) 'Number of contacts in reference conformation:',nci268 write (logString, *) 'Number of contacts in reference conformation:',nci 269 269 270 270 ! Read in fields with multicanonical parameter … … 282 282 vlvr(iv) = x 283 283 end do 284 write (*,*) 'Last iteration, energy:',nswm,eol_old284 write (logString, *) 'Last iteration, energy:',nswm,eol_old 285 285 else 286 286 ! _________________________________ random start … … 294 294 295 295 eol = energy() 296 write ( *,'(e12.5,/)') eol296 write (logString, '(e12.5,/)') eol 297 297 call contacts(nhy,nhx,dham) 298 write (*,*) 'Number of contacts in start configuration:',nhy299 write (*,*) 'Number of native contacts in start configuration:', &298 write (logString, *) 'Number of contacts in start configuration:',nhy 299 write (logString, *) 'Number of native contacts in start configuration:', & 300 300 & nhx 301 301 do i=1,nresi 302 write (*,'(62I1)') (ijcont(i,j), j=1,nresi)303 end do 304 write (*,*)302 write (logString, '(62I1)') (ijcont(i,j), j=1,nresi) 303 end do 304 write (logString, *) 305 305 306 306 … … 355 355 356 356 acz = acz/dble(nsw*nvr) 357 write (*,*) 'last energy',eol358 write (*,*) 'acceptance rate:',acz357 write (logString, *) 'last energy',eol 358 write (logString, *) 'acceptance rate:',acz 359 359 360 360 ! WRITE DOWN (UN-REWEIGHTED) HISTOGRAM OF MULTICANONICAL SIMULATION 361 361 do i=kmin,kmax 362 362 if(xhist(i).gt.0.0d0) then 363 write (*,*) i,xhist(i)363 write (logString, *) i,xhist(i) 364 364 end if 365 365 end do -
mulcan_sim.f
r32289cd r38d77eb 72 72 end do 73 73 end do 74 write (*,*) 'Number of contacts in reference conformation:',nci74 write (logString, *) 'Number of contacts in reference conformation:',nci 75 75 76 76 ! READ IN FIELDS WITH MULTICANONICAL PARAMETER … … 88 88 vlvr(iv) = x 89 89 end do 90 write (*,*) 'Last iteration, energy:',nswm,eol_old90 write (logString, *) 'Last iteration, energy:',nswm,eol_old 91 91 else 92 92 ! _________________________________ random start … … 100 100 ! 101 101 eol = energy() 102 write ( *,'(e12.5,/)') eol102 write (logString, '(e12.5,/)') eol 103 103 call contacts(nhy,nhx,dham) 104 write (*,*) 'Number of contacts in start configuration:',nhy105 write (*,*) 'Number of native contacts in start configuration:',104 write (logString, *) 'Number of contacts in start configuration:',nhy 105 write (logString, *) 'Number of native contacts in start configuration:', 106 106 & nhx 107 107 do i=1,nresi 108 write (*,'(62I1)') (ijcont(i,j), j=1,nresi)109 end do 110 write (*,*)108 write (logString, '(62I1)') (ijcont(i,j), j=1,nresi) 109 end do 110 write (logString, *) 111 111 ! 112 112 … … 165 165 ! FINAL OUTPUT: 166 166 acz = acz/dble(nsw*nvr) 167 write (*,*) 'last energy',eol168 write (*,*) 'aczeptance rate:',acz167 write (logString, *) 'last energy',eol 168 write (logString, *) 'aczeptance rate:',acz 169 169 170 170 ! WRITE DOWN (UN-REWEIGHTED) HISTOGRAM OF MULTICANONICAL SIMULATION 171 171 do i=kmin,kmax 172 172 if(xhist(i).gt.0.0d0) then 173 write (*,*) i,xhist(i)173 write (logString, *) i,xhist(i) 174 174 end if 175 175 end do -
nursvr.f
r32289cd r38d77eb 33 33 enddo 34 34 35 write (*,'(a,i5)') ' nursvr > Cannot find variable # ',ivr 35 write (logString, '(a,i5)') ' nursvr > Cannot find variable # ' 36 & ,ivr 36 37 stop 37 38 … … 70 71 enddo 71 72 72 write ( *,'(a,i5)') ' nursat > Cannot find atom # ',iat73 write (logString, '(a,i5)') ' nursat > Cannot find atom # ',iat 73 74 stop 74 75 -
opeflx.f
r32289cd r38d77eb 60 60 ntlvr=nvrml(nml) 61 61 if (ntlvr.eq.0) then 62 write ( *,'(a,i4)')62 write (logString, '(a,i4)') 63 63 & ' opeflx> No variables defined in molecule #',nml 64 64 return … … 504 504 gda=gdeyvr(iv) ! analytical der. 505 505 506 write ( *,'(1x,2a,2(e12.6,a))') nmvr(iv),': ',gda,' (',506 write (logString, '(1x,2a,2(e12.6,a))') nmvr(iv),': ',gda,' (', 507 507 & abs(gda-gdn),')' 508 508 -
opereg.f
r32289cd r38d77eb 54 54 ntlvr=nvrml(nml) 55 55 if (ntlvr.eq.0) then 56 write ( *,'(a,i4)')56 write (logString, '(a,i4)') 57 57 & ' opereg> No variables defined in molecule #',nml 58 58 return … … 330 330 gdn = ( enyreg(nml) - eyrg ) / del 331 331 332 write ( *,*) ' Gb. var #',(ii+i),': ',gdeygb(ii+i),gdn,332 write (logString, *) ' Gb. var #',(ii+i),': ',gdeygb(ii+i),gdn, 333 333 & abs(gdn-gdeygb(ii+i)) 334 334 ! ----------------------------- restore … … 382 382 gda=gdeyrg(iv) ! analytical der. 383 383 384 write ( *,'(1x,2a,2(e12.6,a))') nmvr(iv),': ',gda,' (',384 write (logString, '(1x,2a,2(e12.6,a))') nmvr(iv),': ',gda,' (', 385 385 & abs(gda-gdn),')' 386 386 -
opeshe.f
r32289cd r38d77eb 51 51 ntlvr=nvrml(nml) 52 52 if (ntlvr.eq.0) then 53 write ( *,'(a,i4)')53 write (logString, '(a,i4)') 54 54 & ' opeshe> No variables defined in molecule #',nml 55 55 return … … 377 377 gda=gdeyvr(iv) ! analytical der. 378 378 379 write ( *,'(1x,2a,2(e12.6,a))') nmvr(iv),': ',gda,' (',379 write (logString, '(1x,2a,2(e12.6,a))') nmvr(iv),': ',gda,' (', 380 380 & abs(gda-gdn),')' 381 381 -
opesol.f
r32289cd r38d77eb 51 51 ntlvr=nvrml(nml) 52 52 if (ntlvr.eq.0) then 53 write ( *,'(a,i4)')53 write (logString, '(a,i4)') 54 54 & ' opesol> No variables defined in molecule #',nml 55 55 return … … 283 283 gdn=(eynw-eysl)/del ! numerical derivative 284 284 285 write ( *,'(1x,2a,2(e12.6,a))') nmvr(iv),': ',gda,' (',285 write (logString, '(1x,2a,2(e12.6,a))') nmvr(iv),': ',gda,' (', 286 286 & abs(gda-gdn),')' 287 287 -
outpdb.f
r32289cd r38d77eb 43 43 44 44 if (nml.lt.0.or.nml.gt.ntlml) then 45 write (*,*) ' outpdb> No such molecule #',nml,' !'45 write (logString, *) ' outpdb> No such molecule #',nml,' !' 46 46 return 47 47 elseif (nml.gt.0) then -
outvar.f
r32289cd r38d77eb 30 30 31 31 if (nml.lt.0.or.nml.gt.ntlml) then 32 write (*,*) ' outvar> No such molecule #',nml,' !'32 write (logString, *) ' outvar> No such molecule #',nml,' !' 33 33 return 34 34 endif … … 57 57 58 58 if (nml.lt.0.or.nml.gt.ntlml) then 59 write (*,*) ' outvbs> No such molecule #',nml,' !'59 write (logString, *) ' outvbs> No such molecule #',nml,' !' 60 60 return 61 61 elseif (nml.gt.0) then -
partem_p.f
r32289cd r38d77eb 95 95 trackID = 1 96 96 odd = 1 97 write ( *,*) 'Starting parallel tempering.'98 write ( *,*) 'parameters, ',switch,newsta,nmes,nswp,nmes,97 write (logString, *) 'Starting parallel tempering.' 98 write (logString, *) 'parameters, ',switch,newsta,nmes,nswp,nmes, 99 99 & rep_id, num_rep, partem_comm, myrank 100 100 call flush(6) … … 167 167 do i=1,num_rep 168 168 read(13,*) j,inode(i),intem(i),yol(i),e_minp(i),h_maxp(i) 169 write ( *,*) "par_R.in:",i,j169 write (logString, *) "par_R.in:",i,j 170 170 end do 171 171 jold=(iold/nmes)*num_rep … … 178 178 & ,idum1, idum2, idum3, e_min 179 179 & ,dummy, dummy 180 write ( *,*) i180 write (logString, *) i 181 181 call flush(6) 182 182 end do … … 197 197 e_min = e_minp(rep_id+1) 198 198 h_max = h_maxp(rep_id+1) 199 write ( *,*) "E_min=",e_min," for ", rep_id + 1199 write (logString, *) "E_min=",e_min," for ", rep_id + 1 200 200 eol=energy() 201 201 if(.not.newsta.and.abs(yol(rep_id + 1) - eol).gt.0.1) then 202 write (*,*) rep_id, ' Warning: yol(rep_id).ne.eol:'203 write (*,*) rep_id, yol(rep_id + 1), eol202 write (logString, *) rep_id, ' Warning: yol(rep_id).ne.eol:' 203 write (logString, *) rep_id, yol(rep_id + 1), eol 204 204 endif 205 205 ! Start of simulation 206 write ( *,*) '[',rep_id, myrank, beta, partem_comm,206 write (logString, *) '[',rep_id, myrank, beta, partem_comm, 207 207 & '] Energy before equilibration:', eol 208 208 ! =====================Equilibration by canonical Metropolis … … 211 211 end do 212 212 CALL MPI_BARRIER(MPI_COMM_WORLD,IERR) 213 write (*,*) '[',rep_id,'] Energy after equilibration:', eol 213 write (logString, *) '[',rep_id,'] Energy after equilibration:', 214 & eol 214 215 call flush(6) 215 216 ! … … 222 223 eol0 = eol 223 224 if (myrank.eq.0.and.rep_id.eq.0) then 224 write ( *,*) "Finished sweep", nsw225 write (logString, *) "Finished sweep", nsw 225 226 call flush(6) 226 227 endif … … 494 495 & IERR) 495 496 if (myrank.ne.0) then 496 ! write ( *,*) '[', myrank,'] Missed', randomCount,497 ! write (logString, *) '[', myrank,'] Missed', randomCount, 497 498 ! & 'random numbers.' 498 499 do i = 1, randomCount 499 500 rd = grnd() 500 ! write ( *,*) '[', myrank,'] rd=', rd501 ! write (logString, *) '[', myrank,'] rd=', rd 501 502 enddo 502 503 endif … … 519 520 e_final=energy() 520 521 if (partem_comm.ne.MPI_COMM_NULL) then 521 write ( *,*) rep_id, ' E_final', e_final522 write (logString, *) rep_id, ' E_final', e_final 522 523 endif 523 524 eol0 = eol -
partem_s.f
r32289cd r38d77eb 148 148 CALL METROPOLIS(energ,acz,can_weight) 149 149 end do 150 write (*,*) 'Start energy after equilibration for replica:',151 & 150 write (logString, *) 151 & 'Start energy after equilibration for replica:',k, energ 152 152 do i=1,nvr 153 153 iv = idvr(i) -
pdbread.f
r32289cd r38d77eb 32 32 dimension cor(3) 33 33 character atm*4,rsn*3,rsno*3,chn,chno, 34 & rsid*5,rsido*5,line*132 34 & rsid*5,rsido*5,line*132, logString*255 35 35 36 36 natp=0 … … 48 48 lunpdb = 99 49 49 else 50 write ( *,'(a)')50 write (logString, '(a)') 51 51 & ' pdbread> empty file name to read pdb-structure' 52 52 … … 57 57 58 58 if (io.le.0) then 59 write ( *,'(a,/,a)')59 write (logString, '(a,/,a)') 60 60 & ' pdbread> ERROR opening file to read pdb-structure: ', 61 61 & pdbfil(1:iendst(pdbfil)) … … 70 70 71 71 if ( line(17:17).ne.' ' ) then 72 write ( *,'(a,/,a,/,a,/,2a)')72 write (logString, '(a,/,a,/,a,/,2a)') 73 73 & ' pdbread> found alternate atom location: ', 74 74 & ' !', … … 86 86 87 87 if ((natp+1).gt.MXATP) then 88 write ( *,'(a,i5,a,/,a)')88 write (logString, '(a,i5,a,/,a)') 89 89 & ' pdbread> >MXATP (',MXATP,') ATOM lines in PDB file ', 90 90 & pdbfil(1:iendst(pdbfil)) … … 97 97 98 98 if ((nchp+1).gt.MXCHP) then 99 write ( *,'(a,i3,a,/,a)')99 write (logString, '(a,i3,a,/,a)') 100 100 & ' pdbread> >MXCHP (',MXCHP,') chains in PDB file ', 101 101 & pdbfil(1:iendst(pdbfil)) … … 106 106 107 107 if ((nrsp+1).gt.MXRSP) then 108 write ( *,'(a,i3,a,/,a)')108 write (logString, '(a,i3,a,/,a)') 109 109 & ' pdbread> >MXRSP (',MXRSP,') residues in PDB file ', 110 110 & pdbfil(1:iendst(pdbfil)) … … 141 141 142 142 if ((nrsp+1).gt.MXRSP) then 143 write ( *,'(a,i3,a,/,a)')143 write (logString, '(a,i3,a,/,a)') 144 144 & ' pdbread> >MXRSP (',MXRSP,') residues in PDB file ', 145 145 & pdbfil(1:iendst(pdbfil)) … … 172 172 goto 1 173 173 174 2 write ( *,'(a,/,a,/,2a)')174 2 write (logString, '(a,/,a,/,2a)') 175 175 & ' pdbread> ERROR reading ATOM line ', 176 176 & line(:l), … … 195 195 else 196 196 197 write ( *,'(a,/,a)')197 write (logString, '(a,/,a)') 198 198 & ' pdbread> NO atom coordinates selected from file ', 199 199 & pdbfil(1:iendst(pdbfil)) … … 245 245 nml=nml+1 246 246 if (nml.gt.mxml) then 247 write (*,'(a,i4,2a)')' pdbvars> NUMBER of chains > '247 write (logString, '(a,i4,2a)')' pdbvars> NUMBER of chains > ' 248 248 & ,mxml,' in ',' ?' 249 249 stop … … 266 266 267 267 if (nrs.gt.mxrs) then 268 write (*,'(a,i4,2a)') ' pdbvars> NUMBER of residues > '269 & ,mxrs,' in ',' ?'268 write (logString, '(a,i4,2a)') 269 & ' pdbvars> NUMBER of residues > ', mxrs, ' in ',' ?' 270 270 stop 271 271 endif … … 421 421 zat(ii)=zatp(ix) 422 422 else 423 write (*,'(3a)') ' pdbvars> missing PDB atom ',nmat(ii),424 & ' is ref. point for SMMP - cannot proceed !'423 write (logString, '(3a)') ' pdbvars> missing PDB atom ', 424 & nmat(ii), ' is ref. point for SMMP - cannot proceed !' 425 425 endif 426 426 enddo … … 436 436 ! ++++++++++ 437 437 438 write (*,*) ' '439 write (*,*) ' Initial RMSD ',rmsd438 write (logString, *) ' ' 439 write (logString, *) ' Initial RMSD ',rmsd 440 440 441 441 enddo ! chains(molecules) … … 485 485 enddo 486 486 487 ! write (*,'(8a)') ' pdbvars> ',atm,' not found in '487 ! write (logString, '(8a)') ' pdbvars> ',atm,' not found in ' 488 488 ! # ,chnp(nc),' ',rsidp(irs),' ',rsnmp(irs) 489 489 -
redseq.f
r32289cd r38d77eb 36 36 37 37 if (iopfil(lunseq,seqfil,'old','formatted').le.izero) then 38 write ( *,'(a,/,a,i3,2a)')38 write (logString, '(a,/,a,i3,2a)') 39 39 & ' redseq> ERROR opening sequence file:', 40 40 & ' LUN=',lunseq,' FILE=',seqfil(1:iendst(seqfil)) … … 67 67 68 68 if ((nrs-irsml1(ntlml)+1).eq.0) then 69 write (*,'(2a)') ' redseq> IGNORE molecule: ',69 write (logString, '(2a)') ' redseq> IGNORE molecule: ', 70 70 & nmml(ntlml)(1:iendst(nmml(ntlml))) 71 71 ntlml=ntlml-1 … … 74 74 ntlml=ntlml+1 75 75 if (ntlml.gt.mxml) then 76 write(*,'(a,i4,2a)')' redseq> NUMBER of molecules > ' 76 write (logString, '(a,i4,2a)') 77 & ' redseq> NUMBER of molecules > ' 77 78 & ,mxml,' in ',seqfil(1:iendst(seqfil)) 78 79 close(lunseq) … … 124 125 125 126 if (id.gt.4) then 126 write ( *,'(4a)') ' redseq> INVALID residue NAME >',127 write (logString, '(4a)') ' redseq> INVALID residue NAME >', 127 128 & line(ib:ii),'< in ', 128 129 & seqfil(1:iendst(seqfil)) … … 133 134 nrs=nrs+1 134 135 if (nrs.gt.mxrs) then 135 write(*,'(a,i4,2a)') ' redseq> NUMBER of residues > ' 136 write (logString, '(a,i4,2a)') 137 & ' redseq> NUMBER of residues > ' 136 138 & ,mxrs,' in ',seqfil(1:iendst(seqfil)) 137 139 close(lunseq) … … 162 164 163 165 if (nrs.eq.0) then 164 write ( *,'(2a)') ' redseq> no residues found in ',166 write (logString, '(2a)') ' redseq> no residues found in ', 165 167 & seqfil(1:iendst(seqfil)) 166 168 stop … … 179 181 if (i.eq.ntlml) then ! Check last molecule 180 182 if ((nrs-ifirs+1).eq.0) then 181 write (*,'(2a)') ' redseq> IGNORE molecule '183 write (logString, '(2a)') ' redseq> IGNORE molecule ' 182 184 & ,nmml(ntlml)(1:iendst(nmml(ntlml))) 183 185 ntlml=ntlml-1 184 186 if (ntlml.eq.0) then 185 write (*,'(2a)') ' redseq> no residues found in ', 186 & seqfil(1:iendst(seqfil)) 187 write (logString, '(2a)') 188 & ' redseq> no residues found in ', 189 & seqfil(1:iendst(seqfil)) 187 190 stop 188 191 endif … … 192 195 endif 193 196 194 ! write ( *,'(/,a,i4,2a)') ' redseq> ',irsml2(i)-irsml1(i)+1,197 ! write (logString, '(/,a,i4,2a)') ' redseq> ',irsml2(i)-irsml1(i)+1, 195 198 ! & ' residue(s) in molecule: ', 196 199 ! & nmml(i)(1:iendst(nmml(i))) 197 ! write ( *,'(15(1x,a))') (seq(j),j=irsml1(i),irsml2(i))200 ! write (logString, '(15(1x,a))') (seq(j),j=irsml1(i),irsml2(i)) 198 201 199 202 enddo … … 203 206 ! _______________________________________________ error 204 207 205 4 write ( *,'(a,i4,2a)') ' redseq> ERROR reading line No. ',nln,208 4 write (logString, '(a,i4,2a)') ' redseq> ERROR reading line No. ',nln, 206 209 & ' in ',seqfil(1:iendst(seqfil)) 207 210 close(lunseq) -
redstr.f
r32289cd r38d77eb 30 30 31 31 character spr,blnk,str*(*),strn*(*) 32 character*255 logString 32 33 33 34 data blnk/' '/ … … 36 37 37 38 if (spr.eq.blnk) then 38 write ( *,*) ' extstr> Separator should not be blank'39 write (logString, *) ' extstr> Separator should not be blank' 39 40 stop 40 41 endif … … 79 80 return 80 81 ! ______________________________________________________________ Error 81 1 write (*,'(a)') ' extstr> Substring to be extracted is too long !' 82 1 write (logString, '(a)') 83 & ' extstr> Substring to be extracted is too long !' 82 84 stop 83 85 -
redvar.f
r32289cd r38d77eb 101 101 ntlvr=ivrml1(ntlml)+nvrml(ntlml)-1 102 102 if (ntlvr.eq.0) then 103 write (*,*) 'redvar> No variables defined in molecule(s)'103 write(logString,*)'redvar> No variables defined in molecule(s)' 104 104 return 105 105 endif … … 108 108 io=iopfil(lunvar,varfil,'old','formatted') 109 109 if (io.eq.0) then 110 write ( *,'(a,/,a,i3,2a)')110 write (logString, '(a,/,a,i3,2a)') 111 111 & ' redvar> ERROR opening file to set variables:', 112 112 & ' LUN=',lunvar,' FILE=',varfil(1:iendst(varfil)) … … 136 136 vr=blat(iatvr(i)) 137 137 else 138 write( *,*) 'redvar> unknown variable type: ',it,' !'138 write(logString,*) 'redvar> unknown variable type: ',it,' !' 139 139 stop 140 140 endif … … 159 159 if (iredin(lincmd,nml).le.0.or. 160 160 & nml.le.0.or.nml.gt.ntlml) then 161 write (*,*) 'redvar> ','Incorrect molecule number >', 161 write (logString, *) 162 & 'redvar> ','Incorrect molecule number >', 162 163 & lincmd(1:l),'< Must be in range [1,', 163 164 & ntlml,'] !' … … 310 311 311 312 if (inum.le.0.or.inum.gt.ntlml) then 312 write ( *,*) ' # 1: ',inum313 write (logString, *) ' # 1: ',inum 313 314 goto 104 314 315 endif … … 324 325 325 326 if (k.lt.nfi.or.k.gt.irsml2(j)) then 326 write ( *,*) ' # 2: ',inum327 write (logString, *) ' # 2: ',inum 327 328 goto 104 328 329 endif … … 343 344 if (l.lt.nfi.or. 344 345 & l.gt.nfi+nvrrs(k)-1) then 345 write ( *,*) ' # 3: ',inum346 write (logString, *) ' # 3: ',inum 346 347 goto 104 347 348 endif … … 427 428 428 429 if (ide.eq.1.and.ihy.eq.ide) then 429 write ( *,*) ' # 4: ',ide430 write (logString, *) ' # 4: ',ide 430 431 goto 104 431 432 endif … … 441 442 if (iredin(linh,ibz).le.0.or.ibz.le.0) 442 443 & then 443 write ( *,*) ' # 5 '444 write (logString, *) ' # 5 ' 444 445 goto 104 445 446 endif … … 456 457 if (iredin(linh,iez).le.0.or.iez.le.0.or. 457 458 & iez.lt.ibz) then 458 write ( *,*) ' # 6 '459 write (logString, *) ' # 6 ' 459 460 goto 104 460 461 endif … … 524 525 endif 525 526 enddo 526 if (.not.did) write ( *,'(3a)')527 if (.not.did) write (logString, '(3a)') 527 528 & ' redvar> No variables affected by command >', 528 529 & lincmd(1:ice),'<' … … 531 532 ll1=ibegst(linfld(nfld)) 532 533 ll2=iendst(linfld(nfld)) 533 write ( *,*) 'll1,ll2, linfld(nfld): ',ll1,ll2,534 write (logString, *) 'll1,ll2, linfld(nfld): ',ll1,ll2, 534 535 & '>',linfld(nfld)(ll1:ll2),'<' 535 536 … … 559 560 enddo 560 561 561 write (*,'(3a,/,1x,5(a,2x),a)') ' redvar> ',nmml(i)(1:ie), 562 write (logString, '(3a,/,1x,5(a,2x),a)') ' redvar> ', 563 & nmml(i)(1:ie), 562 564 & ' with global parameters:', 563 565 & (strg(k)(ibegst(strg(k)):),k=1,6) … … 579 581 did=.true. 580 582 if (fxvr(iv)) then 581 write (*,'(3a,i4,1x,4a,f10.3,a)') ' redvar> ',583 write(logString,'(3a,i4,1x,4a,f10.3,a)') ' redvar> ', 582 584 & nmml(i)(1:ie),': residue ',j-jb,seq(j), 583 585 & ': ',nmvr(iv),' set ',vlvrx(iv),' Fixed' 584 586 else 585 write ( *,'(3a,i4,1x,4a,f10.3)') ' redvar> ',587 write (logString, '(3a,i4,1x,4a,f10.3)') ' redvar> ', 586 588 & nmml(i)(1:ie),': residue ',j-jb,seq(j), 587 589 & ': ',nmvr(iv),' set ',vlvrx(iv) … … 597 599 enddo 598 600 if (did) then 599 if (in.gt.0) write ( *,'(3a,i5,a)')601 if (in.gt.0) write (logString, '(3a,i5,a)') 600 602 & ' redvar> Molecule ',nmml(i)(1:ie),': ',in, 601 603 & ' variable(s) remain unchanged' 602 604 call setvar(iml,vlvrx) 603 605 else 604 write ( *,'(3a)') ' redvar> Molecule ',606 write (logString, '(3a)') ' redvar> Molecule ', 605 607 & nmml(i)(1:ie),': No internal variables changed' 606 608 endif … … 610 612 return 611 613 ! ____________________________________________________________ Errors 612 100 write ( *,'(3a)') ' redvar> Cannot interpret command >',614 100 write (logString, '(3a)') ' redvar> Cannot interpret command >', 613 615 & lincmd(1:ice),'<' 614 616 close(lunvar) 615 617 stop 616 101 write (*,'(a,i5,a)') ' redvar> Command number ',ncmd,' reached' 618 101 write (logString, '(a,i5,a)') ' redvar> Command number ',ncmd, 619 & ' reached' 617 620 close(lunvar) 618 621 stop 619 102 write ( *,'(3a)') ' redvar> Cannot read value from >',622 102 write (logString, '(3a)') ' redvar> Cannot read value from >', 620 623 & lincmd(1:ice),'<' 621 624 close(lunvar) 622 625 stop 623 103 write ( *,'(a,i3,3a)') ' redvar> Cannot read >',maxide,626 103 write (logString, '(a,i3,3a)') ' redvar> Cannot read >',maxide, 624 627 & ' identifiers from >',linfld(ii)(1:ife),'<' 625 628 close(lunvar) 626 629 stop 627 104 write ( *,'(5a)') ' redvar> Error in identifier >',630 104 write (logString, '(5a)') ' redvar> Error in identifier >', 628 631 & linide(1:ide),'< of command >',lincmd(1:ice),'<' 629 632 close(lunvar) 630 633 stop 631 105 write (*,'(a,/,a,/,2a,/)') ' redvar> line with global paramters:', 634 105 write (logString, '(a,/,a,/,2a,/)') 635 & ' redvar> line with global paramters:', 632 636 & line(1:ile),' must contain 6 floating', 633 637 & ' point numbers separated by commas !' … … 635 639 stop 636 640 637 106 write (*,'(a,/,a,/,2a,/)') ' redvar> line with global paramters:', 641 106 write (logString, '(a,/,a,/,2a,/)') 642 & ' redvar> line with global paramters:', 638 643 & line(1:ile),' angles must be inside ', 639 644 &'ranges [-180,180], [-90,90], and [-180,180] Deg., respectively !' -
regul.f
r32289cd r38d77eb 44 44 wtey = 0.d0 45 45 46 write (*,'(/,a,2(a,f4.2),/)')46 write (logString, '(/,a,2(a,f4.2),/)') 47 47 & ' ====================== Regularization only', 48 48 & ' Wt(energy) = ',wtey,' Wt(regul.) = ',wtrg … … 50 50 call minim(2, nsteps, acc) 51 51 52 write (*,*) ' '53 write (*,*) ' ---------- contacts after 1st regularization'54 write (*,*) ' '52 write (logString, *) ' ' 53 write (logString, *) ' -------- contacts after 1st regularization' 54 write (logString, *) ' ' 55 55 call cnteny(nml) 56 write (*,*) ' '56 write (logString, *) ' ' 57 57 58 58 nrs = irsml2(nml)-irsml1(nml)+1 59 59 call rmsdopt(nml,1,nrs,ixatp,xatp,yatp,zatp,0,rm,av1,av2,rmsd) 60 60 61 write (*,*) ' RMSD = ',rmsd61 write (logString, *) ' RMSD = ',rmsd 62 62 63 63 ! --------------------------------------- fix vars. defined in PDB … … 70 70 ireg = 0 71 71 72 write (*,'(/,a,2(a,f4.2),/)')72 write (logString, '(/,a,2(a,f4.2),/)') 73 73 & ' ====================== Internal Energy for Hydrogens only', 74 74 & ' Wt(energy) = ',wtey,' Wt(regul.) = ',wtrg … … 76 76 call minim(1, nsteps, acc) 77 77 78 write (*,*) ' '79 write (*,*) ' ---------- contacs after Emin. for hydrogens'80 write (*,*) ' '78 write (logString, *) ' ' 79 write (logString, *) ' -------- contacs after Emin. for hydrogens' 80 write (logString, *) ' ' 81 81 call cnteny(nml) 82 82 … … 98 98 wtey = 1.d0 - wtrg 99 99 100 write (*,'(/,a,i2,2(a,e11.3),/)')100 write (logString, '(/,a,i2,2(a,e11.3),/)') 101 101 & ' ================ Minimization #',it, 102 102 & ' Wt(energy) = ',wtey,' Wt(regul.) = ',wtrg … … 107 107 call rmsdopt(nml,1,nrs,ixatp,xatp,yatp,zatp,0,rm,av1,av2,rmsd) 108 108 109 write (*,*) ' '110 write (*,*) ' RMSD = ',rmsd109 write (logString, *) ' ' 110 write (logString, *) ' RMSD = ',rmsd 111 111 112 112 enddo 113 113 114 write (*,*) ' '115 write (*,*) ' ---------- contacts after full regularization'116 write (*,*) ' '114 write (logString, *) ' ' 115 write (logString, *) ' ------- contacts after full regularization' 116 write (logString, *) ' ' 117 117 call cnteny(nml) 118 118 … … 120 120 121 121 ! Output of dihedral angles of the regularized structure 122 write(*,*) 'Dihedral angles of the regularized structure;' 122 write (logString, *) 123 & 'Dihedral angles of the regularized structure;' 123 124 call outvar(nml, 'regd.var') 124 125 -
rgyr.f
r32289cd r38d77eb 48 48 49 49 if (nat.le.0) then 50 write ( *,'(a,i4)')50 write (logString, '(a,i4)') 51 51 & ' rgyr> No atoms found for molecule #',nml 52 52 return -
rmsdfun.f
r32289cd r38d77eb 82 82 83 83 if (nml.lt.1.or.nml.gt.ntlml) then 84 write(*,*) ' rmsdopt> Sorry, there is no molecule #',nml 84 write (logString, *) ' rmsdopt> Sorry, there is no molecule #', 85 & nml 85 86 stop 86 87 endif … … 137 138 138 139 if (n.lt.3) then 139 write (*,*) ' rmsdopt> <3 atoms selected !'140 write (logString, *) ' rmsdopt> <3 atoms selected !' 140 141 stop 141 142 endif … … 290 291 integer n,nrot,i,ip,iq,j 291 292 292 293 character(255) logString 293 294 real*8 a(n,n),d(n),v(n,n), 294 295 & c,g,h,s,sm,t,tau,theta,tresh,b(NMAX),z(NMAX),smeps … … 403 404 enddo 404 405 405 write (*,*) ' jacobi> too many iterations'406 write (logString, *) ' jacobi> too many iterations' 406 407 stop 407 408 -
setmvs.f
r32289cd r38d77eb 77 77 78 78 if (ntlvr.eq.0) then 79 write ( *,'(a,i4)')79 write (logString, '(a,i4)') 80 80 & ' setmvs> No variables defined in molecule #',nml 81 81 nmsml(nml)=0 … … 176 176 if (i1.ne.0) then ! combine ranges 177 177 if (j.gt.(i2+1).or.k.lt.(i1-1)) then 178 write ( *,'(3a,/,2a,i4,a,i3)')178 write (logString, '(3a,/,2a,i4,a,i3)') 179 179 & ' setmvs> Cannot combine disjunct ranges of atom', 180 180 & ' indices for torsion ',nmvr(iv),' in residue ', … … 198 198 199 199 if ((nms+1).gt.mxms) then 200 write ( *,'(a,i4,a,i5)') ' setmvs> Molecule # ',nml,200 write (logString, '(a,i4,a,i5)') ' setmvs> Molecule # ',nml, 201 201 & ': Number of moving sets > ',mxms 202 202 stop … … 231 231 nms=nms+1 232 232 if (nms.gt.mxms) then 233 write (*,'(a,i4,a,i5)') ' setmvs> Molecule # ', 233 write (logString, '(a,i4,a,i5)') 234 & ' setmvs> Molecule # ', 234 235 & nml,': Number of moving sets > ',mxms 235 236 stop … … 320 321 nad=nad+1 321 322 if (nad.gt.mxvr) then 322 write (*,'(a,i4,a,i5)') ' setmvs> Molecule # ',nml, 323 write (logString, '(a,i4,a,i5)') ' setmvs> Molecule # ', 324 & nml, 323 325 & ': Number of added variables > ',mxvr 324 326 stop … … 335 337 nad=nad+1 336 338 if (nad.gt.mxvr) then 337 write (*,'(a,i4,a,i5)') ' setmvs> Molecule # ',nml, 339 write (logString, '(a,i4,a,i5)') 340 & ' setmvs> Molecule # ',nml, 338 341 & ': Number of added variables > ',mxvr 339 342 stop … … 349 352 nad=nad+1 350 353 if (nad.gt.mxvr) then 351 write (*,'(a,i4,a,i5)') ' setmvs> Molecule # ',nml, 354 write (logString, '(a,i4,a,i5)') ' setmvs> Molecule # ', 355 & nml, 352 356 & ': Number of added variables > ',mxvr 353 357 stop … … 375 379 ! i2=latms2(i) 376 380 ! if (i.eq.i1s) then 377 ! write ( *,'(a,i3,7a,i4,3a,i4,a)') 'res # ',nursvr(iv),381 ! write (logString, '(a,i3,7a,i4,3a,i4,a)') 'res # ',nursvr(iv), 378 382 ! # ' var: ',nmvr(iv),' base:',nmat(ib),' atoms= ', 379 383 ! # nmat(i1),'(',i1,') - ',nmat(i2),'(',i2,')' 380 384 ! else 381 ! write ( *,'(39x,2a,i4,3a,i4,a)')385 ! write (logString, '(39x,2a,i4,3a,i4,a)') 382 386 ! # nmat(i1),'(',i1,') - ',nmat(i2),'(',i2,')' 383 387 ! endif 384 388 ! enddo 385 389 ! else 386 ! write ( *,'(a,i3,5a)') 'res # ',nursvr(iv),390 ! write (logString, '(a,i3,5a)') 'res # ',nursvr(iv), 387 391 ! # ' var: ',nmvr(iv),' base:',nmat(ib),' No atoms' 388 392 ! endif … … 390 394 ! i2a=iadvr2(iv) 391 395 ! if (i1a.le.i2a) then 392 ! write ( *,'(a,30(1x,a))') ' Depending variables:',396 ! write (logString, '(a,30(1x,a))') ' Depending variables:', 393 397 ! # (nmvr(ladvr(i)),i=i1a,i2a) 394 398 ! else 395 ! write ( *,'(a)') ' No dep. variables'399 ! write (logString, '(a)') ' No dep. variables' 396 400 ! endif 397 401 ! enddo … … 400 404 return 401 405 402 6 write ( *,'(a,i4,/,2(a,i5),a)')406 6 write (logString, '(a,i4,/,2(a,i5),a)') 403 407 & ' setmvs> Error in atom numbering of molecule # ',nml, 404 408 & ': atom ranges for variables # ',iv,' and # ',jv, -
utilities.f
r32289cd r38d77eb 66 66 end do 67 67 ipps = isum / num_ppr 68 write (*,*) "Total number of interactions:", isum 69 write (*,*) "Average # of interactions per processor", ipps 68 write (logString, *) "Total number of interactions:", isum 69 write (logString, *) "Average # of interactions per processor", 70 & ipps 70 71 71 72 totalct = 0 … … 101 102 & .lt.abs(totalct + isum - itarget))) then 102 103 workPerProcessor(nml, irank) = io + 1 103 ! write ( *,*) io + 1, totalct, itarget104 ! write (logString, *) io + 1, totalct, itarget 104 105 else 105 106 workPerProcessor(nml, irank) = io 106 ! write ( *,*) io, totalct + isum, itarget107 ! write (logString, *) io, totalct + isum, itarget 107 108 end if 108 109 irank = irank + 1 … … 127 128 ! rank = 11 128 129 ! fileName = fileNameMP('base_0000.dat', 6, 9, rank) 129 ! write ( *,*), fileName130 ! write (logString, *), fileName 130 131 ! \endcode 131 132 ! will output base_0011.dat.
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