From cfdf99bb8d5233db973de1b78d2905ca5a0ef9cd Mon Sep 17 00:00:00 2001 From: Adam Liwo Date: Sun, 29 Jun 2014 05:35:23 -0400 Subject: [PATCH] Commit Adam 6/29/2014 --- PARAM/scinter_GB_ext.parm | 147 ++++++++------ source/cluster/wham/src-restraint/readrtns.F | 12 +- .../src_MD-M-newcorr/energy_p_new-sep_barrier.F | 44 +++- .../unres/src_MD-M-newcorr/energy_p_new_barrier.F | 14 +- source/unres/src_MD-M-newcorr/geomout.F | 2 +- source/wham/src-M-NEWCORR/DIMENSIONS.FREE | 2 +- source/wham/src-M-NEWCORR/Makefile-ifort-MPICH | 4 +- source/wham/src-M-NEWCORR/enecalc1.F | 31 ++- source/wham/src-M-NEWCORR/energy_p_new.F | 24 ++- source/wham/src-M-NEWCORR/geomout.F | 34 +++- source/wham/src-M-NEWCORR/parmread.F | 2 +- source/wham/src-M/Makefile | 77 +------ source/wham/src-M/tmptmp | 1 - source/wham/src-NEWSC-NEWCORR/energy_p_new.F | 214 ++++++++++---------- source/wham/src-NEWSC-NEWCORR/parmread.F | 8 +- source/wham/src-NEWSC/Makefile | 90 +------- source/wham/src-NEWSC/Makefile_MPICH_ifort | 4 +- source/wham/src-NEWSC/energy_p_new.F | 21 +- source/wham/src-restraints/enecalc1.F | 5 +- 19 files changed, 344 insertions(+), 392 deletions(-) mode change 100644 => 120000 source/wham/src-M/Makefile delete mode 100644 source/wham/src-M/tmptmp mode change 100755 => 100644 source/wham/src-NEWSC/CMakeLists.txt mode change 100755 => 100644 source/wham/src-NEWSC/COMMON.ALLPARM mode change 100755 => 100644 source/wham/src-NEWSC/COMMON.CHAIN mode change 100755 => 100644 source/wham/src-NEWSC/COMMON.COMPAR mode change 100755 => 100644 source/wham/src-NEWSC/COMMON.CONTACTS1 mode change 100755 => 100644 source/wham/src-NEWSC/COMMON.CONTROL mode change 100755 => 100644 source/wham/src-NEWSC/COMMON.CONTROL.org mode change 100755 => 100644 source/wham/src-NEWSC/COMMON.EMP mode change 100755 => 100644 source/wham/src-NEWSC/COMMON.ENEPS mode change 100755 => 100644 source/wham/src-NEWSC/COMMON.ENERGIES mode change 100755 => 100644 source/wham/src-NEWSC/COMMON.FREE mode change 100755 => 100644 source/wham/src-NEWSC/COMMON.IOUNITS mode change 100755 => 100644 source/wham/src-NEWSC/COMMON.MPI mode change 100755 => 100644 source/wham/src-NEWSC/COMMON.OBCINKA mode change 100755 => 100644 source/wham/src-NEWSC/COMMON.PEPTCONT mode change 100755 => 100644 source/wham/src-NEWSC/COMMON.PROT mode change 100755 => 100644 source/wham/src-NEWSC/COMMON.PROTFILES mode change 100755 => 100644 source/wham/src-NEWSC/COMMON.VAR mode change 100755 => 100644 source/wham/src-NEWSC/DIMENSIONS mode change 100755 => 100644 source/wham/src-NEWSC/DIMENSIONS.COMPAR mode change 100755 => 100644 source/wham/src-NEWSC/DIMENSIONS.FREE mode change 100755 => 100644 source/wham/src-NEWSC/DIMENSIONS.FREE.old mode change 100755 => 100644 source/wham/src-NEWSC/DIMENSIONS.ZSCOPT mode change 100755 => 120000 source/wham/src-NEWSC/Makefile mode change 100755 => 100644 source/wham/src-NEWSC/Makefile-pgi mode change 100755 => 100644 source/wham/src-NEWSC/Makefile1_jump mode change 100755 => 100644 source/wham/src-NEWSC/Makefile_MPICH_ifort mode change 100755 => 100644 source/wham/src-NEWSC/Makefile_jubl mode change 100755 => 100644 source/wham/src-NEWSC/Makefile_jump mode change 100755 => 100644 source/wham/src-NEWSC/Makefile_matrix mode change 100755 => 100644 source/wham/src-NEWSC/Makefile_matrix_PGI mode change 100755 => 100644 source/wham/src-NEWSC/Makefile_matrix_PGI-SCT-oldparm mode change 100755 => 100644 source/wham/src-NEWSC/Makefile_matrix_PGI-SCTF-oldparm mode change 100755 => 100644 source/wham/src-NEWSC/Makefile_matrix_PGI-oldparm mode change 100755 => 100644 source/wham/src-NEWSC/a.sh mode change 100755 => 100644 source/wham/src-NEWSC/angnorm.f mode change 100755 => 100644 source/wham/src-NEWSC/arcos.f mode change 100755 => 100644 source/wham/src-NEWSC/bxread.F mode change 100755 => 100644 source/wham/src-NEWSC/cartder.f mode change 100755 => 100644 source/wham/src-NEWSC/cartprint.f mode change 100755 => 100644 source/wham/src-NEWSC/chainbuild.F mode change 100755 => 100644 source/wham/src-NEWSC/chainbuild.f mode change 100755 => 100644 source/wham/src-NEWSC/compinfo.c mode change 100755 => 100644 source/wham/src-NEWSC/conf_compar.F mode change 100755 => 100644 source/wham/src-NEWSC/cont_frag.f mode change 100755 => 100644 source/wham/src-NEWSC/contact.f mode change 100755 => 100644 source/wham/src-NEWSC/contfunc.f mode change 100755 => 100644 source/wham/src-NEWSC/cxread.F mode change 100755 => 100644 source/wham/src-NEWSC/cxread.F.org mode change 100755 => 100644 source/wham/src-NEWSC/define_pairs.f mode change 100755 => 100644 source/wham/src-NEWSC/elecont.f mode change 100755 => 100644 source/wham/src-NEWSC/enecalc1.F mode change 100755 => 100644 source/wham/src-NEWSC/energy_p_new.F mode change 100755 => 100644 source/wham/src-NEWSC/energy_p_new.F.org mode change 100755 => 100644 source/wham/src-NEWSC/fitsq.f mode change 100755 => 100644 source/wham/src-NEWSC/geomout.F mode change 100755 => 100644 source/wham/src-NEWSC/gnmr1.f mode change 100755 => 100644 source/wham/src-NEWSC/icant.f mode change 100755 => 100644 source/wham/src-NEWSC/initialize_p.F mode change 100755 => 100644 source/wham/src-NEWSC/initialize_p.F.org mode change 100755 => 100644 source/wham/src-NEWSC/int_from_cart.f mode change 100755 => 100644 source/wham/src-NEWSC/intcor.f mode change 100755 => 100644 source/wham/src-NEWSC/make_ensemble1.F mode change 100755 => 100644 source/wham/src-NEWSC/match_contact.f mode change 100755 => 100644 source/wham/src-NEWSC/matmult.f mode change 100755 => 100644 source/wham/src-NEWSC/misc.f mode change 100755 => 100644 source/wham/src-NEWSC/molread_zs.F mode change 100755 => 100644 source/wham/src-NEWSC/mygetenv.F mode change 100755 => 100644 source/wham/src-NEWSC/mysort.f mode change 100755 => 100644 source/wham/src-NEWSC/odlodc.f mode change 100755 => 100644 source/wham/src-NEWSC/openunits.F mode change 100755 => 100644 source/wham/src-NEWSC/parmread.F mode change 100755 => 100644 source/wham/src-NEWSC/pinorm.f mode change 100755 => 100644 source/wham/src-NEWSC/printmat.f mode change 100755 => 100644 source/wham/src-NEWSC/proc_cont.f mode change 100755 => 100644 source/wham/src-NEWSC/proc_proc.c mode change 100755 => 100644 source/wham/src-NEWSC/promienie.f mode change 100755 => 100644 source/wham/src-NEWSC/qwolynes.f mode change 100755 => 100644 source/wham/src-NEWSC/read_ref_str.F mode change 100755 => 100644 source/wham/src-NEWSC/readpdb.f mode change 100755 => 100644 source/wham/src-NEWSC/readrtns.F mode change 100755 => 100644 source/wham/src-NEWSC/readrtns.F.org mode change 100755 => 100644 source/wham/src-NEWSC/readrtns_compar.F mode change 100755 => 100644 source/wham/src-NEWSC/rescode.f mode change 100755 => 100644 source/wham/src-NEWSC/rmscalc.f mode change 100755 => 100644 source/wham/src-NEWSC/secondary.f mode change 100755 => 100644 source/wham/src-NEWSC/setup_var.f mode change 100755 => 100644 source/wham/src-NEWSC/slices.F mode change 100755 => 100644 source/wham/src-NEWSC/store_parm.F mode change 100755 => 100644 source/wham/src-NEWSC/timing.F mode change 100755 => 100644 source/wham/src-NEWSC/wham_calc1.F mode change 100755 => 100644 source/wham/src-NEWSC/wham_calc1.F.safe mode change 100755 => 100644 source/wham/src-NEWSC/wham_multparm.F mode change 100755 => 100644 source/wham/src-NEWSC/xread.F diff --git a/PARAM/scinter_GB_ext.parm b/PARAM/scinter_GB_ext.parm index bbb6d91..7f3e726 100644 --- a/PARAM/scinter_GB_ext.parm +++ b/PARAM/scinter_GB_ext.parm @@ -1,109 +1,136 @@ - 4 6 +4 6 5.6053537261 6.2200032154 6.2159898496 6.4386968963 6.2098101231 5.9596374798 5.4310222662 4.8790085257 5.2638423822 5.4961954124 4.2928124162 4.3582250540 4.2667755921 3.6813845958 3.5405429647 3.7026985912 4.7177596156 3.3811992227 3.7936085458 4.5157490585 - 6.2200032154 5.4310222662 5.2638423822 5.2638423822 + 6.2200032154 6.2159898496 5.2638423822 5.2638423822 + 6.6296746680 6.6717260508 6.8168876945 6.8378960152 6.3512039986 6.1425192423 5.5200206406 5.4858936024 4.9382573262 4.2795129166 4.0534857018 4.2086428525 3.5388086279 3.4209730327 2.7995744193 4.8164268553 3.8790755071 3.5878262177 4.6457432555 6.6296746680 - 6.1425192423 5.4858936024 5.4858936024 + 6.6717260508 5.4858936024 5.4858936024 + 6.6424306340 6.9715947250 6.9241225787 6.5291325353 6.1394821460 5.4415971840 5.2914044780 4.7881880526 4.1302408718 3.9405275117 3.9022731880 3.6078928145 3.0809713206 3.0182595342 4.7935507272 3.8711928134 - 3.6826168780 4.4872661030 6.6717260508 6.1394821460 + 3.6826168780 4.4872661030 6.6717260508 6.6424306340 5.2914044780 5.2914044780 + 7.3271707934 7.2970176793 7.0494948235 6.2565687662 5.8133715113 5.8845382769 5.3463553241 4.7146928716 4.4864793359 4.3092352779 3.6928361281 4.0100566871 3.6584608489 4.5901676001 4.4681844010 4.6334334282 - 4.9023945082 6.8168876945 6.2565687662 5.8845382769 + 4.9023945082 6.8168876945 6.9715947250 5.8845382769 5.8845382769 + 7.0106342493 6.8341607204 6.2047876082 5.5802122247 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a/source/cluster/wham/src-restraint/readrtns.F b/source/cluster/wham/src-restraint/readrtns.F index 7112c47..30f5009 100644 --- a/source/cluster/wham/src-restraint/readrtns.F +++ b/source/cluster/wham/src-restraint/readrtns.F @@ -861,19 +861,19 @@ c====------------------------------------------------------------------- model_ki_dist="model"//kic2//".dist" model_ki_angle="model"//kic2//".angle" - open (ientin,file=model_ki_dist,status='old') + open (imol2,file=model_ki_dist,status='old') do irec=1,maxdim !petla do czytania wiezow na odleglosc - read (ientin,*,end=1401) i, j, odl_temp(i+nnt-1,j+nnt-1,ki), + read (imol2,*,end=1401) i, j, odl_temp(i+nnt-1,j+nnt-1,ki), & sigma_odl_temp(i+nnt-1,j+nnt-1,ki) odl_temp(j+nnt-1,i+nnt-1,ki)=odl_temp(i+nnt-1,j+nnt-1,ki) sigma_odl_temp(j+nnt-1,i+nnt-1,ki)= & sigma_odl_temp(i+nnt-1,j+nnt-1,ki) enddo 1401 continue - close (ientin) - open (ientin,file=model_ki_angle,status='old') + close (imol2) + open (imol2,file=model_ki_angle,status='old') do irec=1,maxres-3 !petla do czytania wiezow na katy torsyjne - read (ientin,*,end=1402) i, j, k,l,dih(ki,i+nnt-1), + read (imol2,*,end=1402) i, j, k,l,dih(ki,i+nnt-1), & sigma_dih(ki,i+nnt-1) write (iout,*) i, j, k,l,dih(ki,i+nnt-1), & sigma_dih(ki,i+nnt-1) @@ -881,7 +881,7 @@ c====------------------------------------------------------------------- sigma_dih(ki,i+nnt-1)=1.0d0/sigma_dih(ki,i+nnt-1)**2 enddo 1402 continue - close (ientin) + close (imol2) enddo ii=0 write (iout,*) "nnt",nnt," nct",nct diff --git a/source/unres/src_MD-M-newcorr/energy_p_new-sep_barrier.F b/source/unres/src_MD-M-newcorr/energy_p_new-sep_barrier.F index 6592ace..5f9a128 100644 --- a/source/unres/src_MD-M-newcorr/energy_p_new-sep_barrier.F +++ b/source/unres/src_MD-M-newcorr/energy_p_new-sep_barrier.F @@ -1352,7 +1352,8 @@ C------------------------------------------------------------------------------- dimension ggg(3),gggp(3),gggm(3),erij(3),dcosb(3),dcosg(3), & erder(3,3),uryg(3,3),urzg(3,3),vryg(3,3),vrzg(3,3) double precision acipa(2,2),agg(3,4),aggi(3,4),aggi1(3,4), - & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4) + & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4),gmuij1(4),gmuji1(4), + & gmuij2(4),gmuji2(4) common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33, & dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi, & num_conti,j1,j2 @@ -1582,6 +1583,14 @@ C do l=1,2 kkk=kkk+1 muij(kkk)=mu(k,i)*mu(l,j) +#ifdef NEWCORR + gmuij1(kkk)=gtb1(k,i+1)*mu(l,j) +c write(iout,*) 'kkk=', gtb1(k,i)*mu(l,j),gtb1(k,i),k,i + gmuij2(kkk)=gUb2(k,i)*mu(l,j) + gmuji1(kkk)=mu(k,i)*gtb1(l,j+1) +c write(iout,*) 'kkk=', gtb1(k,i)*mu(l,j),gtb1(l,j),l,j + gmuji2(kkk)=mu(k,i)*gUb2(l,j) +#endif enddo enddo cd write (iout,*) 'EELEC: i',i,' j',j @@ -1748,7 +1757,40 @@ C Contribution to the local-electrostatic energy coming from the i-j pair eel_loc_ij=a22*muij(1)+a23*muij(2)+a32*muij(3) & +a33*muij(4) cd write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij +C Calculate patrial derivative for theta angle +#ifdef NEWCORR + geel_loc_ij=a22*gmuij1(1) + & +a23*gmuij1(2) + & +a32*gmuij1(3) + & +a33*gmuij1(4) +c write(iout,*) "derivative over thatai" +c write(iout,*) a22*gmuij1(1), a23*gmuij1(2) ,a32*gmuij1(3), +c & a33*gmuij1(4) + gloc(nphi+i,icg)=gloc(nphi+i,icg)+ + & geel_loc_ij*wel_loc +c write(iout,*) "derivative over thatai-1" +c write(iout,*) a22*gmuij2(1), a23*gmuij2(2) ,a32*gmuij2(3), +c & a33*gmuij2(4) + geel_loc_ij=a22*gmuij2(1)+a23*gmuij2(2)+a32*gmuij2(3) + & +a33*gmuij2(4) + gloc(nphi+i-1,icg)=gloc(nphi+i-1,icg)+ + & geel_loc_ij*wel_loc + geel_loc_ji=a22*gmuji1(1)+a23*gmuji1(2)+a32*gmuji1(3) + & +a33*gmuji1(4) +c write(iout,*) "derivative over thataj" +c write(iout,*) a22*gmuji1(1), a23*gmuji1(2) ,a32*gmuji1(3), +c & a33*gmuji1(4) + gloc(nphi+j,icg)=gloc(nphi+j,icg)+ + & geel_loc_ji*wel_loc + geel_loc_ji=a22*gmuji2(1)+a23*gmuji2(2)+a32*gmuji2(3) + & +a33*gmuji2(4) +c write(iout,*) "derivative over thataj-1" +c write(iout,*) a22*gmuji2(1), a23*gmuji2(2) ,a32*gmuji2(3), +c & a33*gmuji2(4) + gloc(nphi+j-1,icg)=gloc(nphi+j-1,icg)+ + & geel_loc_ji*wel_loc +#endif if (energy_dec) write (iout,'(a6,2i5,0pf7.3)') & 'eelloc',i,j,eel_loc_ij diff --git a/source/unres/src_MD-M-newcorr/energy_p_new_barrier.F b/source/unres/src_MD-M-newcorr/energy_p_new_barrier.F index 97c4144..c9140a6 100644 --- a/source/unres/src_MD-M-newcorr/energy_p_new_barrier.F +++ b/source/unres/src_MD-M-newcorr/energy_p_new_barrier.F @@ -710,7 +710,6 @@ c enddo do i=1,4*nres glocbuf(i)=gloc(i,icg) enddo -#define DEBUG #ifdef DEBUG write (iout,*) "gloc_sc before reduce" do i=1,nres @@ -719,7 +718,6 @@ c enddo enddo enddo #endif -#undef DEBUG do i=1,nres do j=1,3 gloc_scbuf(j,i)=gloc_sc(j,i,icg) @@ -739,7 +737,6 @@ c enddo call MPI_Reduce(gloc_scbuf(1,1),gloc_sc(1,1,icg),3*nres, & MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR) time_reduce=time_reduce+MPI_Wtime()-time00 -#define DEBUG #ifdef DEBUG write (iout,*) "gloc_sc after reduce" do i=1,nres @@ -748,7 +745,6 @@ c enddo enddo enddo #endif -#undef DEBUG #ifdef DEBUG write (iout,*) "gloc after reduce" do i=1,4*nres @@ -5808,7 +5804,7 @@ c---------------------------------------------------------------------------- logical lprn C Set lprn=.true. for debugging lprn=.false. -c lprn=.true. +c lprn=.true. etors=0.0D0 do i=iphi_start,iphi_end if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1 @@ -5856,12 +5852,12 @@ C C Subtract the constant term etors=etors-v0(itori,itori1,iblock) if (energy_dec) write (iout,'(a6,i5,0pf7.3)') - & 'etor',i,etors_ii-v0(itori,itori1,iblock) + & 'etor',i,etors_ii if (lprn) - & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)') + & write (iout,'(2(a3,2x,i3,2x),2i3,f10.2,6f8.3/36x,6f8.3/)') & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1, - & (v1(j,itori,itori1,iblock),j=1,6), - & (v2(j,itori,itori1,iblock),j=1,6) + & rad2deg*phii, + & (v1(j,itori,itori1,1),j=1,6),(v2(j,itori,itori1,1),j=1,6) gloc(i-3,icg)=gloc(i-3,icg)+wtor*gloci c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg) enddo diff --git a/source/unres/src_MD-M-newcorr/geomout.F b/source/unres/src_MD-M-newcorr/geomout.F index c6a3944..b5d8732 100644 --- a/source/unres/src_MD-M-newcorr/geomout.F +++ b/source/unres/src_MD-M-newcorr/geomout.F @@ -206,7 +206,7 @@ c------------------------------------------------------------------------ & ' Phi',' Dsc',' Alpha',' Omega' do i=1,nres iti=itype(i) - write (iout,'(a3,i4,6f10.3)') restyp(iti),i,vbld(i), + write (iout,'(a3,i4,6f10.3)') restyp(iti),i,vbld(i+1), & rad2deg*theta(i),rad2deg*phi(i),vbld(nres+i),rad2deg*alph(i), & rad2deg*omeg(i) enddo diff --git a/source/wham/src-M-NEWCORR/DIMENSIONS.FREE b/source/wham/src-M-NEWCORR/DIMENSIONS.FREE index 691d9b2..2ccf317 100644 --- a/source/wham/src-M-NEWCORR/DIMENSIONS.FREE +++ b/source/wham/src-M-NEWCORR/DIMENSIONS.FREE @@ -4,7 +4,7 @@ integer MaxSlice parameter (Max_Parm=1) parameter (MaxQ=1,MaxQ1=MaxQ+2) - parameter(MaxR=1,MaxT_h=32) + parameter(MaxR=4,MaxT_h=32) parameter(MaxSlice=40) integer MaxN parameter (MaxN=100) diff --git a/source/wham/src-M-NEWCORR/Makefile-ifort-MPICH b/source/wham/src-M-NEWCORR/Makefile-ifort-MPICH index 866565f..7abfc9d 100644 --- a/source/wham/src-M-NEWCORR/Makefile-ifort-MPICH +++ b/source/wham/src-M-NEWCORR/Makefile-ifort-MPICH @@ -1,8 +1,8 @@ INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh BIN = /users/adam/unres/bin/wham FC= ifort -#OPT = -mcmodel=medium -O3 -ip -w -OPT = -mcmodel=medium -g -CA -CB +OPT = -mcmodel=medium -O3 -ip -w +#OPT = -mcmodel=medium -g -CA -CB FFLAGS = ${OPT} -c -I. -I./include_unres -I$(INSTALL_DIR)/include LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpmpich xdrf/libxdrf.a diff --git a/source/wham/src-M-NEWCORR/enecalc1.F b/source/wham/src-M-NEWCORR/enecalc1.F index 8e4fa74..4372c6f 100644 --- a/source/wham/src-M-NEWCORR/enecalc1.F +++ b/source/wham/src-M-NEWCORR/enecalc1.F @@ -33,7 +33,7 @@ double precision rmsnat,gyrate external rmsnat,gyrate double precision tole /1.0d-1/ - integer i,itj,ii,iii,j,k,l,licz + integer i,itj,ii,iii,j,k,l,licz,itmp integer ir,ib,ipar,iparm integer iscor,islice real*4 csingle(3,maxres2) @@ -157,15 +157,23 @@ c & " kfac",kfac,"quot",quot," fT",fT call etotal(energia(0),fT) #ifdef DEBUG write (iout,*) "Conformation",i - write (iout,'(8f10.5)') ((c(l,k),l=1,3),k=1,nres) - write (iout,'(8f10.5)') ((c(l,k+nres),l=1,3),k=nnt,nct) +c write (iout,'(8f10.5)') ((c(l,k),l=1,3),k=1,nres) +c write (iout,'(8f10.5)') ((c(l,k+nres),l=1,3),k=nnt,nct) call enerprint(energia(0),fT) - write (iout,'(2i5,21f8.2)') i,iparm,(energia(k),k=1,21) - write (iout,*) "ftors",ftors - call briefout(i,energia(0)) - temp=1.0d0/(beta_h(ib,ipar)*1.987D-3) - write (iout,*) "temp", temp - call pdbout(i,temp,energia(0),energia(0),0.0d0,0.0d0) +c write (iout,'(2i5,21f8.2)') i,iparm,(energia(k),k=1,21) +c write (iout,*) "ftors",ftors + itmp=igeom + igeom=iout + call cartout(i) +c call briefout(i,energia(0)) + igeom=itmp + call intout +c temp=1.0d0/(beta_h(ib,ipar)*1.987D-3) +c write (iout,*) "temp", temp + itmp=ipdb + ipdb=iout + call pdbout(i,temp,energia(0),energia(0),0.0d0,0.0d0) + ipdb=itmp #endif if (energia(0).ge.1.0d20) then write (iout,*) "NaNs detected in some of the energy", @@ -202,10 +210,15 @@ c call pdbout(ii+1,beta_h(ib,ipar),efree,energia(0),0.0d0,rmsdev) & iii+1,indstart(me1)+iii," T", & 1.0d0/(1.987D-3*beta_h(ib,ipar)) c call intout +#ifdef DEBUG + itmp=ipdb + ipdb=iout call pdbout(indstart(me1)+iii, & 1.0d0/(1.987D-3*beta_h(ib,ipar)), &energia(0),eini,0.0d0,0.0d0) + ipdb=itmp call enerprint(energia(0),fT) +#endif errmsg_count=errmsg_count+1 if (errmsg_count.gt.maxerrmsg_count) & write (iout,*) "Too many warning messages" diff --git a/source/wham/src-M-NEWCORR/energy_p_new.F b/source/wham/src-M-NEWCORR/energy_p_new.F index 0dddd7f..917b6a6 100644 --- a/source/wham/src-M-NEWCORR/energy_p_new.F +++ b/source/wham/src-M-NEWCORR/energy_p_new.F @@ -1718,8 +1718,8 @@ c write (iout,*) 'theta=', theta(i-1) iti1=ntortyp+1 endif cd write (iout,*) '*******i',i,' iti1',iti -cd write (iout,*) 'b1',b1(:,iti) -cd write (iout,*) 'b2',b2(:,iti) +cd write (iout,*) 'b1',b1(:,i-2) +cd write (iout,*) 'b2',b2(:,i-2) cd write (iout,*) 'Ug',Ug(:,:,i-2) c print *,"itilde1 i iti iti1",i,iti,iti1 if (i .gt. iatel_s+2) then @@ -4362,7 +4362,6 @@ C----------------------------------------------------------------------------- include 'COMMON.IOUNITS' include 'COMMON.FFIELD' include 'COMMON.TORCNSTR' - logical lprn C Set lprn=.true. for debugging lprn=.false. c lprn=.true. @@ -4447,10 +4446,11 @@ c------------------------------------------------------------------------------ include 'COMMON.IOUNITS' include 'COMMON.FFIELD' include 'COMMON.TORCNSTR' - logical lprn + logical lprn,energy_dec C Set lprn=.true. for debugging lprn=.false. c lprn=.true. + energy_dec=.false. etors=0.0D0 do i=iphi_start,iphi_end if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1 @@ -4465,6 +4465,7 @@ c lprn=.true. itori1=itortyp(itype(i-1)) phii=phi(i) gloci=0.0D0 + etors_ii=0.0d0 C Regular cosine and sine terms do j=1,nterm(itori,itori1,iblock) v1ij=v1(j,itori,itori1,iblock) @@ -4472,6 +4473,8 @@ C Regular cosine and sine terms cosphi=dcos(j*phii) sinphi=dsin(j*phii) etors=etors+v1ij*cosphi+v2ij*sinphi + if (energy_dec) etors_ii=etors_ii+ + & v1ij*cosphi+v2ij*sinphi gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi) enddo C Lorentz terms @@ -4488,16 +4491,19 @@ C pom=vl2ij*cosphi+vl3ij*sinphi pom1=1.0d0/(pom*pom+1.0d0) etors=etors+vl1ij*pom1 -c if (energy_dec) etors_ii=etors_ii+ -c & vl1ij*pom1 + if (energy_dec) etors_ii=etors_ii+ + & vl1ij*pom1 pom=-pom*pom1*pom1 gloci=gloci+vl1ij*(vl3ij*cosphi-vl2ij*sinphi)*pom enddo C Subtract the constant term etors=etors-v0(itori,itori1,iblock) + if (energy_dec) write (iout,'(a6,i5,0pf7.3)') + & 'etor',i,etors_ii if (lprn) - & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)') + & write (iout,'(2(a3,2x,i3,2x),2i3,f10.2,6f8.3/36x,6f8.3/)') & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1, + & rad2deg*phii, & (v1(j,itori,itori1,1),j=1,6),(v2(j,itori,itori1,1),j=1,6) gloc(i-3,icg)=gloc(i-3,icg)+wtor*fact*gloci c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg) @@ -4550,8 +4556,8 @@ C 6/23/01 Compute double torsional energy include 'COMMON.TORCNSTR' logical lprn C Set lprn=.true. for debugging - lprn=.false. -c lprn=.true. +c lprn=.false. + lprn=.true. etors_d=0.0D0 do i=iphi_start,iphi_end-1 if (itype(i-2).eq.ntyp1.or. itype(i-1).eq.ntyp1 diff --git a/source/wham/src-M-NEWCORR/geomout.F b/source/wham/src-M-NEWCORR/geomout.F index 0f729e4..28e1fa7 100644 --- a/source/wham/src-M-NEWCORR/geomout.F +++ b/source/wham/src-M-NEWCORR/geomout.F @@ -156,9 +156,9 @@ c--------------------------------------------------------------------------- include 'COMMON.SBRIDGE' print '(a,i5)',intname,igeom #if defined(AIX) || defined(PGI) - open (igeom,file=intname,position='append') +c open (igeom,file=intname,position='append') #else - open (igeom,file=intname,access='append') +c open (igeom,file=intname,access='append') #endif iii=igeom igeom=iout @@ -175,9 +175,37 @@ c if (nvar.gt.nphi+ntheta) then write (igeom,200) (rad2deg*alph(i),i=2,nres-1) write (igeom,200) (rad2deg*omeg(i),i=2,nres-1) c endif - close(igeom) +c close(igeom) 180 format (I5,F12.3,I2,9(1X,2I3)) 190 format (3X,11(1X,2I3)) 200 format (8F10.4) return end +c---------------------------------------------------------------- + subroutine cartout(i) + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' + include 'DIMENSIONS.ZSCOPT' + include 'COMMON.CHAIN' + include 'COMMON.INTERACT' + include 'COMMON.NAMES' + include 'COMMON.IOUNITS' + include 'COMMON.HEADER' + include 'COMMON.SBRIDGE' + double precision time +#if defined(AIX) || defined(PGI) +c open(igeom,file=cartname,position="append") +#else +c open(igeom,file=cartname,access="append") +#endif + write (igeom,'("Conformation",i10)') i + write (igeom,'(i4,$)') + & nss,(ihpb(j),jhpb(j),j=1,nss) + write(igeom,*) + write (igeom,'(8f10.5)') + & ((c(k,j),k=1,3),j=1,nres), + & ((c(k,j+nres),k=1,3),j=nnt,nct) +c close(igeom) + return + end + diff --git a/source/wham/src-M-NEWCORR/parmread.F b/source/wham/src-M-NEWCORR/parmread.F index 34d68d1..3a6b14c 100644 --- a/source/wham/src-M-NEWCORR/parmread.F +++ b/source/wham/src-M-NEWCORR/parmread.F @@ -917,7 +917,7 @@ c write(iout,*) "TU DOCHODZE" enddo c lprint=.true. if (lprint) then - do i=1,nloctyp + do i=0,nloctyp-1 write (iout,*) 'Type',i write (iout,*) 'BNEW1(1)' write (iout,*) (BNEW1(ii,1,i),ii=1,3) diff --git a/source/wham/src-M/Makefile b/source/wham/src-M/Makefile deleted file mode 100644 index 11aac6c..0000000 --- a/source/wham/src-M/Makefile +++ /dev/null @@ -1,76 +0,0 @@ -INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh -BIN = ../bin -CC = cc -FC = ifort -#OPT = -O3 -ip -w -OPT = -g -CB -FFLAGS = -c ${OPT} -I. -I./include_unres -I$(INSTALL_DIR)/include -#FFLAGS = -c -g -C -I. -I./include_unres -I$(INSTALL_DIR)/include -LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdrf.a -#LIBS = -L$(INSTALL_DIR)/lib_pgi -lmpich -lpmpich -Vaxlib -#CPPFLAGS = -DMPI -DLINUX -DUNRES -DMOMENT -DCHECKGRAD -DPGI -#CPPFLAGS = -DMPI -DLINUX -DUNRES -DCHECKGRAD -DPGI -DMYGETENV -CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI -DCRYST_BOND -DCRYST_SC -DCRYST_THETA -#CPPFLAGS = -DMPI -DLINUX -DUNRES -DPGI -#CPPFLAGS = -DMPI -DLINUX -DUNRES - -.f.o: - ${FC} ${FFLAGS} $*.f - -.F.o: - ${FC} ${FFLAGS} ${CPPFLAGS} $*.F - -all: make_dbase - -objects = \ - wham_multparm.o \ - bxread.o \ - xread.o \ - cxread.o \ - enecalc1.o \ - energy_p_new.o \ - gnmr1.o \ - initialize_p.o \ - molread_zs.o \ - openunits.o \ - readrtns.o \ - read_dist_constr.o \ - arcos.o \ - cartder.o \ - cartprint.o \ - chainbuild.o \ - geomout.o \ - icant.o \ - intcor.o \ - int_from_cart.o \ - make_ensemble1.o \ - matmult.o \ - misc.o \ - mygetenv.o \ - parmread.o \ - pinorm.o \ - printmat.o \ - proc_proc.o \ - rescode.o \ - setup_var.o \ - slices.o \ - store_parm.o \ - timing.o \ - wham_calc1.o - -objects_compar = \ - readrtns_compar.o \ - readpdb.o permut.o fitsq.o contact.o \ - elecont.o contfunc.o cont_frag.o conf_compar.o match_contact.o \ - angnorm.o odlodc.o promienie.o qwolynes.o read_ref_str.o \ - rmscalc.o secondary.o proc_cont.o define_pairs.o mysort.o - -make_dbase: ${objects} ${objects_compar} - cc -o compinfo compinfo.c - ./compinfo - ${FC} -c ${FFLAGS} cinfo.f - $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \ - ${LIBS} -o ${BIN}/wham_multparm-D-sccor-oldparm - -clean: - /bin/rm *.o diff --git a/source/wham/src-M/Makefile b/source/wham/src-M/Makefile new file mode 120000 index 0000000..7018157 --- /dev/null +++ b/source/wham/src-M/Makefile @@ -0,0 +1 @@ +Makefile-ifort-MPICH \ No newline at end of file diff --git a/source/wham/src-M/tmptmp b/source/wham/src-M/tmptmp deleted file mode 100644 index fb6f043..0000000 --- a/source/wham/src-M/tmptmp +++ /dev/null @@ -1 +0,0 @@ -aks255 diff --git a/source/wham/src-NEWSC-NEWCORR/energy_p_new.F b/source/wham/src-NEWSC-NEWCORR/energy_p_new.F index 0ee066f..b847313 100644 --- a/source/wham/src-NEWSC-NEWCORR/energy_p_new.F +++ b/source/wham/src-NEWSC-NEWCORR/energy_p_new.F @@ -3406,11 +3406,11 @@ C iti1=ntortyp+1 endif cd write (iout,*) '*******i',i,' iti1',iti -cd write (iout,*) 'b1',b1(:,iti) -cd write (iout,*) 'b2',b2(:,iti) +cd write (iout,*) 'b1',b1(:,i-2) +cd write (iout,*) 'b2',b2(:,i-2) cd write (iout,*) 'Ug',Ug(:,:,i-2) if (i .gt. iatel_s+2) then - call matvec2(Ug(1,1,i-2),b2(1,iti),Ub2(1,i-2)) + call matvec2(Ug(1,1,i-2),b2(1,i-2),Ub2(1,i-2)) call matmat2(EE(1,1,iti),Ug(1,1,i-2),EUg(1,1,i-2)) call matmat2(CC(1,1,iti),Ug(1,1,i-2),CUg(1,1,i-2)) call matmat2(DD(1,1,iti),Ug(1,1,i-2),DUg(1,1,i-2)) @@ -3430,7 +3430,7 @@ cd write (iout,*) 'Ug',Ug(:,:,i-2) enddo enddo endif - call matvec2(Ugder(1,1,i-2),b2(1,iti),Ub2der(1,i-2)) + call matvec2(Ugder(1,1,i-2),b2(1,i-2),Ub2der(1,i-2)) call matmat2(EE(1,1,iti),Ugder(1,1,i-2),EUgder(1,1,i-2)) call matmat2(CC(1,1,iti1),Ugder(1,1,i-2),CUgder(1,1,i-2)) call matmat2(DD(1,1,iti),Ugder(1,1,i-2),DUgder(1,1,i-2)) @@ -3446,10 +3446,10 @@ cd write (iout,*) 'Ug',Ug(:,:,i-2) iti1=ntortyp+1 endif do k=1,2 - mu(k,i-2)=Ub2(k,i-2)+b1(k,iti1) + mu(k,i-2)=Ub2(k,i-2)+b1(k,i-1) enddo C Vectors and matrices dependent on a single virtual-bond dihedral. - call matvec2(DD(1,1,iti),b1tilde(1,iti1),auxvec(1)) + call matvec2(DD(1,1,iti),b1tilde(1,i-1),auxvec(1)) call matvec2(Ug2(1,1,i-2),auxvec(1),Ug2Db1t(1,i-2)) call matvec2(Ug2der(1,1,i-2),auxvec(1),Ug2Db1tder(1,i-2)) call matvec2(CC(1,1,iti1),Ub2(1,i-2),CUgb2(1,i-2)) @@ -4346,10 +4346,10 @@ cd call checkint_turn4(i,a_temp,eello_turn4_num) call transpose2(Eug(1,1,i+3),e3t(1,1)) call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1)) call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1)) - s1=scalar2(b1(1,iti2),auxvec(1)) + s1=scalar2(b1(1,i+2),auxvec(1)) call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1)) call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1)) - s2=scalar2(b1(1,iti1),auxvec(1)) + s2=scalar2(b1(1,i+1),auxvec(1)) call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1)) call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) @@ -4361,14 +4361,14 @@ C Derivatives in gamma(i) call transpose2(EUgder(1,1,i+1),e1tder(1,1)) call matmat2(e1tder(1,1),a_temp(1,1),auxmat(1,1)) call matvec2(auxmat(1,1),Ub2(1,i+3),auxvec(1)) - s1=scalar2(b1(1,iti2),auxvec(1)) + s1=scalar2(b1(1,i+2),auxvec(1)) call matmat2(ae3e2(1,1),e1tder(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) gel_loc_turn4(i)=gel_loc_turn4(i)-(s1+s3) C Derivatives in gamma(i+1) call transpose2(EUgder(1,1,i+2),e2tder(1,1)) call matvec2(ae3(1,1),Ub2der(1,i+2),auxvec(1)) - s2=scalar2(b1(1,iti1),auxvec(1)) + s2=scalar2(b1(1,i+1),auxvec(1)) call matmat2(ae3(1,1),e2tder(1,1),auxmat(1,1)) call matmat2(auxmat(1,1),e1t(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) @@ -4376,10 +4376,10 @@ C Derivatives in gamma(i+1) C Derivatives in gamma(i+2) call transpose2(EUgder(1,1,i+3),e3tder(1,1)) call matvec2(e1a(1,1),Ub2der(1,i+3),auxvec(1)) - s1=scalar2(b1(1,iti2),auxvec(1)) + s1=scalar2(b1(1,i+2),auxvec(1)) call matmat2(a_temp(1,1),e3tder(1,1),auxmat(1,1)) call matvec2(auxmat(1,1),Ub2(1,i+2),auxvec(1)) - s2=scalar2(b1(1,iti1),auxvec(1)) + s2=scalar2(b1(1,i+1),auxvec(1)) call matmat2(auxmat(1,1),e2t(1,1),auxmat(1,1)) call matmat2(auxmat(1,1),e1t(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) @@ -4394,10 +4394,10 @@ C Derivatives of this turn contributions in DC(i+2) a_temp(2,2)=agg(l,4) call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1)) call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1)) - s1=scalar2(b1(1,iti2),auxvec(1)) + s1=scalar2(b1(1,i+2),auxvec(1)) call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1)) call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1)) - s2=scalar2(b1(1,iti1),auxvec(1)) + s2=scalar2(b1(1,i+1),auxvec(1)) call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1)) call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) @@ -4413,10 +4413,10 @@ C Remaining derivatives of this turn contribution a_temp(2,2)=aggi(l,4) call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1)) call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1)) - s1=scalar2(b1(1,iti2),auxvec(1)) + s1=scalar2(b1(1,i+2),auxvec(1)) call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1)) call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1)) - s2=scalar2(b1(1,iti1),auxvec(1)) + s2=scalar2(b1(1,i+1),auxvec(1)) call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1)) call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) @@ -4427,10 +4427,10 @@ C Remaining derivatives of this turn contribution a_temp(2,2)=aggi1(l,4) call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1)) call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1)) - s1=scalar2(b1(1,iti2),auxvec(1)) + s1=scalar2(b1(1,i+2),auxvec(1)) call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1)) call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1)) - s2=scalar2(b1(1,iti1),auxvec(1)) + s2=scalar2(b1(1,i+1),auxvec(1)) call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1)) call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) @@ -4441,10 +4441,10 @@ C Remaining derivatives of this turn contribution a_temp(2,2)=aggj(l,4) call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1)) call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1)) - s1=scalar2(b1(1,iti2),auxvec(1)) + s1=scalar2(b1(1,i+2),auxvec(1)) call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1)) call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1)) - s2=scalar2(b1(1,iti1),auxvec(1)) + s2=scalar2(b1(1,i+1),auxvec(1)) call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1)) call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) @@ -4455,10 +4455,10 @@ C Remaining derivatives of this turn contribution a_temp(2,2)=aggj1(l,4) call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1)) call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1)) - s1=scalar2(b1(1,iti2),auxvec(1)) + s1=scalar2(b1(1,i+2),auxvec(1)) call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1)) call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1)) - s2=scalar2(b1(1,iti1),auxvec(1)) + s2=scalar2(b1(1,i+1),auxvec(1)) call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1)) call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) @@ -7013,10 +7013,10 @@ C--------------------------------------------------------------------------- do iii=1,2 dipi(iii,1)=Ub2(iii,i) dipderi(iii)=Ub2der(iii,i) - dipi(iii,2)=b1(iii,iti1) + dipi(iii,2)=b1(iii,i+1) dipj(iii,1)=Ub2(iii,j) dipderj(iii)=Ub2der(iii,j) - dipj(iii,2)=b1(iii,itj1) + dipj(iii,2)=b1(iii,j+1) enddo kkk=0 do iii=1,2 @@ -7195,26 +7195,26 @@ C They are needed only when the fifth- or the sixth-order cumulants are C indluded. IF (wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0) THEN call transpose2(AEA(1,1,1),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,iti),AEAb1(1,1,1)) + call matvec2(auxmat(1,1),b1(1,i),AEAb1(1,1,1)) call matvec2(auxmat(1,1),Ub2(1,i),AEAb2(1,1,1)) call matvec2(auxmat(1,1),Ub2der(1,i),AEAb2derg(1,2,1,1)) call transpose2(AEAderg(1,1,1),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,iti),AEAb1derg(1,1,1)) + call matvec2(auxmat(1,1),b1(1,i),AEAb1derg(1,1,1)) call matvec2(auxmat(1,1),Ub2(1,i),AEAb2derg(1,1,1,1)) - call matvec2(AEA(1,1,1),b1(1,itk1),AEAb1(1,2,1)) - call matvec2(AEAderg(1,1,1),b1(1,itk1),AEAb1derg(1,2,1)) + call matvec2(AEA(1,1,1),b1(1,k+1),AEAb1(1,2,1)) + call matvec2(AEAderg(1,1,1),b1(1,k+1),AEAb1derg(1,2,1)) call matvec2(AEA(1,1,1),Ub2(1,k+1),AEAb2(1,2,1)) call matvec2(AEAderg(1,1,1),Ub2(1,k+1),AEAb2derg(1,1,2,1)) call matvec2(AEA(1,1,1),Ub2der(1,k+1),AEAb2derg(1,2,2,1)) call transpose2(AEA(1,1,2),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,itj),AEAb1(1,1,2)) + call matvec2(auxmat(1,1),b1(1,j),AEAb1(1,1,2)) call matvec2(auxmat(1,1),Ub2(1,j),AEAb2(1,1,2)) call matvec2(auxmat(1,1),Ub2der(1,j),AEAb2derg(1,2,1,2)) call transpose2(AEAderg(1,1,2),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,itj),AEAb1derg(1,1,2)) + call matvec2(auxmat(1,1),b1(1,j),AEAb1derg(1,1,2)) call matvec2(auxmat(1,1),Ub2(1,j),AEAb2derg(1,1,1,2)) - call matvec2(AEA(1,1,2),b1(1,itl1),AEAb1(1,2,2)) - call matvec2(AEAderg(1,1,2),b1(1,itl1),AEAb1derg(1,2,2)) + call matvec2(AEA(1,1,2),b1(1,l+1),AEAb1(1,2,2)) + call matvec2(AEAderg(1,1,2),b1(1,l+1),AEAb1derg(1,2,2)) call matvec2(AEA(1,1,2),Ub2(1,l+1),AEAb2(1,2,2)) call matvec2(AEAderg(1,1,2),Ub2(1,l+1),AEAb2derg(1,1,2,2)) call matvec2(AEA(1,1,2),Ub2der(1,l+1),AEAb2derg(1,2,2,2)) @@ -7223,20 +7223,20 @@ C Calculate the Cartesian derivatives of the vectors. do kkk=1,5 do lll=1,3 call transpose2(AEAderx(1,1,lll,kkk,iii,1),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,iti), + call matvec2(auxmat(1,1),b1(1,i), & AEAb1derx(1,lll,kkk,iii,1,1)) call matvec2(auxmat(1,1),Ub2(1,i), & AEAb2derx(1,lll,kkk,iii,1,1)) - call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,itk1), + call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,k+1), & AEAb1derx(1,lll,kkk,iii,2,1)) call matvec2(AEAderx(1,1,lll,kkk,iii,1),Ub2(1,k+1), & AEAb2derx(1,lll,kkk,iii,2,1)) call transpose2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,itj), + call matvec2(auxmat(1,1),b1(1,j), & AEAb1derx(1,lll,kkk,iii,1,2)) call matvec2(auxmat(1,1),Ub2(1,j), & AEAb2derx(1,lll,kkk,iii,1,2)) - call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,itl1), + call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,l+1), & AEAb1derx(1,lll,kkk,iii,2,2)) call matvec2(AEAderx(1,1,lll,kkk,iii,2),Ub2(1,l+1), & AEAb2derx(1,lll,kkk,iii,2,2)) @@ -7333,26 +7333,26 @@ C indluded. IF (wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0 .or. & (wturn6.gt.0.0d0 .and. j.eq.i+4 .and. l.eq.i+3)) THEN call transpose2(AEA(1,1,1),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,iti),AEAb1(1,1,1)) + call matvec2(auxmat(1,1),b1(1,i),AEAb1(1,1,1)) call matvec2(auxmat(1,1),Ub2(1,i),AEAb2(1,1,1)) call matvec2(auxmat(1,1),Ub2der(1,i),AEAb2derg(1,2,1,1)) call transpose2(AEAderg(1,1,1),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,iti),AEAb1derg(1,1,1)) + call matvec2(auxmat(1,1),b1(1,i),AEAb1derg(1,1,1)) call matvec2(auxmat(1,1),Ub2(1,i),AEAb2derg(1,1,1,1)) - call matvec2(AEA(1,1,1),b1(1,itk1),AEAb1(1,2,1)) - call matvec2(AEAderg(1,1,1),b1(1,itk1),AEAb1derg(1,2,1)) + call matvec2(AEA(1,1,1),b1(1,k+1),AEAb1(1,2,1)) + call matvec2(AEAderg(1,1,1),b1(1,k+1),AEAb1derg(1,2,1)) call matvec2(AEA(1,1,1),Ub2(1,k+1),AEAb2(1,2,1)) call matvec2(AEAderg(1,1,1),Ub2(1,k+1),AEAb2derg(1,1,2,1)) call matvec2(AEA(1,1,1),Ub2der(1,k+1),AEAb2derg(1,2,2,1)) call transpose2(AEA(1,1,2),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,itj1),AEAb1(1,1,2)) + call matvec2(auxmat(1,1),b1(1,j+1),AEAb1(1,1,2)) call matvec2(auxmat(1,1),Ub2(1,l),AEAb2(1,1,2)) call matvec2(auxmat(1,1),Ub2der(1,l),AEAb2derg(1,2,1,2)) call transpose2(AEAderg(1,1,2),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,itl),AEAb1(1,1,2)) + call matvec2(auxmat(1,1),b1(1,l),AEAb1(1,1,2)) call matvec2(auxmat(1,1),Ub2(1,l),AEAb2derg(1,1,1,2)) - call matvec2(AEA(1,1,2),b1(1,itj1),AEAb1(1,2,2)) - call matvec2(AEAderg(1,1,2),b1(1,itj1),AEAb1derg(1,2,2)) + call matvec2(AEA(1,1,2),b1(1,j+1),AEAb1(1,2,2)) + call matvec2(AEAderg(1,1,2),b1(1,j+1),AEAb1derg(1,2,2)) call matvec2(AEA(1,1,2),Ub2(1,j),AEAb2(1,2,2)) call matvec2(AEAderg(1,1,2),Ub2(1,j),AEAb2derg(1,1,2,2)) call matvec2(AEA(1,1,2),Ub2der(1,j),AEAb2derg(1,2,2,2)) @@ -7361,20 +7361,20 @@ C Calculate the Cartesian derivatives of the vectors. do kkk=1,5 do lll=1,3 call transpose2(AEAderx(1,1,lll,kkk,iii,1),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,iti), + call matvec2(auxmat(1,1),b1(1,i), & AEAb1derx(1,lll,kkk,iii,1,1)) call matvec2(auxmat(1,1),Ub2(1,i), & AEAb2derx(1,lll,kkk,iii,1,1)) - call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,itk1), + call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,k+1), & AEAb1derx(1,lll,kkk,iii,2,1)) call matvec2(AEAderx(1,1,lll,kkk,iii,1),Ub2(1,k+1), & AEAb2derx(1,lll,kkk,iii,2,1)) call transpose2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,itl), + call matvec2(auxmat(1,1),b1(1,l), & AEAb1derx(1,lll,kkk,iii,1,2)) call matvec2(auxmat(1,1),Ub2(1,l), & AEAb2derx(1,lll,kkk,iii,1,2)) - call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,itj1), + call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,j+1), & AEAb1derx(1,lll,kkk,iii,2,2)) call matvec2(AEAderx(1,1,lll,kkk,iii,2),Ub2(1,j), & AEAb2derx(1,lll,kkk,iii,2,2)) @@ -7679,7 +7679,7 @@ C Contribution from graph II call matmat2(auxmat(1,1),AEA(1,1,1),pizda(1,1)) vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) - eello5_2=scalar2(AEAb1(1,2,1),b1(1,itk)) + eello5_2=scalar2(AEAb1(1,2,1),b1(1,k)) & -0.5d0*scalar2(vv(1),Ctobr(1,k)) if (calc_grad) then C Explicit gradient in virtual-dihedral angles. @@ -7690,11 +7690,11 @@ C Explicit gradient in virtual-dihedral angles. vv(2)=pizda(2,1)-pizda(1,2) if (l.eq.j+1) then g_corr5_loc(l-1)=g_corr5_loc(l-1) - & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,itk)) + & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,k)) & -0.5d0*scalar2(vv(1),Ctobr(1,k))) else g_corr5_loc(j-1)=g_corr5_loc(j-1) - & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,itk)) + & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,k)) & -0.5d0*scalar2(vv(1),Ctobr(1,k))) endif C Cartesian gradient @@ -7706,7 +7706,7 @@ C Cartesian gradient vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) derx(lll,kkk,iii)=derx(lll,kkk,iii) - & +scalar2(AEAb1derx(1,lll,kkk,iii,2,1),b1(1,itk)) + & +scalar2(AEAb1derx(1,lll,kkk,iii,2,1),b1(1,k)) & -0.5d0*scalar2(vv(1),Ctobr(1,k)) enddo enddo @@ -7764,7 +7764,7 @@ cd1110 continue call matmat2(auxmat(1,1),AEA(1,1,2),pizda(1,1)) vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) - eello5_4=scalar2(AEAb1(1,2,2),b1(1,itl)) + eello5_4=scalar2(AEAb1(1,2,2),b1(1,l)) & -0.5d0*scalar2(vv(1),Ctobr(1,l)) if (calc_grad) then C Explicit gradient in virtual-dihedral angles. @@ -7774,7 +7774,7 @@ C Explicit gradient in virtual-dihedral angles. vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) g_corr5_loc(k-1)=g_corr5_loc(k-1) - & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,itl)) + & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,l)) & -0.5d0*scalar2(vv(1),Ctobr(1,l))) C Cartesian gradient do iii=1,2 @@ -7785,7 +7785,7 @@ C Cartesian gradient vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) derx(lll,kkk,iii)=derx(lll,kkk,iii) - & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,itl)) + & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,l)) & -0.5d0*scalar2(vv(1),Ctobr(1,l)) enddo enddo @@ -7841,7 +7841,7 @@ C Contribution from graph IV call matmat2(auxmat(1,1),AEA(1,1,2),pizda(1,1)) vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) - eello5_4=scalar2(AEAb1(1,2,2),b1(1,itj)) + eello5_4=scalar2(AEAb1(1,2,2),b1(1,j)) & -0.5d0*scalar2(vv(1),Ctobr(1,j)) if (calc_grad) then C Explicit gradient in virtual-dihedral angles. @@ -7851,7 +7851,7 @@ C Explicit gradient in virtual-dihedral angles. vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) g_corr5_loc(k-1)=g_corr5_loc(k-1) - & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,itj)) + & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,j)) & -0.5d0*scalar2(vv(1),Ctobr(1,j))) C Cartesian gradient do iii=1,2 @@ -7862,7 +7862,7 @@ C Cartesian gradient vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii) - & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,itj)) + & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,j)) & -0.5d0*scalar2(vv(1),Ctobr(1,j)) enddo enddo @@ -8127,8 +8127,8 @@ CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC vv1(1)=pizda1(1,1)-pizda1(2,2) vv1(2)=pizda1(1,2)+pizda1(2,1) s4=0.5d0*scalar2(vv1(1),Dtobr2(1,i)) - vv(1)=AEAb1(1,2,imat)*b1(1,itk)-AEAb1(2,2,imat)*b1(2,itk) - vv(2)=AEAb1(1,2,imat)*b1(2,itk)+AEAb1(2,2,imat)*b1(1,itk) + vv(1)=AEAb1(1,2,imat)*b1(1,k)-AEAb1(2,2,imat)*b1(2,k) + vv(2)=AEAb1(1,2,imat)*b1(2,k)+AEAb1(2,2,imat)*b1(1,k) s5=scalar2(vv(1),Dtobr2(1,i)) cd write (2,*) 's1',s1,' s2',s2,' s3',s3,' s4', s4,' s5',s5 eello6_graph1=-0.5d0*(s1+s2+s3+s4+s5) @@ -8142,8 +8142,8 @@ cd write (2,*) 's1',s1,' s2',s2,' s3',s3,' s4', s4,' s5',s5 call matmat2(AEAderg(1,1,imat),auxmat(1,1),pizda1(1,1)) vv1(1)=pizda1(1,1)-pizda1(2,2) vv1(2)=pizda1(1,2)+pizda1(2,1) - vv(1)=AEAb1derg(1,2,imat)*b1(1,itk)-AEAb1derg(2,2,imat)*b1(2,itk) - vv(2)=AEAb1derg(1,2,imat)*b1(2,itk)+AEAb1derg(2,2,imat)*b1(1,itk) + vv(1)=AEAb1derg(1,2,imat)*b1(1,k)-AEAb1derg(2,2,imat)*b1(2,k) + vv(2)=AEAb1derg(1,2,imat)*b1(2,k)+AEAb1derg(2,2,imat)*b1(1,k) if (l.eq.j+1) then g_corr6_loc(l-1)=g_corr6_loc(l-1) & +ekont*(-0.5d0*(scalar2(AEAb1derg(1,2,imat),CUgb2(1,i)) @@ -8182,10 +8182,10 @@ cd write (2,*) 's1',s1,' s2',s2,' s3',s3,' s4', s4,' s5',s5 vv1(1)=pizda1(1,1)-pizda1(2,2) vv1(2)=pizda1(1,2)+pizda1(2,1) s4=0.5d0*scalar2(vv1(1),Dtobr2(1,i)) - vv(1)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(1,itk) - & -AEAb1derx(2,lll,kkk,iii,2,imat)*b1(2,itk) - vv(2)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(2,itk) - & +AEAb1derx(2,lll,kkk,iii,2,imat)*b1(1,itk) + vv(1)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(1,k) + & -AEAb1derx(2,lll,kkk,iii,2,imat)*b1(2,k) + vv(2)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(2,k) + & +AEAb1derx(2,lll,kkk,iii,2,imat)*b1(1,k) s5=scalar2(vv(1),Dtobr2(1,i)) derx(lll,kkk,ind)=derx(lll,kkk,ind)-0.5d0*(s1+s2+s3+s4+s5) enddo @@ -8428,10 +8428,10 @@ C energy moment and not to the cluster cumulant. #ifdef MOMENT s1=dip(4,jj,i)*dip(4,kk,k) #endif - call matvec2(AECA(1,1,1),b1(1,itk1),auxvec(1)) - s2=0.5d0*scalar2(b1(1,itk),auxvec(1)) - call matvec2(AECA(1,1,2),b1(1,itl1),auxvec(1)) - s3=0.5d0*scalar2(b1(1,itj1),auxvec(1)) + call matvec2(AECA(1,1,1),b1(1,k+1),auxvec(1)) + s2=0.5d0*scalar2(b1(1,k),auxvec(1)) + call matvec2(AECA(1,1,2),b1(1,l+1),auxvec(1)) + s3=0.5d0*scalar2(b1(1,j+1),auxvec(1)) call transpose2(EE(1,1,itk),auxmat(1,1)) call matmat2(auxmat(1,1),AECA(1,1,1),pizda(1,1)) vv(1)=pizda(1,1)+pizda(2,2) @@ -8446,13 +8446,13 @@ cd write (2,*) 'eello6_graph3:','s1',s1,' s2',s2,' s3',s3,' s4',s4 c eello6_graph3=-s4 if (.not. calc_grad) return C Derivatives in gamma(k-1) - call matvec2(AECAderg(1,1,2),b1(1,itl1),auxvec(1)) - s3=0.5d0*scalar2(b1(1,itj1),auxvec(1)) + call matvec2(AECAderg(1,1,2),b1(1,l+1),auxvec(1)) + s3=0.5d0*scalar2(b1(1,j+1),auxvec(1)) s4=-0.25d0*scalar2(vv(1),Ctobrder(1,k)) g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s3+s4) C Derivatives in gamma(l-1) - call matvec2(AECAderg(1,1,1),b1(1,itk1),auxvec(1)) - s2=0.5d0*scalar2(b1(1,itk),auxvec(1)) + call matvec2(AECAderg(1,1,1),b1(1,k+1),auxvec(1)) + s2=0.5d0*scalar2(b1(1,k),auxvec(1)) call matmat2(auxmat(1,1),AECAderg(1,1,1),pizda(1,1)) vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) @@ -8469,12 +8469,12 @@ C Cartesian derivatives. s1=dip(4,jj,i)*dipderx(lll,kkk,4,kk,k) endif #endif - call matvec2(AECAderx(1,1,lll,kkk,iii,1),b1(1,itk1), + call matvec2(AECAderx(1,1,lll,kkk,iii,1),b1(1,k+1), & auxvec(1)) - s2=0.5d0*scalar2(b1(1,itk),auxvec(1)) - call matvec2(AECAderx(1,1,lll,kkk,iii,2),b1(1,itl1), + s2=0.5d0*scalar2(b1(1,k),auxvec(1)) + call matvec2(AECAderx(1,1,lll,kkk,iii,2),b1(1,l+1), & auxvec(1)) - s3=0.5d0*scalar2(b1(1,itj1),auxvec(1)) + s3=0.5d0*scalar2(b1(1,j+1),auxvec(1)) call matmat2(auxmat(1,1),AECAderx(1,1,lll,kkk,iii,1), & pizda(1,1)) vv(1)=pizda(1,1)+pizda(2,2) @@ -8563,11 +8563,11 @@ cd & ' itl',itl,' itl1',itl1 call matvec2(AECA(1,1,imat),Ub2(1,k),auxvec(1)) s2=0.5d0*scalar2(Ub2(1,i),auxvec(1)) if (j.eq.l+1) then - call matvec2(ADtEA1(1,1,3-imat),b1(1,itj1),auxvec1(1)) - s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1)) + call matvec2(ADtEA1(1,1,3-imat),b1(1,j+1),auxvec1(1)) + s3=-0.5d0*scalar2(b1(1,j),auxvec1(1)) else - call matvec2(ADtEA1(1,1,3-imat),b1(1,itl1),auxvec1(1)) - s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1)) + call matvec2(ADtEA1(1,1,3-imat),b1(1,l+1),auxvec1(1)) + s3=-0.5d0*scalar2(b1(1,l),auxvec1(1)) endif call transpose2(EUg(1,1,k),auxmat(1,1)) call matmat2(AECA(1,1,imat),auxmat(1,1),pizda(1,1)) @@ -8592,11 +8592,11 @@ C Derivatives in gamma(i-1) #endif s2=0.5d0*scalar2(Ub2der(1,i),auxvec(1)) if (j.eq.l+1) then - call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,itj1),auxvec1(1)) - s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1)) + call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,j+1),auxvec1(1)) + s3=-0.5d0*scalar2(b1(1,j),auxvec1(1)) else - call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,itl1),auxvec1(1)) - s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1)) + call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,l+1),auxvec1(1)) + s3=-0.5d0*scalar2(b1(1,l),auxvec1(1)) endif s4=0.25d0*scalar2(vv(1),Dtobr2der(1,i)) if (wturn6.gt.0.0d0 .and. k.eq.l+4 .and. i.eq.j+2) then @@ -8625,11 +8625,11 @@ C Derivatives in gamma(k-1) call matvec2(AECA(1,1,imat),Ub2der(1,k),auxvec1(1)) s2=0.5d0*scalar2(Ub2(1,i),auxvec1(1)) if (j.eq.l+1) then - call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,itj1),auxvec1(1)) - s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1)) + call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,j+1),auxvec1(1)) + s3=-0.5d0*scalar2(b1(1,j),auxvec1(1)) else - call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,itl1),auxvec1(1)) - s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1)) + call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,l+1),auxvec1(1)) + s3=-0.5d0*scalar2(b1(1,tl),auxvec1(1)) endif call transpose2(EUgder(1,1,k),auxmat1(1,1)) call matmat2(AECA(1,1,imat),auxmat1(1,1),pizda(1,1)) @@ -8695,12 +8695,12 @@ C Cartesian derivatives. s2=0.5d0*scalar2(Ub2(1,i),auxvec(1)) if (j.eq.l+1) then call matvec2(ADtEA1derx(1,1,lll,kkk,iii,3-imat), - & b1(1,itj1),auxvec(1)) - s3=-0.5d0*scalar2(b1(1,itj),auxvec(1)) + & b1(1,j+1),auxvec(1)) + s3=-0.5d0*scalar2(b1(1,j),auxvec(1)) else call matvec2(ADtEA1derx(1,1,lll,kkk,iii,3-imat), - & b1(1,itl1),auxvec(1)) - s3=-0.5d0*scalar2(b1(1,itl),auxvec(1)) + & b1(1,l+1),auxvec(1)) + s3=-0.5d0*scalar2(b1(1,l),auxvec(1)) endif call matmat2(AECAderx(1,1,lll,kkk,iii,imat),auxmat(1,1), & pizda(1,1)) @@ -8797,14 +8797,14 @@ cd write (2,*) 'eello6_5',eello6_5 #ifdef MOMENT call transpose2(AEA(1,1,1),auxmat(1,1)) call matmat2(EUg(1,1,i+1),auxmat(1,1),auxmat(1,1)) - ss1=scalar2(Ub2(1,i+2),b1(1,itl)) + ss1=scalar2(Ub2(1,i+2),b1(1,l)) s1 = (auxmat(1,1)+auxmat(2,2))*ss1 #else s1 = 0.0d0 #endif - call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1(1)) + call matvec2(EUg(1,1,i+2),b1(1,l),vtemp1(1)) call matvec2(AEA(1,1,1),vtemp1(1),vtemp1(1)) - s2 = scalar2(b1(1,itk),vtemp1(1)) + s2 = scalar2(b1(1,k),vtemp1(1)) #ifdef MOMENT call transpose2(AEA(1,1,2),atemp(1,1)) call matmat2(atemp(1,1),EUg(1,1,i+4),atemp(1,1)) @@ -8821,7 +8821,7 @@ cd write (2,*) 'eello6_5',eello6_5 call matmat2(achuj_temp(1,1),EUg(1,1,i+2),gtemp(1,1)) call matmat2(gtemp(1,1),EUg(1,1,i+3),gtemp(1,1)) call matvec2(a_chuj(1,1,jj,i),Ub2(1,i+4),vtemp4(1)) - ss13 = scalar2(b1(1,itk),vtemp4(1)) + ss13 = scalar2(b1(1,k),vtemp4(1)) s13 = (gtemp(1,1)+gtemp(2,2))*ss13 #else s13=0.0d0 @@ -8858,14 +8858,14 @@ C Derivatives in gamma(i+3) #ifdef MOMENT call transpose2(AEA(1,1,1),auxmatd(1,1)) call matmat2(EUg(1,1,i+1),auxmatd(1,1),auxmatd(1,1)) - ss1d=scalar2(Ub2der(1,i+2),b1(1,itl)) + ss1d=scalar2(Ub2der(1,i+2),b1(1,l)) s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1d #else s1d=0.0d0 #endif - call matvec2(EUgder(1,1,i+2),b1(1,itl),vtemp1d(1)) + call matvec2(EUgder(1,1,i+2),b1(1,l),vtemp1d(1)) call matvec2(AEA(1,1,1),vtemp1d(1),vtemp1d(1)) - s2d = scalar2(b1(1,itk),vtemp1d(1)) + s2d = scalar2(b1(1,k),vtemp1d(1)) #ifdef MOMENT call matvec2(Ug2der(1,1,i+2),dd(1,1,itk1),vtemp2d(1)) s8d = -(atemp(1,1)+atemp(2,2))*scalar2(cc(1,1,itl),vtemp2d(1)) @@ -8919,9 +8919,9 @@ C Derivatives in gamma(i+5) #else s1d = 0.0d0 #endif - call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1d(1)) + call matvec2(EUg(1,1,i+2),b1(1,l),vtemp1d(1)) call matvec2(AEAderg(1,1,1),vtemp1d(1),vtemp1d(1)) - s2d = scalar2(b1(1,itk),vtemp1d(1)) + s2d = scalar2(b1(1,k),vtemp1d(1)) #ifdef MOMENT call transpose2(AEA(1,1,2),atempd(1,1)) call matmat2(atempd(1,1),EUgder(1,1,i+4),atempd(1,1)) @@ -8933,7 +8933,7 @@ C Derivatives in gamma(i+5) s12d = scalar2(Ub2(1,i+2),vtemp3d(1)) #ifdef MOMENT call matvec2(a_chuj(1,1,jj,i),Ub2der(1,i+4),vtemp4d(1)) - ss13d = scalar2(b1(1,itk),vtemp4d(1)) + ss13d = scalar2(b1(1,k),vtemp4d(1)) s13d = (gtemp(1,1)+gtemp(2,2))*ss13d #else s13d = 0.0d0 @@ -8961,10 +8961,10 @@ C Cartesian derivatives #else s1d = 0.0d0 #endif - call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1(1)) + call matvec2(EUg(1,1,i+2),b1(1,l),vtemp1(1)) call matvec2(AEAderx(1,1,lll,kkk,iii,1),vtemp1(1), & vtemp1d(1)) - s2d = scalar2(b1(1,itk),vtemp1d(1)) + s2d = scalar2(b1(1,k),vtemp1d(1)) #ifdef MOMENT call transpose2(AEAderx(1,1,lll,kkk,iii,2),atempd(1,1)) call matmat2(atempd(1,1),EUg(1,1,i+4),atempd(1,1)) @@ -9010,7 +9010,7 @@ c s13d=0.0d0 derx_turn(lll,kkk,2) = derx_turn(lll,kkk,2)-0.5d0*s13d call matvec2(a_chuj_der(1,1,lll,kkk,jj,i),Ub2(1,i+4), & vtemp4d(1)) - ss13d = scalar2(b1(1,itk),vtemp4d(1)) + ss13d = scalar2(b1(1,k),vtemp4d(1)) s13d = (gtemp(1,1)+gtemp(2,2))*ss13d derx_turn(lll,kkk,1) = derx_turn(lll,kkk,1)-0.5d0*s13d enddo diff --git a/source/wham/src-NEWSC-NEWCORR/parmread.F b/source/wham/src-NEWSC-NEWCORR/parmread.F index ba6ec3e..43a24b8 100644 --- a/source/wham/src-NEWSC-NEWCORR/parmread.F +++ b/source/wham/src-NEWSC-NEWCORR/parmread.F @@ -694,10 +694,10 @@ C EEold(2,2,i)=-b(10,i)+b(11,i) EEold(2,1,i)= b(12,i)-b(13,i) EEold(1,2,i)= b(12,i)+b(13,i) - EEold(1,1,-i)= b(10,i)+b(11,i) - EEold(2,2,-i)=-b(10,i)+b(11,i) - EEold(2,1,-i)=-b(12,i)+b(13,i) - EEold(1,2,-i)=-b(12,i)-b(13,i) +c EEold(1,1,-i)= b(10,i)+b(11,i) +c EEold(2,2,-i)=-b(10,i)+b(11,i) +c EEold(2,1,-i)=-b(12,i)+b(13,i) +c EEold(1,2,-i)=-b(12,i)-b(13,i) #else EE(1,1,i)= b(10,i)+b(11,i) EE(2,2,i)=-b(10,i)+b(11,i) diff --git a/source/wham/src-NEWSC/CMakeLists.txt b/source/wham/src-NEWSC/CMakeLists.txt old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/COMMON.ALLPARM b/source/wham/src-NEWSC/COMMON.ALLPARM old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/COMMON.CHAIN b/source/wham/src-NEWSC/COMMON.CHAIN old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/COMMON.COMPAR b/source/wham/src-NEWSC/COMMON.COMPAR old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/COMMON.CONTACTS1 b/source/wham/src-NEWSC/COMMON.CONTACTS1 old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/COMMON.CONTROL b/source/wham/src-NEWSC/COMMON.CONTROL old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/COMMON.CONTROL.org b/source/wham/src-NEWSC/COMMON.CONTROL.org old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/COMMON.EMP b/source/wham/src-NEWSC/COMMON.EMP old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/COMMON.ENEPS b/source/wham/src-NEWSC/COMMON.ENEPS old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/COMMON.ENERGIES b/source/wham/src-NEWSC/COMMON.ENERGIES old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/COMMON.FREE b/source/wham/src-NEWSC/COMMON.FREE old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/COMMON.IOUNITS b/source/wham/src-NEWSC/COMMON.IOUNITS old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/COMMON.MPI b/source/wham/src-NEWSC/COMMON.MPI old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/COMMON.OBCINKA b/source/wham/src-NEWSC/COMMON.OBCINKA old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/COMMON.PEPTCONT b/source/wham/src-NEWSC/COMMON.PEPTCONT old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/COMMON.PROT b/source/wham/src-NEWSC/COMMON.PROT old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/COMMON.PROTFILES b/source/wham/src-NEWSC/COMMON.PROTFILES old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/COMMON.VAR b/source/wham/src-NEWSC/COMMON.VAR old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/DIMENSIONS b/source/wham/src-NEWSC/DIMENSIONS old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/DIMENSIONS.COMPAR b/source/wham/src-NEWSC/DIMENSIONS.COMPAR old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/DIMENSIONS.FREE b/source/wham/src-NEWSC/DIMENSIONS.FREE old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/DIMENSIONS.FREE.old b/source/wham/src-NEWSC/DIMENSIONS.FREE.old old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/DIMENSIONS.ZSCOPT b/source/wham/src-NEWSC/DIMENSIONS.ZSCOPT old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/Makefile b/source/wham/src-NEWSC/Makefile deleted file mode 100755 index 8b92f57..0000000 --- a/source/wham/src-NEWSC/Makefile +++ /dev/null @@ -1,89 +0,0 @@ -INSTALL_DIR = /users/local/mpi64/mpich-1.2.7p1 -BIN = /users/adam/bin -FC= ifort -OPT = -mcmodel=medium -O3 -ip -w -#OPT = -mcmodel=medium -g -CA -CB -FFLAGS = ${OPT} -c -I. -I./include_unres -I$(INSTALL_DIR)/include -LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpmpich xdrf/libxdrf.a - -.f.o: - ${FC} ${FFLAGS} $*.f - -.F.o: - ${FC} ${FFLAGS} ${CPPFLAGS} $*.F - -objects = \ - wham_multparm.o \ - bxread.o \ - xread.o \ - cxread.o \ - enecalc1.o \ - energy_p_new.o \ - gnmr1.o \ - initialize_p.o \ - molread_zs.o \ - openunits.o \ - readrtns.o \ - arcos.o \ - cartder.o \ - cartprint.o \ - chainbuild.o \ - geomout.o \ - icant.o \ - intcor.o \ - int_from_cart.o \ - make_ensemble1.o \ - matmult.o \ - misc.o \ - mygetenv.o \ - parmread.o \ - pinorm.o \ - printmat.o \ - proc_proc.o \ - rescode.o \ - setup_var.o \ - slices.o \ - store_parm.o \ - timing.o \ - wham_calc1.o - -objects_compar = \ - readrtns_compar.o \ - readpdb.o fitsq.o contact.o \ - elecont.o contfunc.o cont_frag.o conf_compar.o match_contact.o \ - angnorm.o odlodc.o promienie.o qwolynes.o read_ref_str.o \ - rmscalc.o secondary.o proc_cont.o define_pairs.o mysort.o - -GABs: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI -DISNAN -DAMD64 \ - -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DSCALREP -GABs: ${objects} ${objects_compar} xdrf/libxdrf.a - cc -o compinfo compinfo.c - ./compinfo - ${FC} -c ${FFLAGS} cinfo.f - $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \ - ${LIBS} -static-intel -o ${BIN}/wham_ifort_MPICH_MM-KN-DEBUG-scalrep.exe - -GAB: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI -DISNAN -DAMD64 \ - -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -GAB: ${objects} ${objects_compar} xdrf/libxdrf.a - cc -o compinfo compinfo.c - ./compinfo - ${FC} -c ${FFLAGS} cinfo.f - $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \ - ${LIBS} -static-intel -o ${BIN}/wham_ifort_MPICH_MM-KN-DEBUG.exe - -E0LL2Y: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI -DISNAN -DAMD64 -E0LL2Y: ${objects} ${objects_compar} xdrf/libxdrf.a - cc -o compinfo compinfo.c - ./compinfo - ${FC} -c ${FFLAGS} cinfo.f - $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \ - ${LIBS} -static-intel -o ${BIN}/wham_ifort_MPICH_MM-PH.exe - -xdrf/libxdrf.a: - cd xdrf && make - - -clean: - /bin/rm -f *.o && /bin/rm -f compinfo && cd xdrf && make clean - diff --git a/source/wham/src-NEWSC/Makefile b/source/wham/src-NEWSC/Makefile new file mode 120000 index 0000000..8453cdd --- /dev/null +++ b/source/wham/src-NEWSC/Makefile @@ -0,0 +1 @@ +Makefile_MPICH_ifort \ No newline at end of file diff --git a/source/wham/src-NEWSC/Makefile-pgi b/source/wham/src-NEWSC/Makefile-pgi old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/Makefile1_jump b/source/wham/src-NEWSC/Makefile1_jump old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/Makefile_MPICH_ifort b/source/wham/src-NEWSC/Makefile_MPICH_ifort old mode 100755 new mode 100644 index 8b92f57..6cd313d --- a/source/wham/src-NEWSC/Makefile_MPICH_ifort +++ b/source/wham/src-NEWSC/Makefile_MPICH_ifort @@ -1,5 +1,5 @@ -INSTALL_DIR = /users/local/mpi64/mpich-1.2.7p1 -BIN = /users/adam/bin +INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh +BIN = /users/adam/unres/bin/wham FC= ifort OPT = -mcmodel=medium -O3 -ip -w #OPT = -mcmodel=medium -g -CA -CB diff --git a/source/wham/src-NEWSC/Makefile_jubl b/source/wham/src-NEWSC/Makefile_jubl old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/Makefile_jump b/source/wham/src-NEWSC/Makefile_jump old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/Makefile_matrix b/source/wham/src-NEWSC/Makefile_matrix old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/Makefile_matrix_PGI b/source/wham/src-NEWSC/Makefile_matrix_PGI old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/Makefile_matrix_PGI-SCT-oldparm b/source/wham/src-NEWSC/Makefile_matrix_PGI-SCT-oldparm old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/Makefile_matrix_PGI-SCTF-oldparm b/source/wham/src-NEWSC/Makefile_matrix_PGI-SCTF-oldparm old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/Makefile_matrix_PGI-oldparm b/source/wham/src-NEWSC/Makefile_matrix_PGI-oldparm old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/a.sh b/source/wham/src-NEWSC/a.sh old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/angnorm.f b/source/wham/src-NEWSC/angnorm.f old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/arcos.f b/source/wham/src-NEWSC/arcos.f old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/bxread.F b/source/wham/src-NEWSC/bxread.F old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/cartder.f b/source/wham/src-NEWSC/cartder.f old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/cartprint.f b/source/wham/src-NEWSC/cartprint.f old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/chainbuild.F b/source/wham/src-NEWSC/chainbuild.F old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/chainbuild.f b/source/wham/src-NEWSC/chainbuild.f old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/compinfo.c b/source/wham/src-NEWSC/compinfo.c old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/conf_compar.F b/source/wham/src-NEWSC/conf_compar.F old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/cont_frag.f b/source/wham/src-NEWSC/cont_frag.f old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/contact.f b/source/wham/src-NEWSC/contact.f old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/contfunc.f b/source/wham/src-NEWSC/contfunc.f old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/cxread.F b/source/wham/src-NEWSC/cxread.F old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/cxread.F.org b/source/wham/src-NEWSC/cxread.F.org old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/define_pairs.f b/source/wham/src-NEWSC/define_pairs.f old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/elecont.f b/source/wham/src-NEWSC/elecont.f old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/enecalc1.F b/source/wham/src-NEWSC/enecalc1.F old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/energy_p_new.F b/source/wham/src-NEWSC/energy_p_new.F old mode 100755 new mode 100644 index 113d499..37bd887 --- a/source/wham/src-NEWSC/energy_p_new.F +++ b/source/wham/src-NEWSC/energy_p_new.F @@ -6256,8 +6256,8 @@ c amino-acid residues. include 'COMMON.CONTROL' logical lprn C Set lprn=.true. for debugging - lprn=.false. -c lprn=.true. +c lprn=.false. + lprn=.true. c write (iout,*) "EBACK_SC_COR",itau_start,itau_end,nterm_sccor esccor=0.0D0 do i=itau_start,itau_end @@ -6289,22 +6289,27 @@ c 3 = SC...Ca...Ca...SCi if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.21)) cycle if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.21)) & cycle + esccori=0.0d0 do j=1,nterm_sccor(isccori,isccori1) v1ij=v1sccor(j,intertyp,isccori,isccori1) v2ij=v2sccor(j,intertyp,isccori,isccori1) cosphi=dcos(j*tauangle(intertyp,i)) sinphi=dsin(j*tauangle(intertyp,i)) - esccor=esccor+v1ij*cosphi+v2ij*sinphi + esccori=esccori+v1ij*cosphi+v2ij*sinphi gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi) enddo + esccor=esccor+esccori gloc_sc(intertyp,i-3,icg)=gloc_sc(intertyp,i-3,icg)+wsccor*gloci c write (iout,*) "WTF",intertyp,i,itype(i),v1ij*cosphi+v2ij*sinphi c &gloc_sc(intertyp,i-3,icg) - if (lprn) - & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)') - & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1, - & (v1sccor(j,intertyp,itori,itori1),j=1,6) - & ,(v2sccor(j,intertyp,itori,itori1),j=1,6) + if (lprn) then + write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)') + & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,isccori,isccori1, + & (v1sccor(j,intertyp,isccori,isccori1),j=1,6) + & ,(v2sccor(j,intertyp,isccori,isccori1),j=1,6) + write (iout,*) "esccori",esccori + call flush(iout) + endif gsccor_loc(i-3)=gsccor_loc(i-3)+gloci enddo !intertyp enddo diff --git a/source/wham/src-NEWSC/energy_p_new.F.org b/source/wham/src-NEWSC/energy_p_new.F.org old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/fitsq.f b/source/wham/src-NEWSC/fitsq.f old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/geomout.F b/source/wham/src-NEWSC/geomout.F old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/gnmr1.f b/source/wham/src-NEWSC/gnmr1.f old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/icant.f b/source/wham/src-NEWSC/icant.f old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/initialize_p.F b/source/wham/src-NEWSC/initialize_p.F old mode 100755 new mode 100644 diff --git a/source/wham/src-NEWSC/initialize_p.F.org b/source/wham/src-NEWSC/initialize_p.F.org old mode 100755 new mode 100644 diff --git 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b/source/wham/src-restraints/enecalc1.F index 6c39f6c..3a4a3a3 100644 --- a/source/wham/src-restraints/enecalc1.F +++ b/source/wham/src-restraints/enecalc1.F @@ -33,7 +33,7 @@ double precision rmsnat,gyrate external rmsnat,gyrate double precision tole /1.0d-1/ - integer i,itj,ii,iii,j,k,l,licz + integer i,itj,ii,iii,j,k,l,licz,scme integer ir,ib,ipar,iparm integer iscor,islice real*4 csingle(3,maxres2) @@ -154,7 +154,6 @@ c & " kfac",kfac,"quot",quot," fT",fT & wtor_d,wsccor,wbond #endif call etotal(energia(0),fT) -#define DEBUG #ifdef DEBUG write (iout,*) "Conformation",i call enerprint(energia(0),fT) @@ -162,7 +161,6 @@ c write (iout,'(2i5,21f8.2)') i,iparm,(energia(k),k=1,21) c write (iout,*) "ftors",ftors c call intout #endif -#undef DEBUG if (energia(0).ge.1.0d20) then write (iout,*) "NaNs detected in some of the energy", & " components for conformation",ii+1 @@ -275,6 +273,7 @@ c & " snk",snk_p(iR,ib,ipar) write (iout,*) "Me",me," scount",scount(me) call flush(iout) c Master gathers updated numbers of conformations written by all procs. + scme = scount(me) call MPI_AllGather( scount(me), 1, MPI_INTEGER, scount(0), 1, & MPI_INTEGER, WHAM_COMM, IERROR) indstart(0)=1 -- 1.7.9.5