Introduced itype2loc table to denote local fourier types; now different from itortyp
Fixed gradients near gamma=180
& sideadd,lsecondary,read_cart,unres_pdb,
& vdisulf,searchsc,lmuca,dccart,extconf,out1file,
& gnorm_check,gradout,split_ene,with_theta_constr
- common /cntrl/ modecalc,iscode,indpdb,indback,indphi,iranconf,
+ double precision aincr
+ common /cntrl/ aincr,modecalc,iscode,indpdb,indback,indphi,
+ & iranconf,
& icheckgrad,minim,i2ndstr,refstr,pdbref,outpdb,outmol2,iprint,
& overlapsc,energy_dec,sideadd,lsecondary,read_cart,unres_pdb
& ,vdisulf,searchsc,lmuca,dccart,mucadyn,extconf,out1file,
integer inp,iout,igeom,intin,ipdb,imol2,ipdbin,ithep,irotam,
& itorp,itordp,ifourier,ielep,isidep,iscpp,icbase,istat,
& ientin,ientout,izs1,isecpred,ibond,irest2,iifrag,icart,
- & irest1,isccor,ithep_pdb,irotam_pdb,itorkcc,ithetkcc
+ & irest1,isccor,ithep_pdb,irotam_pdb,itorkcc,ithetkcc,
+ & iliptranpar
common /iounits/ inp,iout,igeom,intin,ipdb,imol2,ipdbin,ithep,
& irotam,itorp,itordp,ifourier,ielep,isidep,iscpp,icbase,
& istat,ientin,ientout,izs1,isecpred,ibond,irest2,iifrag,
& icart,irest1,isccor,ithep_pdb,irotam_pdb,
- & itorkcc,ithetkcc
+ & itorkcc,ithetkcc,iliptranpar
character*256 outname,intname,pdbname,mol2name,statname,intinname,
& entname,prefix,secpred,rest2name,qname,cartname,tmpdir,
& mremd_rst_name,curdir,pref_orig
C Torsional constants of the rotation about virtual-bond dihedral angles
double precision v1,v2,vlor1,vlor2,vlor3,v0,v1_kcc,v2_kcc,
- & v1_chyb,v2_chyb,v1bend_chyb
+ & v11_chyb,v21_chyb,v12_chyb,v22_chyb,v1bend_chyb
integer itortyp,ntortyp,nterm,nlor,nterm_old,nterm_kcc_Tb,
& nterm_kcc,itortyp_kcc,nbend_kcc_Tb
common/torsion/v0(-maxtor:maxtor,-maxtor:maxtor,2),
& vlor2(maxlor,maxtor,maxtor),vlor3(maxlor,maxtor,maxtor),
& v1_kcc(maxtermkcc,-maxtor:maxtor,-maxtor:maxtor),
& v2_kcc(maxtermkcc,-maxtor:maxtor,-maxtor:maxtor),
- & v1_chyb(maxtermkcc,maxtermkcc,-maxtor:maxtor,-maxtor:maxtor),
- & v2_chyb(maxtermkcc,maxtermkcc,-maxtor:maxtor,-maxtor:maxtor),
+ & v11_chyb(maxtermkcc,maxtermkcc,-maxtor:maxtor,-maxtor:maxtor),
+ & v21_chyb(maxtermkcc,maxtermkcc,-maxtor:maxtor,-maxtor:maxtor),
+ & v12_chyb(maxtermkcc,maxtermkcc,-maxtor:maxtor,-maxtor:maxtor),
+ & v22_chyb(maxtermkcc,maxtermkcc,-maxtor:maxtor,-maxtor:maxtor),
& v1bend_chyb(maxtermkcc,-maxtor:maxtor),
& itortyp(-ntyp1:ntyp1),ntortyp,
& itortyp_kcc(-ntyp1:ntyp1),
C 9/18/99 - added Fourier coeffficients of the expansion of local energy
C surface
double precision b1,b2,cc,dd,ee,ctilde,dtilde,b2tilde,b1tilde,
- &bnew1,bnew2,eenew,gtb1,gtb2,eeold,gtee
- integer nloctyp
- common/fourier/ b1(2,0:maxres),b2(2,0:maxres),b(13,0:maxtor),
- & bnew1(3,2,-maxtor:maxtor),bnew2(3,2,-maxtor:maxtor),
- & cc(2,2,-maxtor:maxtor),
- & dd(2,2,-maxtor:maxtor),eeold(2,2,-maxtor:maxtor),
- & eenew(2,-maxtor:maxtor),
+ & b,bnew1,bnew2,eenew,gtb1,gtb2,eeold,gtee
+ integer nloctyp,iloctyp(-ntyp1:ntyp1),itype2loc(-ntyp1:ntyp1)
+ common/fourier/ b1(2,maxres),b2(2,maxres),b(13,-ntyp:ntyp),
+ & bnew1(3,2,-ntyp:ntyp),bnew2(3,2,-ntyp:ntyp),
+ & cc(2,2,-ntyp:ntyp),
+ & dd(2,2,-ntyp:ntyp),eeold(2,2,-ntyp:ntyp),
+ & eenew(2,-ntyp:ntyp),
& ee(2,2,maxres),
- & ctilde(2,2,-maxtor:maxtor),
- & dtilde(2,2,-maxtor:maxtor),b1tilde(2,0:maxres),
+ & ctilde(2,2,-ntyp:ntyp),
+ & dtilde(2,2,-ntyp:ntyp),b1tilde(2,maxres),
& b2tilde(2,maxres),
& gtb1(2,maxres),gtb2(2,maxres),gtEE(2,2,maxres),
- & nloctyp
-
+ & nloctyp,iloctyp,itype2loc
+++ /dev/null
-#source /opt/pgi/linux86-64/13.7/mpi.csh
-###################################################################
-
-
-FC= mpif90
-OPT = -Minfo
-
-FFLAGS = -c ${OPT}
-FFLAGS1 = -c -g
-FFLAGS2 = -c -g -O0
-FFLAGSE = -c -fast -Minline=name:scalar2,scalar,transpose2,matvec2,prodmat3 -Minfo
-
-
-LIBS = xdrf/libxdrf.a
-
-ARCH = LINUX
-PP = /lib/cpp -P
-
-
-all: no_option
- @echo "give optin GAB or E0LL2Y"
-
-.SUFFIXES: .F
-.F.o:
- ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
-
-
-object = unres.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \
- matmult.o readrtns_CSA.o parmread.o gen_rand_conf.o printmat.o map.o \
- pinorm.o randgens.o rescode.o intcor.o timing.o misc.o intlocal.o \
- cartder.o checkder_p.o econstr_local.o energy_p_new_barrier.o \
- energy_p_new-sep_barrier.o gradient_p.o minimize_p.o sumsld.o \
- cored.o rmdd.o geomout.o readpdb.o regularize.o thread.o fitsq.o mcm.o \
- mc.o bond_move.o refsys.o check_sc_distr.o check_bond.o contact.o djacob.o \
- eigen.o blas.o add.o entmcm.o minim_mcmf.o \
- MP.o compare_s1.o prng_32.o \
- banach.o rmsd.o elecont.o dihed_cons.o \
- sc_move.o local_move.o \
- intcartderiv.o lagrangian_lesyng.o\
- stochfric.o kinetic_lesyng.o MD_A-MTS.o moments.o int_to_cart.o \
- surfatom.o sort.o muca_md.o MREMD.o rattle.o gauss.o energy_split-sep.o \
- q_measure.o gnmr1.o test.o ssMD.o isnan.o permut.o together.o
-
-no_option:
-
-GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES -DISNAN -DMP -DMPI \
- -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
-GAB: BIN = ../../../bin/unres/MD/unres_pgf90_mpi_GAB.exe
-GAB: ${object} xdrf/libxdrf.a
- cc -o compinfo compinfo.c
- ./compinfo | true
- ${FC} ${FFLAGS} cinfo.f
- ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
-
-E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES -DISNAN -DMP -DMPI \
- -DSPLITELE -DLANG0
-E0LL2Y: BIN = ../../../bin/unres/MD/unres_pgf90_mpi_E0LL2Y.exe
-E0LL2Y: ${object} xdrf/libxdrf.a
- cc -o compinfo compinfo.c
- ./compinfo | true
- ${FC} ${FFLAGS} cinfo.f
- ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
-
-xdrf/libxdrf.a:
- cd xdrf && make
-
-
-clean:
- /bin/rm -f *.o && /bin/rm -f compinfo && cd xdrf && make clean
-
-test.o: test.F
- ${FC} ${FFLAGS} ${CPPFLAGS} test.F
-
-chainbuild.o: chainbuild.F
- ${FC} ${FFLAGS} ${CPPFLAGS} chainbuild.F
-
-matmult.o: matmult.f
- ${FC} ${FFLAGS} ${CPPFLAGS} matmult.f
-
-parmread.o : parmread.F
- ${FC} ${FFLAGS} ${CPPFLAGS} parmread.F
-
-intcor.o : intcor.f
- ${FC} ${FFLAGS} ${CPPFLAGS} intcor.f
-
-cartder.o : cartder.F
- ${FC} ${FFLAGS} ${CPPFLAGS} cartder.F
-
-readpdb.o : readpdb.F
- ${FC} ${FFLAGS2} ${CPPFLAGS} readpdb.F
-
-sumsld.o : sumsld.f
- ${FC} ${FFLAGS} ${CPPFLAGS} sumsld.f
-
-cored.o : cored.f
- ${FC} ${FFLAGS1} ${CPPFLAGS} cored.f
-
-rmdd.o : rmdd.f
- ${FC} ${FFLAGS} ${CPPFLAGS} rmdd.f
-
-energy_p_new_barrier.o : energy_p_new_barrier.F
- ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new_barrier.F
-
-gradient_p.o : gradient_p.F
- ${FC} ${FFLAGSE} ${CPPFLAGS} gradient_p.F
-
-energy_p_new-sep_barrier.o : energy_p_new-sep_barrier.F
- ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new-sep_barrier.F
-
-lagrangian_lesyng.o : lagrangian_lesyng.F
- ${FC} ${FFLAGSE} ${CPPFLAGS} lagrangian_lesyng.F
-
-MD_A-MTS.o : MD_A-MTS.F
- ${FC} ${FFLAGSE} ${CPPFLAGS} MD_A-MTS.F
-
-blas.o : blas.f
- ${FC} ${FFLAGS1} blas.f
-
-add.o : add.f
- ${FC} ${FFLAGS1} add.f
-
-eigen.o : eigen.f
- ${FC} ${FFLAGS2} eigen.f
-
-proc_proc.o: proc_proc.c
- ${CC} ${CFLAGS} proc_proc.c
-
-isnan.o: isnan.f
- ${FC} -Kieee -c isnan.f
-
--- /dev/null
+Makefile_MPICH_ifort
\ No newline at end of file
FC= ifort
OPT = -O3 -ip
+OPT = -g -CA -CB
FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
FFLAGS1 = -c -g -CA -CB -I$(INSTALL_DIR)/include
FFLAGS2 = -c -g -O0 -I$(INSTALL_DIR)/include
FFLAGSE = -c -O3 -ipo -opt_report -I$(INSTALL_DIR)/include
+FFLAGSE = ${FFLAGS}
LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdrf.a
GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
-DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
-GAB: BIN = ../../../bin/unres/MD/unres-mult-symetr_ifort_MPICH_GAB.exe
+GAB: BIN = /users/adam/bin/unres/MD/unres-mult-symetr_KCC_ifort_MPICH_GAB.exe
GAB: ${object} xdrf/libxdrf.a
cc -o compinfo compinfo.c
./compinfo | true
4P: CPPFLAGS = -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
-DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
-4P: BIN = ../../../bin/unres/MD/unres-mult-symetr_ifort_MPICH_4P.exe
+4P: BIN = /users/adam/bin/unres-mult-symetr_KCC_ifort_MPICH_4P.exe
4P: ${object} xdrf/libxdrf.a
cc -o compinfo compinfo.c
./compinfo | true
E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
-DSPLITELE -DLANG0
-E0LL2Y: BIN = ../../../bin/unres/MD/unres-mult-symetr_ifort_MPICH_E0LL2Y.exe
+E0LL2Y: BIN = /users/adam/bin/unres-mult-symetr_KCC_ifort_MPICH_E0LL2Y.exe
E0LL2Y: ${object} xdrf/libxdrf.a
cc -o compinfo compinfo.c
./compinfo | true
${FC} ${FFLAGS} cinfo.f
${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+NEWCORR: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0 -DNEWCORR
+NEWCORR: BIN = /users/adam/bin/unres-mult-symetr_KCC_ifort_MPICH_E0LL2Y-NEWCORR.exe
+NEWCORR: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
xdrf/libxdrf.a:
cd xdrf && make
C Check the gradient of Cartesian coordinates in internal coordinates.
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
+ include 'COMMON.CONTROL'
include 'COMMON.IOUNITS'
include 'COMMON.VAR'
include 'COMMON.CHAIN'
* Check the gradient of the virtual-bond and SC vectors in the internal
* coordinates.
*
- aincr=1.5d-7
- aincr2=2.5d-8
+ print '("Calling CHECK_ECART",1pd12.3)',aincr
+ write (iout,'("Calling CHECK_ECART",1pd12.3)') aincr
+ aincr2=0.5d0*aincr
call cartder
write (iout,'(a)') '**************** dx/dalpha'
write (iout,'(a)')
C Check the gradient of the energy in Cartesian coordinates.
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
+ include 'COMMON.CONTROL'
include 'COMMON.CHAIN'
include 'COMMON.DERIV'
include 'COMMON.IOUNITS'
nf=0
nfl=0
call zerograd
- aincr=1.0D-7
- print '(a)','CG processor',me,' calling CHECK_CART.'
+ print '("Calling CHECK_ECART",1pd12.3)',aincr
+ write (iout,'("Calling CHECK_ECART",1pd12.3)') aincr
nf=0
icall=0
call geom_to_var(nvar,x)
c call intcartderiv
c call checkintcartgrad
call zerograd
- aincr=8.0D-7
- write(iout,*) 'Calling CHECK_ECARTINT.'
+c aincr=8.0D-7
+c aincr=1.0D-7
+ print '("Calling CHECK_ECARTINT",1pd12.3)',aincr
+ write (iout,'("Calling CHECK_ECARTINT",1pd12.3)') aincr
nf=0
icall=0
call geom_to_var(nvar,x)
write (iout,*) "exit cartgrad"
call flush(iout)
icall =1
+ write (iout,*) "gcard and gxcart"
do i=1,nres
- write (iout,'(i5,3f10.5)') i,(gradxorr(j,i),j=1,3)
+ write (iout,'(i5,3f10.5,5x,3f10.5)') i,(gcart(j,i),j=1,3),
+ & (gxcart(j,i),j=1,3)
enddo
do j=1,3
grad_s(j,0)=gcart(j,0)
C Check the gradient of energy in internal coordinates.
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
+ include 'COMMON.CONTROL'
include 'COMMON.CHAIN'
include 'COMMON.DERIV'
include 'COMMON.IOUNITS'
character*6 key
external fdum
call zerograd
- aincr=1.0D-7
- print '(a)','Calling CHECK_INT.'
+c aincr=1.0D-7
+ print '("Calling CHECK_INT",1pd12.3)',aincr
+ write (iout,'("Calling CHECK_INT",1pd12.3)') aincr
nf=0
nfl=0
icg=1
xi=x(i)
x(i)=xi-0.5D0*aincr
call var_to_geom(nvar,x)
- call chainbuild
+ call chainbuild_extconf
call etotal(energia1(0))
etot1=energia1(0)
x(i)=xi+0.5D0*aincr
call var_to_geom(nvar,x)
- call chainbuild
+ call chainbuild_extconf
call etotal(energia2(0))
etot2=energia2(0)
gg(i)=(etot2-etot1)/aincr
C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
-C 0 40360 18
+C 0 40360 71
subroutine cinfo
include 'COMMON.IOUNITS'
write(iout,*)'++++ Compile info ++++'
- write(iout,*)'Version 0.40360 build 18'
- write(iout,*)'compiled Fri Nov 27 10:42:05 2015'
- write(iout,*)'compiled by adasko@cuda1'
+ write(iout,*)'Version 0.40360 build 71'
+ write(iout,*)'compiled Sun Jan 3 21:03:16 2016'
+ write(iout,*)'compiled by adam@piasek4'
write(iout,*)'OS name: Linux '
- write(iout,*)'OS release: 3.2.0-32-generic '
+ write(iout,*)'OS release: 3.2.0-91-generic '
write(iout,*)'OS version:',
- & ' #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 '
+ & ' #129-Ubuntu SMP Wed Sep 9 10:56:06 UTC 2015 '
write(iout,*)'flags:'
- write(iout,*)'FC= mpif90'
- write(iout,*)'OPT = -Minfo'
- write(iout,*)'FFLAGS = -c ${OPT} '
- write(iout,*)'FFLAGS1 = -c -g '
- write(iout,*)'FFLAGS2 = -c -g -O0 '
- write(iout,*)'FFLAGSE = -c -fast -Minline=name:scalar2,scala...'
- write(iout,*)'LIBS = xdrf/libxdrf.a'
+ write(iout,*)'INSTALL_DIR = /users/software/mpich-1.2.7p1_int...'
+ write(iout,*)'FC= ifort'
+ write(iout,*)'OPT = -O3 -ip '
+ write(iout,*)'OPT = -g -CA -CB'
+ write(iout,*)'FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include '
+ write(iout,*)'FFLAGS1 = -c -g -CA -CB -I$(INSTALL_DIR)/inclu...'
+ write(iout,*)'FFLAGS2 = -c -g -O0 -I$(INSTALL_DIR)/include '
+ write(iout,*)'FFLAGSE = -c -O3 -ipo -opt_report -I$(INSTALL...'
+ write(iout,*)'FFLAGSE = ${FFLAGS}'
+ write(iout,*)'LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr...'
write(iout,*)'ARCH = LINUX'
write(iout,*)'PP = /lib/cpp -P'
write(iout,*)'object = unres.o arcos.o cartprint.o chainbuild...'
- write(iout,*)'GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES ...'
- write(iout,*)'GAB: BIN = ../../../bin/unres/MD/unres_pgf90_mp...'
- write(iout,*)'E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR...'
- write(iout,*)'E0LL2Y: BIN = ../../../bin/unres/MD/unres_pgf90...'
+ write(iout,*)'GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 ...'
+ write(iout,*)'GAB: BIN = /users/adam/bin/unres/MD/unres-mult-...'
+ write(iout,*)'4P: CPPFLAGS = -DLINUX -DPGI -DAMD64 -DUNRES -D...'
+ write(iout,*)'4P: BIN = /users/adam/bin/unres-mult-symetr_KCC...'
+ write(iout,*)'E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD...'
+ write(iout,*)'E0LL2Y: BIN = /users/adam/bin/unres-mult-symetr...'
+ write(iout,*)'NEWCORR: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAM...'
+ write(iout,*)'NEWCORR: BIN = /users/adam/bin/unres-mult-symet...'
write(iout,*)'++++ End of compile info ++++'
return
end
#endif
#ifdef NEWCORR
if (i.gt. nnt+2 .and. i.lt.nct+2) then
- iti = itortyp(itype(i-2))
+ iti = itype2loc(itype(i-2))
else
- iti=ntortyp+1
+ iti=nloctyp
endif
c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then
if (i.gt. nnt+1 .and. i.lt.nct+1) then
- iti1 = itortyp(itype(i-1))
+ iti1 = itype2loc(itype(i-1))
else
- iti1=ntortyp+1
+ iti1=nloctyp
endif
c write(iout,*),i
- b1(1,i-2)=bnew1(1,1,iti)*dsin(theta(i-1)/2.0)
+ b1(1,i-2)=bnew1(1,1,iti)*dsin(theta(i-1)/2.0d0)
& +bnew1(2,1,iti)*dsin(theta(i-1))
- & +bnew1(3,1,iti)*dcos(theta(i-1)/2.0)
+ & +bnew1(3,1,iti)*dcos(theta(i-1)/2.0d0)
gtb1(1,i-2)=bnew1(1,1,iti)*dcos(theta(i-1)/2.0d0)/2.0d0
& +bnew1(2,1,iti)*dcos(theta(i-1))
& -bnew1(3,1,iti)*dsin(theta(i-1)/2.0d0)/2.0d0
c & +bnew1(3,1,iti)*sin(alpha(i))*cos(beta(i))
c &*(cos(theta(i)/2.0)
- b2(1,i-2)=bnew2(1,1,iti)*dsin(theta(i-1)/2.0)
+ b2(1,i-2)=bnew2(1,1,iti)*dsin(theta(i-1)/2.0d0)
& +bnew2(2,1,iti)*dsin(theta(i-1))
- & +bnew2(3,1,iti)*dcos(theta(i-1)/2.0)
+ & +bnew2(3,1,iti)*dcos(theta(i-1)/2.0d0)
c & +bnew2(3,1,iti)*sin(alpha(i))*cos(beta(i))
c &*(cos(theta(i)/2.0)
gtb2(1,i-2)=bnew2(1,1,iti)*dcos(theta(i-1)/2.0d0)/2.0d0
enddo
#else
if (i.gt. nnt+2 .and. i.lt.nct+2) then
- iti = itortyp(itype(i-2))
+ iti = itype2loc(itype(i-2))
else
- iti=ntortyp+1
+ iti=nloctyp
endif
c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then
if (i.gt. nnt+1 .and. i.lt.nct+1) then
- iti1 = itortyp(itype(i-1))
+ iti1 = itype2loc(itype(i-1))
else
- iti1=ntortyp+1
+ iti1=nloctyp
endif
b1(1,i-2)=b(3,iti)
b1(2,i-2)=b(5,iti)
endif
c if (i.gt. iatel_s+2 .and. i.lt.iatel_e+5) then
if (i.gt. nnt+2 .and. i.lt.nct+2) then
- iti = itortyp(itype(i-2))
+ iti = itype2loc(itype(i-2))
else
- iti=ntortyp
+ iti=nloctyp
endif
c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then
if (i.gt. nnt+1 .and. i.lt.nct+1) then
- iti1 = itortyp(itype(i-1))
+ iti1 = itype2loc(itype(i-1))
else
- iti1=ntortyp
+ iti1=nloctyp
endif
cd write (iout,*) '*******i',i,' iti1',iti
cd write (iout,*) 'b1',b1(:,iti)
call matvec2(Ug(1,1,i-2),gtb2(1,i-2),gUb2(1,i-2))
c write (iout,*) Ug(1,1,i-2),gtb2(1,i-2),gUb2(1,i-2),"chuj"
#endif
-c write(iout,*) "co jest kurwa", iti, EE(1,1,iti),EE(2,1,iti),
-c & EE(1,2,iti),EE(2,2,iti)
+c write(iout,*) "co jest kurwa", iti, EE(1,1,i),EE(2,1,i),
+c & EE(1,2,iti),EE(2,2,i)
call matmat2(EE(1,1,i-2),Ug(1,1,i-2),EUg(1,1,i-2))
call matmat2(gtEE(1,1,i-2),Ug(1,1,i-2),gtEUg(1,1,i-2))
c write(iout,*) "Macierz EUG",
c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then
if (i.gt. nnt+1 .and. i.lt.nct+1) then
if (itype(i-1).le.ntyp) then
- iti1 = itortyp(itype(i-1))
+ iti1 = itype2loc(itype(i-1))
else
- iti1=ntortyp
+ iti1=nloctyp
endif
else
- iti1=ntortyp
+ iti1=nloctyp
endif
do k=1,2
mu(k,i-2)=Ub2(k,i-2)+b1(k,i-1)
enddo
-C write (iout,*) 'mumu',i,b1(1,i-1),Ub2(1,i-2)
-c write (iout,*) 'mu ',mu(:,i-2),i-2
+#ifdef MUOUT
+ write (iout,'(2hmu,i3,3f8.1,12f10.5)') i-2,rad2deg*theta(i-1),
+ & rad2deg*theta(i),rad2deg*phi(i),mu(1,i-2),mu(2,i-2),
+ & -b2(1,i-2),b2(2,i-2),b1(1,i-2),b1(2,i-2),
+ & dsqrt(b2(1,i-1)**2+b2(2,i-1)**2)
+ & +dsqrt(b1(1,i-1)**2+b1(2,i-1)**2),
+ & ((ee(l,k,i-2),l=1,2),k=1,2),eenew(1,itype2loc(iti))
+#endif
cd write (iout,*) 'mu1',mu1(:,i-2)
cd write (iout,*) 'mu2',mu2(:,i-2)
if (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or.wcorr6.gt.0.0d0)
#endif
#endif
cd do i=1,nres
-cd iti = itortyp(itype(i))
+cd iti = itype2loc(itype(i))
cd write (iout,*) i
cd do j=1,2
cd write (iout,'(2f10.5,5x,2f10.5,5x,2f10.5)')
-cd & (EE(j,k,iti),k=1,2),(Ug(j,k,i),k=1,2),(EUg(j,k,i),k=1,2)
+cd & (EE(j,k,i),k=1,2),(Ug(j,k,i),k=1,2),(EUg(j,k,i),k=1,2)
cd enddo
cd enddo
return
C
C 14/01/2014 TURN3,TUNR4 does no go under periodic boundry condition
do i=iturn3_start,iturn3_end
- if (i.le.1) cycle
+c if (i.le.1) cycle
C write(iout,*) "tu jest i",i
if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
C changes suggested by Ana to avoid out of bounds
- & .or.((i+4).gt.nres)
- & .or.((i-1).le.0)
+C Adam: Unnecessary: handled by iturn3_end and iturn3_start
+c & .or.((i+4).gt.nres)
+c & .or.((i-1).le.0)
C end of changes by Ana
& .or. itype(i+2).eq.ntyp1
& .or. itype(i+3).eq.ntyp1) cycle
- if(i.gt.1)then
- if(itype(i-1).eq.ntyp1)cycle
- end if
- if(i.LT.nres-3)then
- if (itype(i+4).eq.ntyp1) cycle
- end if
+C Adam: Instructions below will switch off existing interactions
+c if(i.gt.1)then
+c if(itype(i-1).eq.ntyp1)cycle
+c end if
+c if(i.LT.nres-3)then
+c if (itype(i+4).eq.ntyp1) cycle
+c end if
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
if (i.le.1) cycle
if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
C changes suggested by Ana to avoid out of bounds
- & .or.((i+5).gt.nres)
- & .or.((i-1).le.0)
+c & .or.((i+5).gt.nres)
+c & .or.((i-1).le.0)
C end of changes suggested by Ana
& .or. itype(i+3).eq.ntyp1
& .or. itype(i+4).eq.ntyp1
- & .or. itype(i+5).eq.ntyp1
- & .or. itype(i).eq.ntyp1
- & .or. itype(i-1).eq.ntyp1
+c & .or. itype(i+5).eq.ntyp1
+c & .or. itype(i).eq.ntyp1
+c & .or. itype(i-1).eq.ntyp1
& ) cycle
dxi=dc(1,i)
dyi=dc(2,i)
CTU KURWA
do i=iatel_s,iatel_e
C do i=75,75
- if (i.le.1) cycle
+c if (i.le.1) cycle
if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
C changes suggested by Ana to avoid out of bounds
- & .or.((i+2).gt.nres)
- & .or.((i-1).le.0)
+c & .or.((i+2).gt.nres)
+c & .or.((i-1).le.0)
C end of changes by Ana
- & .or. itype(i+2).eq.ntyp1
- & .or. itype(i-1).eq.ntyp1
+c & .or. itype(i+2).eq.ntyp1
+c & .or. itype(i-1).eq.ntyp1
& ) cycle
dxi=dc(1,i)
dyi=dc(2,i)
if (j.le.1) cycle
if (itype(j).eq.ntyp1.or. itype(j+1).eq.ntyp1
C changes suggested by Ana to avoid out of bounds
- & .or.((j+2).gt.nres)
- & .or.((j-1).le.0)
+c & .or.((j+2).gt.nres)
+c & .or.((j-1).le.0)
C end of changes by Ana
- & .or.itype(j+2).eq.ntyp1
- & .or.itype(j-1).eq.ntyp1
+c & .or.itype(j+2).eq.ntyp1
+c & .or.itype(j-1).eq.ntyp1
&) cycle
call eelecij(i,j,ees,evdw1,eel_loc)
enddo ! j
a_temp(1,2)=a23
a_temp(2,1)=a32
a_temp(2,2)=a33
- iti1=itortyp(itype(i+1))
- iti2=itortyp(itype(i+2))
- iti3=itortyp(itype(i+3))
+ iti1=itype2loc(itype(i+1))
+ iti2=itype2loc(itype(i+2))
+ iti3=itype2loc(itype(i+3))
c write(iout,*) "iti1",iti1," iti2",iti2," iti3",iti3
call transpose2(EUg(1,1,i+1),e1t(1,1))
call transpose2(Eug(1,1,i+2),e2t(1,1))
include 'COMMON.TORCNSTR'
include 'COMMON.CONTROL'
logical lprn
- double precision thybt1(maxtermkcc),thybt2(maxtermkcc)
+c double precision thybt1(maxtermkcc),thybt2(maxtermkcc)
C Set lprn=.true. for debugging
lprn=.false.
c lprn=.true.
C print *,"wchodze kcc"
+ if (lprn) write (iout,*) "etor_kcc tor_mode",tor_mode
if (tor_mode.ne.2) then
etors=0.0D0
endif
sumnonchebyshev=0.0d0
sumchebyshev=0.0d0
C to avoid multiple devision by 2
- theti22=0.5d0*theta(i)
+c theti22=0.5d0*theta(i)
C theta 12 is the theta_1 /2
C theta 22 is theta_2 /2
- theti12=0.5d0*theta(i-1)
+c theti12=0.5d0*theta(i-1)
C and appropriate sinus function
- sinthet2=dsin(theta(i))
sinthet1=dsin(theta(i-1))
+ sinthet2=dsin(theta(i))
costhet1=dcos(theta(i-1))
costhet2=dcos(theta(i))
+c Cosines of halves thetas
+ costheti12=0.5d0*(1.0d0+costhet1)
+ costheti22=0.5d0*(1.0d0+costhet2)
C to speed up lets store its mutliplication
- sint1t2=sinthet2*sinthet1
+ sint1t2=sinthet2*sinthet1
+ sint1t2n=1.0d0
C \sum_{i=1}^n (sin(theta_1) * sin(theta_2))^n * (c_n* cos(n*gamma)
C +d_n*sin(n*gamma)) *
C \sum_{i=1}^m (1+a_m*Tb_m(cos(theta_1 /2))+b_m*Tb_m(cos(theta_2 /2)))
C we have two sum 1) Non-Chebyshev which is with n and gamma
+ etori=0.0d0
do j=1,nterm_kcc(itori,itori1)
+ nval=nterm_kcc_Tb(itori,itori1)
v1ij=v1_kcc(j,itori,itori1)
v2ij=v2_kcc(j,itori,itori1)
+c write (iout,*) "i",i," j",j," v1",v1ij," v2",v2ij
C v1ij is c_n and d_n in euation above
cosphi=dcos(j*phii)
sinphi=dsin(j*phii)
- sint1t2n=sint1t2**j
- sumnonchebyshev=
- & sint1t2n*(v1ij*cosphi+v2ij*sinphi)
- actval=sint1t2n*(v1ij*cosphi+v2ij*sinphi)
+ sint1t2n1=sint1t2n
+ sint1t2n=sint1t2n*sint1t2
+ sumth1tyb1=tschebyshev(1,nval,v11_chyb(1,j,itori,itori1),
+ & costheti12)
+ gradth1tyb1=-0.5d0*sinthet1*gradtschebyshev(0,nval-1,
+ & v11_chyb(1,j,itori,itori1),costheti12)
+c write (iout,*) "v11",(v11_chyb(k,j,itori,itori1),k=1,nval),
+c & " sumth1tyb1",sumth1tyb1," gradth1tyb1",gradth1tyb1
+ sumth2tyb1=tschebyshev(1,nval,v21_chyb(1,j,itori,itori1),
+ & costheti22)
+ gradth2tyb1=-0.5d0*sinthet2*gradtschebyshev(0,nval-1,
+ & v21_chyb(1,j,itori,itori1),costheti22)
+c write (iout,*) "v21",(v21_chyb(k,j,itori,itori1),k=1,nval),
+c & " sumth2tyb1",sumth2tyb1," gradth2tyb1",gradth2tyb1
+ sumth1tyb2=tschebyshev(1,nval,v12_chyb(1,j,itori,itori1),
+ & costheti12)
+ gradth1tyb2=-0.5d0*sinthet1*gradtschebyshev(0,nval-1,
+ & v12_chyb(1,j,itori,itori1),costheti12)
+c write (iout,*) "v12",(v12_chyb(k,j,itori,itori1),k=1,nval),
+c & " sumth1tyb2",sumth1tyb2," gradth1tyb2",gradth1tyb2
+ sumth2tyb2=tschebyshev(1,nval,v22_chyb(1,j,itori,itori1),
+ & costheti22)
+ gradth2tyb2=-0.5d0*sinthet2*gradtschebyshev(0,nval-1,
+ & v22_chyb(1,j,itori,itori1),costheti22)
+c write (iout,*) "v22",(v22_chyb(k,j,itori,itori1),k=1,nval),
+c & " sumth2tyb2",sumth2tyb2," gradth2tyb2",gradth2tyb2
C etors=etors+sint1t2n*(v1ij*cosphi+v2ij*sinphi)
C if (energy_dec) etors_ii=etors_ii+
C & v1ij*cosphi+v2ij*sinphi
C glocig is the gradient local i site in gamma
- glocig=j*(v2ij*cosphi-v1ij*sinphi)*sint1t2n
+ actval1=v1ij*cosphi*(1.0d0+sumth1tyb1+sumth2tyb1)
+ actval2=v2ij*sinphi*(1.0d0+sumth1tyb2+sumth2tyb2)
+ etori=etori+sint1t2n*(actval1+actval2)
+ glocig=glocig+
+ & j*sint1t2n*(v2ij*cosphi*(1.0d0+sumth1tyb2+sumth2tyb2)
+ & -v1ij*sinphi*(1.0d0+sumth1tyb1+sumth2tyb1))
C now gradient over theta_1
- glocit1=actval/sinthet1*j*costhet1
- glocit2=actval/sinthet2*j*costhet2
+ glocit1=glocit1+
+ & j*sint1t2n1*costhet1*sinthet2*(actval1+actval2)+
+ & sint1t2n*(v1ij*cosphi*gradth1tyb1+v2ij*sinphi*gradth1tyb2)
+ glocit2=glocit2+
+ & j*sint1t2n1*sinthet1*costhet2*(actval1+actval2)+
+ & sint1t2n*(v1ij*cosphi*gradth2tyb1+v2ij*sinphi*gradth2tyb2)
C now the Czebyshev polinominal sum
- do k=1,nterm_kcc_Tb(itori,itori1)
- thybt1(k)=v1_chyb(k,j,itori,itori1)
- thybt2(k)=v2_chyb(k,j,itori,itori1)
+c do k=1,nterm_kcc_Tb(itori,itori1)
+c thybt1(k)=v1_chyb(k,j,itori,itori1)
+c thybt2(k)=v2_chyb(k,j,itori,itori1)
C thybt1(k)=0.0
C thybt2(k)=0.0
- enddo
- sumth1thyb=tschebyshev
- & (1,nterm_kcc_Tb(itori,itori1),thybt1(1),dcos(theti12)**2)
- gradthybt1=gradtschebyshev
- & (0,nterm_kcc_Tb(itori,itori1)-1,thybt1(1),
- & dcos(theti12)**2)
- & *dcos(theti12)*(-dsin(theti12))
- sumth2thyb=tschebyshev
- & (1,nterm_kcc_Tb(itori,itori1),thybt2(1),dcos(theti22)**2)
- gradthybt2=gradtschebyshev
- & (0,nterm_kcc_Tb(itori,itori1)-1,thybt2(1),
- & dcos(theti22)**2)
- & *dcos(theti22)*(-dsin(theti22))
+c enddo
C print *, sumth1thyb, gradthybt1, sumth2thyb, gradthybt2,
C & gradtschebyshev
C & (0,nterm_kcc_Tb(itori,itori1)-1,thybt2(1),
C & dsin(theti22)
C now overal sumation
- etors=etors+(1.0d0+sumth1thyb+sumth2thyb)*sumnonchebyshev
C print *,"sumnon", sumnonchebyshev,sumth1thyb+sumth2thyb
+ enddo ! j
+ etors=etors+etori
C derivative over gamma
- gloc(i-3,icg)=gloc(i-3,icg)+wtor*glocig
- & *(1.0d0+sumth1thyb+sumth2thyb)
+ gloc(i-3,icg)=gloc(i-3,icg)+wtor*glocig
C derivative over theta1
- gloc(nphi+i-3,icg)=gloc(nphi+i-3,icg)+wtor*
- & (glocit1*(1.0d0+sumth1thyb+sumth2thyb)+
- & sumnonchebyshev*gradthybt1)
+ gloc(nphi+i-3,icg)=gloc(nphi+i-3,icg)+wtor*glocit1
C now derivative over theta2
- gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)+wtor*
- & (glocit2*(1.0d0+sumth1thyb+sumth2thyb)+
- & sumnonchebyshev*gradthybt2)
- enddo
+ gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)+wtor*glocit2
+ if (lprn)
+ & write (iout,*) i-2,i-1,itype(i-2),itype(i-1),itori,itori1,
+ & theta(i-1)*rad2deg,theta(i)*rad2deg,phii*rad2deg,etori
enddo
-
C gloc(i-3,icg)=gloc(i-3,icg)+wtor*gloci
! 6/20/98 - dihedral angle constraints
if (tor_mode.ne.2) then
lprn=.false.
c lprn=.true.
C print *,"wchodze kcc"
- if (tormode.ne.2) etheta=0.0D0
+ if (lprn) write (iout,*) "ebend_kcc tor_mode",tor_mode
+ if (tor_mode.ne.2) etheta=0.0D0
do i=ithet_start,ithet_end
c print *,i,itype(i-1),itype(i),itype(i-2)
if ((itype(i-1).eq.ntyp1).or.itype(i-2).eq.ntyp1
enddo
sumth1thyb=tschebyshev
& (1,nbend_kcc_Tb(iti),thybt1(1),costhet)
+ if (lprn) write (iout,*) i-1,itype(i-1),iti,theta(i)*rad2deg,
+ & sumth1thyb
ihelp=nbend_kcc_Tb(iti)-1
gradthybt1=gradtschebyshev
& (0,ihelp,thybt1(1),costhet)
gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)+wang*
& gradthybt1*sinthet*(-0.5d0)
enddo
- if (tormode.ne.2) then
+ if (tor_mode.ne.2) then
ethetacnstr=0.0d0
C print *,ithetaconstr_start,ithetaconstr_end,"TU"
do i=ithetaconstr_start,ithetaconstr_end
& auxmat(2,2)
iti1 = itortyp(itype(i+1))
if (j.lt.nres-1) then
- itj1 = itortyp(itype(j+1))
+ itj1 = itype2loc(itype(j+1))
else
- itj1=ntortyp
+ itj1=nloctyp
endif
do iii=1,2
dipi(iii,1)=Ub2(iii,i)
if (l.eq.j+1) then
C parallel orientation of the two CA-CA-CA frames.
if (i.gt.1) then
- iti=itortyp(itype(i))
+ iti=itype2loc(itype(i))
else
- iti=ntortyp
+ iti=nloctyp
endif
- itk1=itortyp(itype(k+1))
- itj=itortyp(itype(j))
+ itk1=itype2loc(itype(k+1))
+ itj=itype2loc(itype(j))
if (l.lt.nres-1) then
- itl1=itortyp(itype(l+1))
+ itl1=itype2loc(itype(l+1))
else
- itl1=ntortyp
+ itl1=nloctyp
endif
C A1 kernel(j+1) A2T
cd do iii=1,2
else
C Antiparallel orientation of the two CA-CA-CA frames.
if (i.gt.1) then
- iti=itortyp(itype(i))
+ iti=itype2loc(itype(i))
else
- iti=ntortyp
+ iti=nloctyp
endif
- itk1=itortyp(itype(k+1))
- itl=itortyp(itype(l))
- itj=itortyp(itype(j))
+ itk1=itype2loc(itype(k+1))
+ itl=itype2loc(itype(l))
+ itj=itype2loc(itype(j))
if (j.lt.nres-1) then
- itj1=itortyp(itype(j+1))
+ itj1=itype2loc(itype(j+1))
else
- itj1=ntortyp
+ itj1=nloctyp
endif
C A2 kernel(j-1)T A1T
call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
cd write (iout,*)
cd & 'EELLO5: Contacts have occurred for peptide groups',i,j,
cd & ' and',k,l
- itk=itortyp(itype(k))
- itl=itortyp(itype(l))
- itj=itortyp(itype(j))
+ itk=itype2loc(itype(k))
+ itl=itype2loc(itype(l))
+ itj=itype2loc(itype(j))
eello5_1=0.0d0
eello5_2=0.0d0
eello5_3=0.0d0
c goto 1112
c1111 continue
C Contribution from graph II
- call transpose2(EE(1,1,itk),auxmat(1,1))
+ call transpose2(EE(1,1,k),auxmat(1,1))
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)
cd goto 1112
C Contribution from graph IV
cd1110 continue
- call transpose2(EE(1,1,itl),auxmat(1,1))
+ call transpose2(EE(1,1,l),auxmat(1,1))
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)
cd goto 1112
C Contribution from graph IV
1110 continue
- call transpose2(EE(1,1,itj),auxmat(1,1))
+ call transpose2(EE(1,1,j),auxmat(1,1))
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)
C i i C
C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
- itk=itortyp(itype(k))
+ itk=itype2loc(itype(k))
s1= scalar2(AEAb1(1,2,imat),CUgb2(1,i))
s2=-scalar2(AEAb2(1,1,imat),Ug2Db1t(1,k))
s3= scalar2(AEAb2(1,1,imat),CUgb2(1,k))
C energy moment and not to the cluster cumulant.
iti=itortyp(itype(i))
if (j.lt.nres-1) then
- itj1=itortyp(itype(j+1))
+ itj1=itype2loc(itype(j+1))
else
- itj1=ntortyp
+ itj1=nloctyp
endif
- itk=itortyp(itype(k))
- itk1=itortyp(itype(k+1))
+ itk=itype2loc(itype(k))
+ itk1=itype2loc(itype(k+1))
if (l.lt.nres-1) then
- itl1=itortyp(itype(l+1))
+ itl1=itype2loc(itype(l+1))
else
- itl1=ntortyp
+ itl1=nloctyp
endif
#ifdef MOMENT
s1=dip(4,jj,i)*dip(4,kk,k)
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 transpose2(EE(1,1,k),auxmat(1,1))
call matmat2(auxmat(1,1),AECA(1,1,1),pizda(1,1))
vv(1)=pizda(1,1)+pizda(2,2)
vv(2)=pizda(2,1)-pizda(1,2)
C 4/7/01 AL Component s1 was removed, because it pertains to the respective
C energy moment and not to the cluster cumulant.
cd write (2,*) 'eello_graph4: wturn6',wturn6
- iti=itortyp(itype(i))
- itj=itortyp(itype(j))
+ iti=itype2loc(itype(i))
+ itj=itype2loc(itype(j))
if (j.lt.nres-1) then
- itj1=itortyp(itype(j+1))
+ itj1=itype2loc(itype(j+1))
else
- itj1=ntortyp
+ itj1=nloctyp
endif
- itk=itortyp(itype(k))
+ itk=itype2loc(itype(k))
if (k.lt.nres-1) then
- itk1=itortyp(itype(k+1))
+ itk1=itype2loc(itype(k+1))
else
- itk1=ntortyp
+ itk1=nloctyp
endif
- itl=itortyp(itype(l))
+ itl=itype2loc(itype(l))
if (l.lt.nres-1) then
- itl1=itortyp(itype(l+1))
+ itl1=itype2loc(itype(l+1))
else
- itl1=ntortyp
+ itl1=nloctyp
endif
cd write (2,*) 'eello6_graph4:','i',i,' j',j,' k',k,' l',l
cd write (2,*) 'iti',iti,' itj',itj,' itj1',itj1,' itk',itk,
j=i+4
k=i+1
l=i+3
- iti=itortyp(itype(i))
- itk=itortyp(itype(k))
- itk1=itortyp(itype(k+1))
- itl=itortyp(itype(l))
- itj=itortyp(itype(j))
+ iti=itype2loc(itype(i))
+ itk=itype2loc(itype(k))
+ itk1=itype2loc(itype(k+1))
+ itl=itype2loc(itype(l))
+ itj=itype2loc(itype(j))
cd write (2,*) 'itk',itk,' itk1',itk1,' itl',itl,' itj',itj
cd write (2,*) 'i',i,' k',k,' j',j,' l',l
cd if (i.ne.1 .or. j.ne.3 .or. k.ne.2 .or. l.ne.4) then
include "DIMENSIONS"
integer i,m,n
double precision x(n+1),y,yy(0:maxvar),aux
-c Tschebyshev polynomial. Note that the first term is omitted
+c Tschebyshev polynomial. Note that the first term is omitted
c m=0: the constant term is included
c m=1: the constant term is not included
yy(0)=1.0d0
include 'COMMON.MD'
include 'COMMON.SCCOR'
include 'COMMON.SHIELD'
+ maxshieldlist=0
C
C Initialize Cartesian-coordinate gradient
C
c Obtaining the gamma derivatives from sine derivative
if (phi(i).gt.-pi4.and.phi(i).le.pi4.or.
& phi(i).gt.pi34.and.phi(i).le.pi.or.
- & phi(i).gt.-pi.and.phi(i).le.-pi34) then
+ & phi(i).ge.-pi.and.phi(i).le.-pi34) then
call vecpr(dc_norm(1,i-1),dc_norm(1,i-2),vp1)
call vecpr(dc_norm(1,i-3),dc_norm(1,i-1),vp2)
call vecpr(dc_norm(1,i-3),dc_norm(1,i-2),vp3)
c Obtaining the gamma derivatives from sine derivative
if (tauangle(1,i).gt.-pi4.and.tauangle(1,i).le.pi4.or.
& tauangle(1,i).gt.pi34.and.tauangle(1,i).le.pi.or.
- & tauangle(1,i).gt.-pi.and.tauangle(1,i).le.-pi34) then
+ & tauangle(1,i).ge.-pi.and.tauangle(1,i).le.-pi34) then
call vecpr(dc_norm(1,i-1),dc_norm(1,i-2),vp1)
call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-1),vp2)
call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-2),vp3)
c Obtaining the gamma derivatives from sine derivative
if (tauangle(3,i).gt.-pi4.and.tauangle(3,i).le.pi4.or.
& tauangle(3,i).gt.pi34.and.tauangle(3,i).le.pi.or.
- & tauangle(3,i).gt.-pi.and.tauangle(3,i).le.-pi34) then
+ & tauangle(3,i).ge.-pi.and.tauangle(3,i).le.-pi34) then
call vecpr(dc_norm(1,i-1+nres),dc_norm(1,i-2),vp1)
call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-1+nres),vp2)
call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-2),vp3)
c obtaining the derivatives of omega from sines
if(omeg(i).gt.-pi4.and.omeg(i).le.pi4.or.
& omeg(i).gt.pi34.and.omeg(i).le.pi.or.
- & omeg(i).gt.-pi.and.omeg(i).le.-pi34) then
+ & omeg(i).ge.-pi.and.omeg(i).le.-pi34) then
fac15=dcos(theta(i+1))/(dsin(theta(i+1))*
& dsin(theta(i+1)))
fac16=dcos(alph(i))/(dsin(alph(i))*dsin(alph(i)))
cd print *,'func',nf,nfl,icg
call var_to_geom(n,x)
call zerograd
- call chainbuild
+ call chainbuild_extconf
cd write (iout,*) 'ETOTAL called from FUNC'
call etotal(energia(0))
call sum_gradient
icg=mod(nf,2)+1
call var_to_geom_restr(n,x)
call zerograd
- call chainbuild
+ call chainbuild_extconf
cd write (iout,*) 'ETOTAL called from FUNC'
call etotal(energia(0))
call sum_gradient
enddo
endif
C reading lipid parameters
+ write (iout,*) "iliptranpar",iliptranpar
+ call flush(iout)
read(iliptranpar,*) pepliptran
do i=1,ntyp
read(iliptranpar,*) liptranene(i)
C
read (ithep,*,err=111,end=111) nthetyp,ntheterm,ntheterm2,
& ntheterm3,nsingle,ndouble
+ write (iout,*) "ithep",ithep
+ call flush(iout)
nntheterm=max0(ntheterm,ntheterm2,ntheterm3)
read (ithep,*,err=111,end=111) (ithetyp(i),i=1,ntyp1)
do i=-ntyp1,-1
C
if (lprint) then
write (iout,'(//a)') 'Parameter of virtual-bond-angle potential'
- do i=1,nthetyp+1
- do j=1,nthetyp+1
- do k=1,nthetyp+1
+ do iblock=1,2
+ do i=0,nthetyp
+ do j=-nthetyp,nthetyp
+ do k=-nthetyp,nthetyp
write (iout,'(//4a)')
- & 'Type ',onelett(i),onelett(j),onelett(k)
+ & 'Type ',toronelet(i),toronelet(j),toronelet(k)
write (iout,'(//a,10x,a)') " l","a[l]"
write (iout,'(i2,1pe15.5)') 0,aa0thet(i,j,k,iblock)
write (iout,'(i2,1pe15.5)')
enddo
enddo
enddo
+ enddo
enddo
call flush(iout)
endif
close (itorp)
if (lprint) then
write (iout,'(/a/)') 'Torsional constants:'
- do i=1,ntortyp
- do j=1,ntortyp
+ do iblock=1,2
+ do i=0,ntortyp-1
+ do j=-ntortyp+1,ntortyp-1
write (iout,*) 'ityp',i,' jtyp',j
write (iout,*) 'Fourier constants'
do k=1,nterm(i,j,iblock)
enddo
enddo
enddo
+ enddo
endif
C
endif
#endif
C read Czybyshev torsional parameters
- read (itorkcc,*,end=121,err=121) nkcctyp
- read (itorkcc,*,end=121,err=121) (itortyp_kcc(i),i=1,ntyp)
- do i=-ntyp,-1
+ read (itorkcc,*,end=121,err=121) nkcctyp
+ read (itorkcc,*,end=121,err=121) (itortyp_kcc(i),i=1,ntyp)
+ do i=-ntyp,-1
itortyp_kcc(i)=-itortyp_kcc(-i)
- enddo
- do i=1,nkcctyp
- do j=1,nkcctyp
+ enddo
+ do i=0,nkcctyp
+ do j=0,nkcctyp
C first we read the cos and sin gamma parameters
read (itorkcc,*,end=121,err=121)
& nterm_kcc(j,i),nterm_kcc_Tb(j,i)
C read (itorkcc,*,end=121,err=121) nterm_kcc_Tb(j,i)
- do k=1,nterm_kcc(j,i)
- do l=1,nterm_kcc_Tb(j,i)
- read (itorkcc,*,end=121,err=121)
- & v1_chyb(l,k,j,i)
- enddo
- do l=1,nterm_kcc_Tb(j,i)
- read (itorkcc,*,end=121,err=121)
- & v2_chyb(l,k,j,i)
- enddo
- read (itorkcc,*,end=121,err=121)
- & v1_kcc(k,j,i)
- read (itorkcc,*,end=121,err=121)
- & v2_kcc(k,j,i)
- enddo
+ do k=1,nterm_kcc(j,i)
+ do l=1,nterm_kcc_Tb(j,i)
+ read (itorkcc,*,end=121,err=121) v11_chyb(l,k,j,i)
+ enddo
+ do l=1,nterm_kcc_Tb(j,i)
+ read (itorkcc,*,end=121,err=121) v21_chyb(l,k,j,i)
+ enddo
+ do l=1,nterm_kcc_Tb(j,i)
+ read (itorkcc,*,end=121,err=121) v12_chyb(l,k,j,i)
+ enddo
+ do l=1,nterm_kcc_Tb(j,i)
+ read (itorkcc,*,end=121,err=121) v22_chyb(l,k,j,i)
+ enddo
+ read (itorkcc,*,end=121,err=121) v1_kcc(k,j,i)
+ read (itorkcc,*,end=121,err=121) v2_kcc(k,j,i)
+ enddo
+ enddo
+ enddo
+ if (lprint) then
+c Print valence-torsional parameters
+ write (iout,'(a)')
+ & "Parameters of the valence-torsional potentials"
+ do i=0,nkcctyp
+ do j=0,nkcctyp
+ write (iout,'(3a)') "Type ",toronelet(i),toronelet(j)
+ write (iout,'(2a20,a15)') "v_kcc","v1_chyb","v2_chyb"
+ do k=1,nterm_kcc(j,i)
+ write (iout,'(i5,f15.10,i5,2f15.10)')
+ & k,v1_kcc(k,j,i),1,v11_chyb(1,k,j,i),v21_chyb(1,k,j,i)
+ do l=2,nterm_kcc_Tb(j,i)
+ write (iout,'(20x,i5,2f15.10)')
+ & l,v11_chyb(l,k,j,i),v21_chyb(l,k,j,i)
enddo
- enddo
+ write (iout,'(i5,f15.10,i5,2f15.10)')
+ & k,v2_kcc(k,j,i),1,v12_chyb(1,k,j,i),v22_chyb(1,k,j,i)
+ do l=2,nterm_kcc_Tb(j,i)
+ write (iout,'(20x,i5,2f15.10)')
+ & l,v12_chyb(l,k,j,i),v22_chyb(l,k,j,i)
+ enddo
+ write (iout,'(a)')
+ enddo
+ enddo
+ enddo
+ endif
C here will be the apropriate recalibrating for D-aminoacid
C read (ithetkcc,*,end=121,err=121) nkcctyp
- do i=1,nkcctyp
+ do i=0,nkcctyp
read (ithetkcc,*,end=121,err=121) nbend_kcc_Tb(i)
- do j=1,nbend_kcc_Tb(i)
- read (ithetkcc,*,end=121,err=121)
- & v1bend_chyb(j,i)
- enddo
+ do j=1,nbend_kcc_Tb(i)
+ read (ithetkcc,*,end=121,err=121) v1bend_chyb(j,i)
+ enddo
+ enddo
+ if (lprint) then
+ write (iout,'(a)')
+ & "Parameters of the valence-only potentials"
+ do i=0,nkcctyp
+ write (iout,'(2a)') "Type ",toronelet(i)
+ do k=1,nbend_kcc_Tb(i)
+ write(iout,'(i5,f15.10)') k,v1bend_chyb(k,i)
enddo
+ enddo
+ endif
C Read of Side-chain backbone correlation parameters
C Modified 11 May 2012 by Adasko
CCC
v0ijsccor=v0ijsccor+vlor1sccor(k,i,j)/
&(1+vlor3sccor(k,i,j)**2)
enddo
- v0sccor(i,j,iblock)=v0ijsccor
+ v0sccor(l,i,j)=v0ijsccor
enddo
enddo
enddo
#endif
if (lprint) then
write (iout,'(/a/)') 'Torsional constants:'
+ do l=1,maxinter
do i=1,nsccortyp
do j=1,nsccortyp
write (iout,*) 'ityp',i,' jtyp',j
enddo
enddo
enddo
+ enddo
endif
C
write (iout,*) "Coefficients of the cumulants"
endif
read (ifourier,*) nloctyp
-
+#ifdef NEWCORR
+ read (ifourier,*,end=115,err=115) (itype2loc(i),i=1,ntyp)
+ read (ifourier,*,end=115,err=115) (iloctyp(i),i=0,nloctyp-1)
+ itype2loc(ntyp1)=nloctyp
+ iloctyp(nloctyp)=ntyp1
+#else
+ do i=1,ntyp1
+ itype2loc(i)=itortyp(i)
+ enddo
+ iloctyp(0)=10
+ iloctyp(1)=9
+ iloctyp(2)=20
+ iloctyp(3)=ntyp1
+#endif
+ do i=1,ntyp1
+ itype2loc(-i)=-itype2loc(i)
+ enddo
+ do i=1,nloctyp
+ iloctyp(-i)=-iloctyp(i)
+ enddo
+ write (iout,*) "itype2loc",(itype2loc(i),i=1,ntyp1)
+ write (iout,*) "nloctyp",nloctyp,
+ & " iloctyp",(iloctyp(i),i=0,nloctyp)
do i=0,nloctyp-1
read (ifourier,*,end=115,err=115)
read (ifourier,*,end=115,err=115) (b(ii,i),ii=1,13)
c B2(2,i) = b(4)
c B2(1,-i) =b(2)
c B2(2,-i) =-b(4)
- B1tilde(1,i) = b(3,i)
- B1tilde(2,i) =-b(5,i)
+cc B1tilde(1,i) = b(3,i)
+cc B1tilde(2,i) =-b(5,i)
C B1tilde(1,-i) =-b(3,i)
C B1tilde(2,-i) =b(5,i)
- b1tilde(1,i)=0.0d0
- b1tilde(2,i)=0.0d0
- B2(1,i) = b(2,i)
- B2(2,i) = b(4,i)
+cc b1tilde(1,i)=0.0d0
+cc b1tilde(2,i)=0.0d0
+cc B2(1,i) = b(2,i)
+cc B2(2,i) = b(4,i)
C B2(1,-i) =b(2,i)
C B2(2,-i) =-b(4,i)
else
icheckgrad=3
endif
+ call reada(controlcard,'DELTA',aincr,1.0d-7)
elseif (index(controlcard,'THREAD').gt.0) then
modecalc=2
call readi(controlcard,'THREAD',nthread,0)
projects / unres.git / commitdiff