- FUNCTION ARCOS(X)
+ double precision FUNCTION ARCOS(X)
implicit real*8 (a-h,o-z)
include 'COMMON.GEO'
IF (DABS(X).LT.1.0D0) GOTO 1
c call intcartderiv
c call checkintcartgrad
call zerograd
- aincr=1.0D-5
+ aincr=10.0D-6
write(iout,*) 'Calling CHECK_ECARTINT.'
nf=0
icall=0
endif
write (iout,'(/a/)') 'Gradient in virtual-bond and SC vectors'
do i=0,nres
+ print *,i
do j=1,3
xx(j)=c(j,i+nres)
ddc(j)=dc(j,i)
C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
-C 2 3 3500
+C 0 40360 9
subroutine cinfo
include 'COMMON.IOUNITS'
write(iout,*)'++++ Compile info ++++'
- write(iout,*)'Version 2.3 build 3500'
- write(iout,*)'compiled Wed Jun 18 15:52:43 2014'
- write(iout,*)'compiled by czarek@piasek3'
+ write(iout,*)'Version 0.40360 build 9'
+ write(iout,*)'compiled Fri Jan 23 21:00:08 2015'
+ write(iout,*)'compiled by adam@mmka'
write(iout,*)'OS name: Linux '
- write(iout,*)'OS release: 3.2.0-59-generic '
+ write(iout,*)'OS release: 3.2.0-72-generic '
write(iout,*)'OS version:',
- & ' #90-Ubuntu SMP Tue Jan 7 22:43:51 UTC 2014 '
+ & ' #107-Ubuntu SMP Thu Nov 6 14:24:01 UTC 2014 '
write(iout,*)'flags:'
write(iout,*)'INSTALL_DIR = /users/software/mpich-1.2.7p1_int...'
write(iout,*)'FC= ifort'
- write(iout,*)'OPT = -O3 -ip -w'
- write(iout,*)'CFLAGS = -DSGI -c'
- write(iout,*)'FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include'
- write(iout,*)'FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)...'
- write(iout,*)'FFLAGS2 = -c -w -O0 -I$(INSTALL_DIR)/include'
- write(iout,*)'FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report ...'
- write(iout,*)'LIBS = -L$(INSTALL_DIR)/lib -lmpich ../../lib/x...'
+ write(iout,*)'OPT = -O3 -ip '
+ 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$(INSTALL...'
+ write(iout,*)'LIBS = -L$(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-M/unres_ifort_...'
- write(iout,*)'E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR...'
- write(iout,*)'E0LL2Y: BIN = ../../../bin/unres/MD-M/unres_ifo...'
+ write(iout,*)'GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 ...'
+ write(iout,*)'GAB: BIN = ../../../bin/unres/MD/unres-mult-sym...'
+ write(iout,*)'4P: CPPFLAGS = -DLINUX -DPGI -DAMD64 -DUNRES -D...'
+ write(iout,*)'4P: BIN = ../../../bin/unres/MD/unres-mult-syme...'
+ write(iout,*)'E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD...'
+ write(iout,*)'E0LL2Y: BIN = ../../../bin/unres/MD/unres-mult-...'
write(iout,*)'++++ End of compile info ++++'
return
end
logical lprn /.false./, lprn1 /.false./
etheta=0.0D0
do i=ithet_start,ithet_end
- if (itype(i-1).eq.ntyp1) cycle
+ if ((itype(i-1).eq.ntyp1).or.(itype(i-2).eq.ntyp1).or.
+ &(itype(i).eq.ntyp1)) cycle
+C print *,i,theta(i)
if (iabs(itype(i+1)).eq.20) iblock=2
if (iabs(itype(i+1)).ne.20) iblock=1
dethetai=0.0d0
coskt(k)=dcos(k*theti2)
sinkt(k)=dsin(k*theti2)
enddo
- if (i.gt.3 .and. itype(i-2).ne.ntyp1) then
+C print *,ethetai
+
+ if (i.gt.3 .and. itype(i-3).ne.ntyp1) then
#ifdef OSF
phii=phi(i)
if (phii.ne.phii) phii=150.0
enddo
else
phii=0.0d0
- ityp1=nthetyp+1
do k=1,nsingle
+ ityp1=ithetyp((itype(i-2)))
cosph1(k)=0.0d0
sinph1(k)=0.0d0
enddo
endif
- if (i.lt.nres .and. itype(i).ne.ntyp1) then
+ if (i.lt.nres .and. itype(i+1).ne.ntyp1) then
#ifdef OSF
phii1=phi(i+1)
if (phii1.ne.phii1) phii1=150.0
enddo
else
phii1=0.0d0
- ityp3=nthetyp+1
+ ityp3=ithetyp((itype(i)))
do k=1,nsingle
cosph2(k)=0.0d0
sinph2(k)=0.0d0
enddo
write(iout,*) "ethetai",ethetai
endif
+C print *,ethetai
do m=1,ntheterm2
do k=1,nsingle
aux=bbthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)
& ccthet(k,m,ityp1,ityp2,ityp3,iblock)," ddthet",
& ddthet(k,m,ityp1,ityp2,ityp3,iblock)," eethet",
& eethet(k,m,ityp1,ityp2,ityp3,iblock)," ethetai",ethetai
+C print *,"tu",cosph1(k),sinph1(k),cosph2(k),sinph2(k)
enddo
enddo
+C print *,"cosph1", (cosph1(k), k=1,nsingle)
+C print *,"cosph2", (cosph2(k), k=1,nsingle)
+C print *,"sinph1", (sinph1(k), k=1,nsingle)
+C print *,"sinph2", (sinph2(k), k=1,nsingle)
if (lprn)
& write(iout,*) "ethetai",ethetai
+C print *,"tu",cosph1(k),sinph1(k),cosph2(k),sinph2(k)
do m=1,ntheterm3
do k=2,ndouble
do l=1,k-1
enddo
10 continue
c lprn1=.true.
+C print *,ethetai
if (lprn1)
& write (iout,'(i2,3f8.1,9h ethetai ,f10.5)')
& i,theta(i)*rad2deg,phii*rad2deg,
etheta=etheta+ethetai
if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang*dephii
if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*dephii1
- gloc(nphi+i-2,icg)=wang*dethetai
+ gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)+wang*dethetai
enddo
return
end
include 'COMMON.TIME1'
include 'COMMON.MD'
double precision z(dimen3),d_a_tmp(dimen3),temp(maxres6),time00
- &time01
+ &,time01,zcopy(dimen3)
#ifdef MPI
if (nfgtasks.gt.1) then
if (fg_rank.eq.0) then
time00=MPI_Wtime()
call MPI_Scatterv(z,ng_counts(0),ng_start(0),
& MPI_DOUBLE_PRECISION,
- & z,3*my_ng_count,MPI_DOUBLE_PRECISION,king,FG_COMM,IERR)
+ & zcopy,3*my_ng_count,MPI_DOUBLE_PRECISION,king,FG_COMM,IERR)
c write (2,*) "My chunk of z"
-c do i=1,3*my_ng_count
+ do i=1,3*my_ng_count
+ z(i)=zcopy(i)
c write (2,*) i,z(i)
-c enddo
+ enddo
c write (2,*) "After SCATTERV"
c call flush(2)
c write (2,*) "MPI_Wtime",MPI_Wtime()
include 'COMMON.LANGEVIN.lang0'
#endif
double precision z(dimen3),d_a_tmp(dimen3),temp(maxres6),time00
- &time01
+ &,time01,zcopy(dimen3)
#ifdef MPI
if (nfgtasks.gt.1) then
if (fg_rank.eq.0) then
time00=MPI_Wtime()
call MPI_Scatterv(z,ng_counts(0),ng_start(0),
& MPI_DOUBLE_PRECISION,
- & z,3*my_ng_count,MPI_DOUBLE_PRECISION,king,FG_COMM,IERR)
+ & zcopy,3*my_ng_count,MPI_DOUBLE_PRECISION,king,FG_COMM,IERR)
c write (2,*) "My chunk of z"
-c do i=1,3*my_ng_count
+ do i=1,3*my_ng_count
+ z(i)=zcopy(i)
c write (2,*) i,z(i)
-c enddo
+ enddo
time_scatter=time_scatter+MPI_Wtime()-time00
#ifdef TIMING
time_scatter_fmatmult=time_scatter_fmatmult+MPI_Wtime()-time00
33 write (iout,'(a)') 'Error opening PDB file.'
stop
34 continue
-c print *,'Begin reading pdb data'
+c write (iout,*) 'Begin reading pdb data'
+c call flush(iout)
call readpdb
-c print *,'Finished reading pdb data'
+c write (iout,*) 'Finished reading pdb data'
+c call flush(iout)
if(me.eq.king.or..not.out1file)
& write (iout,'(a,i3,a,i3)')'nsup=',nsup,
& ' nstart_sup=',nstart_sup
- subroutine refsys(fail)
-c This subroutine calculates unit vectors of a local reference system
-c defined by atoms (i2), (i3), and (i4). The x axis is the axis from
+ subroutine refsys(i2,i3,i4,e1,e2,e3,fail)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+c this subroutine calculates unity vectors of a local reference system
+c defined by atoms (i2), (i3), and (i4). the x axis is the axis from
c atom (i3) to atom (i2), and the xy plane is the plane defined by atoms
c (i2), (i3), and (i4). z axis is directed according to the sign of the
-c vector product (i3)-(i2) and (i3)-(i4). Sets fail to .true. if atoms
+c vector product (i3)-(i2) and (i3)-(i4). sets fail to .true. if atoms
c (i2) and (i3) or (i3) and (i4) coincide or atoms (i2), (i3), and (i4)
-c form a linear fragment. Returns vectors e1, e2, and e3.
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
+c form a linear fragment. returns vectors e1, e2, and e3.
logical fail
double precision e1(3),e2(3),e3(3)
double precision u(3),z(3)
include 'COMMON.IOUNITS'
- include 'COMMON.CHAIN'
- double precision coinc/1.0D-13/,align /1.0D-13/
+ include "COMMON.CHAIN"
+ data coinc /1.0d-13/,align /1.0d-13/
fail=.false.
- s1=0.0
- s2=0.0
+ s1=0.0d0
+ s2=0.0d0
do 1 i=1,3
zi=c(i,i2)-c(i,i3)
ui=c(i,i4)-c(i,i3)
if (s1.gt.coinc) goto 2
write (iout,1000) i2,i3,i1
fail=.true.
-c do 3 i=1,3
-c 3 c(i,i1)=0.0D0
return
2 if (s2.gt.coinc) goto 4
write(iout,1000) i3,i4,i1
fail=.true.
- do 5 i=1,3
- 5 c(i,i1)=0.0D0
return
4 s1=1.0/s1
s2=1.0/s2
v1=z(2)*u(3)-z(3)*u(2)
v2=z(3)*u(1)-z(1)*u(3)
v3=z(1)*u(2)-z(2)*u(1)
- anorm=dsqrt(v1*v1+v2*v2+v3*v3)
+ anorm=sqrt(v1*v1+v2*v2+v3*v3)
if (anorm.gt.align) goto 6
write (iout,1010) i2,i3,i4,i1
fail=.true.
-c do 7 i=1,3
-c 7 c(i,i1)=0.0D0
return
- 6 anorm=1.0D0/anorm
+ 6 anorm=1.0/anorm
e3(1)=v1*anorm
e3(2)=v2*anorm
e3(3)=v3*anorm
e2(1)=e1(3)*e3(2)-e1(2)*e3(3)
e2(2)=e1(1)*e3(3)-e1(3)*e3(1)
e2(3)=e1(2)*e3(1)-e1(1)*e3(2)
- 1000 format (/1x,' * * * Error - atoms',i4,' and',i4,' coincide.',
- 1 'coordinates of atom',i4,' are set to zero.')
- 1010 format (/1x,' * * * Error - atoms',2(i4,2h, ),i4,' form a linear',
- 1 ' fragment. coordinates of atom',i4,' are set to zero.')
+ 1000 format (/1x,' * * * error - atoms',i4,' and',i4,' coincide.')
+ 1010 format (/1x,' * * * error - atoms',2(i4,2h, ),i4,' form a linear')
return
end
if (me.eq.king) call cinfo
C Read force field parameters and job setup data
call readrtns
- call flush(iout)
C
if (me.eq.king .or. .not. out1file) then
write (iout,'(2a/)')
include 'COMMON.SETUP'
include 'COMMON.CONTROL'
include 'COMMON.IOUNITS'
- if (me.eq.king .or. .not. out1file)
- & write (iout,*) "Calling chainbuild"
+c if (me.eq.king .or. .not. out1file) then
+c write (iout,*) "Calling chainbuild"
+c call flush(iout)
+c endif
call chainbuild
+c if (me.eq.king .or. .not. out1file) then
+c write (iout,*) "Calling MD"
+c call flush(iout)
+c endif
call MD
return
end
projects / unres.git / commitdiff