project(UNRESPACK Fortran C)
set(UNRES_MAJOR 3)
- set(UNRES_MINOR 1)
- set(UNRES_PATCH 0)
+ set(UNRES_MINOR 2)
+ set(UNRES_PATCH 1)
set(UNRES_VERSION ${UNRES_MAJOR}.${UNRES_MINOR}.${UNRES_PATCH})
#======================================
file(APPEND ${FN} " write(iout,*)'${STR}'\n")
endif(SUMA GREATER 50)
ENDMACRO (CINFO_FORMAT)
+
+ # Some MPI wrappers pass double include paths
+ # This macro fixes broken by semicolon occurence in path
+ MACRO (FIX_DBL_INCLUDE RESULT)
+ string(REPLACE ";" " -I" ${RESULT} "${${RESULT}}")
+ ENDMACRO (FIX_DBL_INCLUDE)
+
#======================================
# CTest stuff
#======================================A
include(CTest)
enable_testing()
- # Set makefile verbose on
- set( CMAKE_VERBOSE_MAKEFILE 1 )
#======================================
# Fortran compilers stuff
# make sure that the default is a RELEASE
if (NOT CMAKE_BUILD_TYPE)
- set (CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: None Debug Release." FORCE)
- set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "None" "Debug" "Release" )
+ set (CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo." FORCE)
+ set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "None" "Debug" "Release" "RelWithDebInfo")
endif (NOT CMAKE_BUILD_TYPE)
-
+
+
+ if (CMAKE_BUILD_TYPE STREQUAL "Release")
+ # Set makefile verbosity off for Release builds
+ set( CMAKE_VERBOSE_MAKEFILE 0 )
+ else()
+ # Set makefile verbosity on for other builds
+ set( CMAKE_VERBOSE_MAKEFILE 1 )
+ endif (CMAKE_BUILD_TYPE STREQUAL "Release")
+
+ # Default Install Path
+
+ set(CMAKE_INSTALL_PREFIX "${CMAKE_SOURCE_DIR}/bin" CACHE PATH "Binary install directory " FORCE)
+
#=======================================
# Set the varous build variables
#=======================================
if (MPI_Fortran_FOUND)
message("MPI found")
+ FIX_DBL_INCLUDE(MPI_Fortran_INCLUDE_PATH)
else()
message("MPI not found - disabling MPI compile flags ")
set ( UNRES_WITH_MPI "OFF")
# used by unres/src_MIN
find_package (Threads)
-
-
- #=======================================
- # Create diractories for build targets
- #=======================================
- #execute_process(COMMAND ${CMAKE_COMMAND} -E make_directory ${CMAKE_BINARY_DIR}/bin/unres/MD )
-
#=======================================
# Add source files
#=======================================
-
add_subdirectory(source/lib/xdrf)
-
if(UNRES_NA_MMCE)
if(UNRES_WITH_MPI)
# Brak MPI dla gfortrana, wiec tylko na ifort sie skompiluje
if (Fortran_COMPILER_NAME STREQUAL "ifort")
add_subdirectory(source/unres/src_MD)
+ add_subdirectory(source/unres/src_MD_DFA)
add_subdirectory(source/unres/src_MD-M)
add_subdirectory(source/unres/src_CSA)
add_subdirectory(source/unres/src_CSA_DiL)
add_subdirectory(source/unres/src_MD)
if(UNRES_WITH_MPI)
add_subdirectory(source/unres/src_MD-M)
+ add_subdirectory(source/unres/src_MD_DFA)
add_subdirectory(source/unres/src_CSA)
add_subdirectory(source/unres/src_CSA_DiL)
add_subdirectory(source/wham/src)
#=========================================
# Set binary name
#=========================================
- set(MAXLIK_BIN "maxlik-opt-multprot")
+ set(MAXLIK_BIN "maxlik_CSA")
#=========================================
#=========================================
add_executable(MAXLIK ${MAXLIK_SRCS} )
set_target_properties(MAXLIK PROPERTIES OUTPUT_NAME ${MAXLIK_BIN})
+ set_property(TARGET MAXLIK PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin )
#=========================================
-# Install Path
+# Install maxlik binary (used by "make install")
#=========================================
+ install(TARGETS MAXLIK DESTINATION ${CMAKE_INSTALL_PREFIX})
+install(TARGETS MAXLIK RUNTIME DESTINATION unrespack/bin)
enable_language (Fortran)
#================================
- # build the xdrf library
- #================================
- #add_subdirectory(xdrf)
-
- #================================
# Set source file lists
#================================
set(UNRES_MDM_SRC0
permut.F
pinorm.f
printmat.f
+ prng_32.F
q_measure.F
ran.f
randgens.f
ssMD.F
)
- if (Fortran_COMPILER_NAME STREQUAL "ifort")
- set(UNRES_MDM_SRC0 ${UNRES_MDM_SRC0} prng.f )
- elseif(Fortran_COMPILER_NAME STREQUAL "mpif90")
- set(UNRES_MDM_SRC0 ${UNRES_MDM_SRC0} prng.f )
- else()
- set(UNRES_MDM_SRC0 ${UNRES_MDM_SRC0} prng_32.F )
- endif (Fortran_COMPILER_NAME STREQUAL "ifort")
-
-
set(UNRES_MDM_SRC3 energy_p_new_barrier.F energy_p_new-sep_barrier.F gradient_p.F )
set(UNRES_MDM_PP_SRC
newconf.f
parmread.F
permut.F
+ prng_32.F
q_measure1.F
q_measure3.F
q_measure.F
#=========================================
if(UNRES_MD_FF STREQUAL "GAB" )
# set preprocesor flags
- set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC" )
+ set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DSCCORPDB -DTIMING -DTIMING_ENE" )
#=========================================
# Settings for E0LL2Y force field
#=========================================
elseif(UNRES_MD_FF STREQUAL "E0LL2Y")
# set preprocesor flags
- set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0" )
+ set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0 -DSCCORPDB" )
endif(UNRES_MD_FF STREQUAL "GAB")
elseif (Fortran_COMPILER_NAME STREQUAL "gfortran")
# Add old gfortran flags
set(CPPFLAGS "${CPPFLAGS} -DG77")
+else (Fortran_COMPILER_NAME STREQUAL "ifort")
+ # Default preprocessor flags
+ set(CPPFLAGS "${CPPFLAGS} -DPGI")
endif (Fortran_COMPILER_NAME STREQUAL "ifort")
endif(UNRES_WITH_MPI)
+ #=========================================
# add 64-bit specific preprocessor flags
+ #=========================================
if (architektura STREQUAL "64")
set(CPPFLAGS "${CPPFLAGS} -DAMD64")
endif (architektura STREQUAL "64")
#========================================
if(UNRES_WITH_MPI)
# binary with mpi
- set(UNRES_BIN "unres_${Fortran_COMPILER_NAME}_MPICH_${UNRES_MD_FF}.exe")
+ set(UNRES_BIN "unresMD-M_${Fortran_COMPILER_NAME}_MPICH_${UNRES_MD_FF}.exe")
else(UNRES_WITH_MPI)
# binary without mpi
- set(UNRES_BIN "unres_${Fortran_COMPILER_NAME}_single_${UNRES_MD_FF}.exe")
+ set(UNRES_BIN "unresMD-M_${Fortran_COMPILER_NAME}_single_${UNRES_MD_FF}.exe")
endif(UNRES_WITH_MPI)
#=========================================
#=========================================
add_executable(UNRES_BIN-MD-M ${UNRES_MDM_SRCS} )
set_target_properties(UNRES_BIN-MD-M PROPERTIES OUTPUT_NAME ${UNRES_BIN})
-
- #set_property(TARGET ${UNRES_BIN} PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin/unres/MD )
+ set_property(TARGET UNRES_BIN-MD-M PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin )
#add_dependencies (${UNRES_BIN} ${UNRES_XDRFLIB})
#=========================================
target_link_libraries( UNRES_BIN-MD-M xdrf )
#=========================================
- # INSTALL
+ # Install Path
#=========================================
-
- install(TARGETS UNRES_BIN-MD-M RUNTIME DESTINATION unrespack/bin)
+ install(TARGETS UNRES_BIN-MD-M DESTINATION ${CMAKE_INSTALL_PREFIX})
#=========================================
# TESTS
energia(17)=estr
energia(20)=Uconst+Uconst_back
energia(21)=esccor
+c Here are the energies showed per procesor if the are more processors
+c per molecule then we sum it up in sum_energy subroutine
c print *," Processor",myrank," calls SUM_ENERGY"
call sum_energy(energia,.true.)
if (dyn_ss) call dyn_set_nss
#ifdef MPI
include 'mpif.h'
double precision gradbufc(3,maxres),gradbufx(3,maxres),
- & glocbuf(4*maxres),gradbufc_sum(3,maxres)
+ & glocbuf(4*maxres),gradbufc_sum(3,maxres),gloc_scbuf(3,maxres)
#endif
include 'COMMON.SETUP'
include 'COMMON.IOUNITS'
include 'COMMON.CONTROL'
include 'COMMON.TIME1'
include 'COMMON.MAXGRAD'
+ include 'COMMON.SCCOR'
#ifdef TIMING
time01=MPI_Wtime()
#endif
& +wturn3*gel_loc_turn3(i)
& +wturn6*gel_loc_turn6(i)
& +wel_loc*gel_loc_loc(i)
- & +wsccor*gsccor_loc(i)
enddo
#ifdef DEBUG
write (iout,*) "gloc after adding corr"
do i=1,4*nres
glocbuf(i)=gloc(i,icg)
enddo
+c#define DEBUG
+#ifdef DEBUG
+ write (iout,*) "gloc_sc before reduce"
+ do i=1,nres
+ do j=1,1
+ write (iout,*) i,j,gloc_sc(j,i,icg)
+ enddo
+ enddo
+#endif
+c#undef DEBUG
+ do i=1,nres
+ do j=1,3
+ gloc_scbuf(j,i)=gloc_sc(j,i,icg)
+ enddo
+ enddo
time00=MPI_Wtime()
call MPI_Barrier(FG_COMM,IERR)
time_barrier_g=time_barrier_g+MPI_Wtime()-time00
call MPI_Reduce(glocbuf(1),gloc(1,icg),4*nres,
& MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR)
time_reduce=time_reduce+MPI_Wtime()-time00
+ 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
+c#define DEBUG
+#ifdef DEBUG
+ write (iout,*) "gloc_sc after reduce"
+ do i=1,nres
+ do j=1,1
+ write (iout,*) i,j,gloc_sc(j,i,icg)
+ enddo
+ enddo
+#endif
+c#undef DEBUG
#ifdef DEBUG
write (iout,*) "gloc after reduce"
do i=1,4*nres
c write(iout,*)'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
cd write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
cd & 'iend=',iend(i,iint)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
c print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
C
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
c endif
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
ind=ind+1
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
c dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
chi1=chi(itypi,itypj)
c if (icall.eq.0) lprn=.false.
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
& 'evdw',i,j,evdwij,' ss'
ELSE
ind=ind+1
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
c dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
c write (iout,*) "j",j,dsc_inv(itypj),dscj_inv,
c if (icall.eq.0) lprn=.true.
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
ind=ind+1
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
c dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
sig0ij=sigma(itypi,itypj)
cd print *,'Entering Esoft_sphere nnt=',nnt,' nct=',nct
evdw=0.0D0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
cd write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
cd & 'iend=',iend(i,iint)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
eello_turn4=0.0d0
ind=0
do i=iatel_s,iatel_e
- if (itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
num_conti=0
c write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
do j=ielstart(i),ielend(i)
- if (itype(j).eq.21 .or. itype(j+1).eq.21) cycle
+ if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1) cycle
ind=ind+1
iteli=itel(i)
itelj=itel(j)
enddo
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))
+ if (itype(i-1).le.ntyp) then
+ iti1 = itortyp(itype(i-1))
+ else
+ iti1=ntortyp+1
+ endif
else
iti1=ntortyp+1
endif
C Loop over i,i+2 and i,i+3 pairs of the peptide groups
C
do i=iturn3_start,iturn3_end
- if (itype(i).eq.21 .or. itype(i+1).eq.21
- & .or. itype(i+2).eq.21 .or. itype(i+3).eq.21) cycle
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
+ & .or. itype(i+2).eq.ntyp1 .or. itype(i+3).eq.ntyp1) cycle
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
num_cont_hb(i)=num_conti
enddo
do i=iturn4_start,iturn4_end
- if (itype(i).eq.21 .or. itype(i+1).eq.21
- & .or. itype(i+3).eq.21
- & .or. itype(i+4).eq.21) cycle
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
+ & .or. itype(i+3).eq.ntyp1
+ & .or. itype(i+4).eq.ntyp1) cycle
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
zmedi=c(3,i)+0.5d0*dzi
num_conti=num_cont_hb(i)
call eelecij(i,i+3,ees,evdw1,eel_loc)
- if (wturn4.gt.0.0d0 .and. itype(i+2).ne.21)
+ if (wturn4.gt.0.0d0 .and. itype(i+2).ne.ntyp1)
& call eturn4(i,eello_turn4)
num_cont_hb(i)=num_conti
enddo ! i
c Loop over all pairs of interacting peptide groups except i,i+2 and i,i+3
c
do i=iatel_s,iatel_e
- if (itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
num_conti=num_cont_hb(i)
do j=ielstart(i),ielend(i)
c write (iout,*) i,j,itype(i),itype(j)
- if (itype(j).eq.21 .or. itype(j+1).eq.21) cycle
+ if (itype(j).eq.ntyp1.or. itype(j+1).eq.ntyp1) cycle
call eelecij(i,j,ees,evdw1,eel_loc)
enddo ! j
num_cont_hb(i)=num_conti
cd & xmedi,ymedi,zmedi,xj,yj,zj
if (energy_dec) then
- write (iout,'(a6,2i5,0pf7.3)') 'evdw1',i,j,evdwij
+ write (iout,'(a6,2i5,0pf7.3,2i5,2e11.3)')
+ &'evdw1',i,j,evdwij
+ &,iteli,itelj,aaa,evdw1
write (iout,'(a6,2i5,0pf7.3)') 'ees',i,j,eesij
endif
if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
& 'eelloc',i,j,eel_loc_ij
+c write (iout,*) a22,muij(1),a23,muij(2),a32,muij(3)
eel_loc=eel_loc+eel_loc_ij
C Partial derivatives in virtual-bond dihedral angles gamma
cd print '(a)','Enter ESCP'
cd write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e
do i=iatscp_s,iatscp_e
- if (itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
iteli=itel(i)
xi=0.5D0*(c(1,i)+c(1,i+1))
yi=0.5D0*(c(2,i)+c(2,i+1))
do iint=1,nscp_gr(i)
do j=iscpstart(i,iint),iscpend(i,iint)
- if (itype(j).eq.21) cycle
- itypj=itype(j)
+ if (itype(j).eq.ntyp1) cycle
+ itypj=iabs(itype(j))
C Uncomment following three lines for SC-p interactions
c xj=c(1,nres+j)-xi
c yj=c(2,nres+j)-yi
cd print '(a)','Enter ESCP'
cd write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e
do i=iatscp_s,iatscp_e
- if (itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
iteli=itel(i)
xi=0.5D0*(c(1,i)+c(1,i+1))
yi=0.5D0*(c(2,i)+c(2,i+1))
do iint=1,nscp_gr(i)
do j=iscpstart(i,iint),iscpend(i,iint)
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
C Uncomment following three lines for SC-p interactions
c xj=c(1,nres+j)-xi
c yj=c(2,nres+j)-yi
endif
evdwij=e1+e2
evdw2=evdw2+evdwij
- if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
- & 'evdw2',i,j,evdwij
+ if (energy_dec) write (iout,'(a6,2i5,0pf7.3,2i3,3e11.3)')
+ & 'evdw2',i,j,evdwij,iteli,itypj,fac,aad(itypj,iteli),
+ & bad(itypj,iteli)
C
C Calculate contributions to the gradient in the virtual-bond and SC vectors.
C
C 18/07/06 MC: Use the convention that the first nss pairs are SS bonds
if (.not.dyn_ss .and. i.le.nss) then
C 15/02/13 CC dynamic SSbond - additional check
++<<<<<<< HEAD
+ if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
+ & iabs(itype(jjj)).eq.1) then
++=======
+ if (ii.gt.nres
+ & .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then
++>>>>>>> prerelease-3.2.1
call ssbond_ene(iii,jjj,eij)
ehpb=ehpb+2*eij
+ endif
cd write (iout,*) "eij",eij
+ endif
else
C Calculate the distance between the two points and its difference from the
C target distance.
- dd=dist(ii,jj)
- rdis=dd-dhpb(i)
+ dd=dist(ii,jj)
+ rdis=dd-dhpb(i)
C Get the force constant corresponding to this distance.
- waga=forcon(i)
+ waga=forcon(i)
C Calculate the contribution to energy.
- ehpb=ehpb+waga*rdis*rdis
+ ehpb=ehpb+waga*rdis*rdis
C
C Evaluate gradient.
C
- fac=waga*rdis/dd
+ fac=waga*rdis/dd
cd print *,'i=',i,' ii=',ii,' jj=',jj,' dhpb=',dhpb(i),' dd=',dd,
cd & ' waga=',waga,' fac=',fac
- do j=1,3
- ggg(j)=fac*(c(j,jj)-c(j,ii))
- enddo
+ do j=1,3
+ ggg(j)=fac*(c(j,jj)-c(j,ii))
+ enddo
cd print '(i3,3(1pe14.5))',i,(ggg(j),j=1,3)
C If this is a SC-SC distance, we need to calculate the contributions to the
C Cartesian gradient in the SC vectors (ghpbx).
- if (iii.lt.ii) then
+ if (iii.lt.ii) then
do j=1,3
ghpbx(j,iii)=ghpbx(j,iii)-ggg(j)
ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
enddo
- endif
+ endif
cgrad do j=iii,jjj-1
cgrad do k=1,3
cgrad ghpbc(k,j)=ghpbc(k,j)+ggg(k)
cgrad enddo
cgrad enddo
- do k=1,3
- ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
- ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
- enddo
+ do k=1,3
+ ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
+ ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
+ enddo
endif
enddo
ehpb=0.5D0*ehpb
include 'COMMON.VAR'
include 'COMMON.IOUNITS'
double precision erij(3),dcosom1(3),dcosom2(3),gg(3)
- itypi=itype(i)
+ itypi=iabs(itype(i))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
dzi=dc_norm(3,nres+i)
c dsci_inv=dsc_inv(itypi)
dsci_inv=vbld_inv(nres+i)
- itypj=itype(j)
+ itypj=iabs(itype(j))
c dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(nres+j)
xj=c(1,nres+j)-xi
estr=0.0d0
estr1=0.0d0
do i=ibondp_start,ibondp_end
- if (itype(i-1).eq.21 .or. itype(i).eq.21) then
+ if (itype(i-1).eq.ntyp1 .or. itype(i).eq.ntyp1) then
estr1=estr1+gnmr1(vbld(i),-1.0d0,distchainmax)
do j=1,3
gradb(j,i-1)=gnmr1prim(vbld(i),-1.0d0,distchainmax)
c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
c
do i=ibond_start,ibond_end
- iti=itype(i)
- if (iti.ne.10 .and. iti.ne.21) then
+ iti=iabs(itype(i))
+ if (iti.ne.10 .and. iti.ne.ntyp1) then
nbi=nbondterm(iti)
if (nbi.eq.1) then
diff=vbld(i+nres)-vbldsc0(1,iti)
etheta=0.0D0
c write (*,'(a,i2)') 'EBEND ICG=',icg
do i=ithet_start,ithet_end
- if (itype(i-1).eq.21) cycle
+ if (itype(i-1).eq.ntyp1) cycle
C Zero the energy function and its derivative at 0 or pi.
call splinthet(theta(i),0.5d0*delta,ss,ssd)
it=itype(i-1)
- if (i.gt.3 .and. itype(i-2).ne.21) then
+ ichir1=isign(1,itype(i-2))
+ ichir2=isign(1,itype(i))
+ if (itype(i-2).eq.10) ichir1=isign(1,itype(i-1))
+ if (itype(i).eq.10) ichir2=isign(1,itype(i-1))
+ if (itype(i-1).eq.10) then
+ itype1=isign(10,itype(i-2))
+ ichir11=isign(1,itype(i-2))
+ ichir12=isign(1,itype(i-2))
+ itype2=isign(10,itype(i))
+ ichir21=isign(1,itype(i))
+ ichir22=isign(1,itype(i))
+ endif
+
+ if (i.gt.3 .and. itype(i-2).ne.ntyp1) then
#ifdef OSF
phii=phi(i)
if (phii.ne.phii) phii=150.0
y(1)=0.0D0
y(2)=0.0D0
endif
- if (i.lt.nres .and. itype(i).ne.21) then
+ if (i.lt.nres .and. itype(i).ne.ntyp1) then
#ifdef OSF
phii1=phi(i+1)
if (phii1.ne.phii1) phii1=150.0
C In following comments this theta will be referred to as t_c.
thet_pred_mean=0.0d0
do k=1,2
- athetk=athet(k,it)
- bthetk=bthet(k,it)
- thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k)
+ athetk=athet(k,it,ichir1,ichir2)
+ bthetk=bthet(k,it,ichir1,ichir2)
+ if (it.eq.10) then
+ athetk=athet(k,itype1,ichir11,ichir12)
+ bthetk=bthet(k,itype2,ichir21,ichir22)
+ endif
+ thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k)
enddo
dthett=thet_pred_mean*ssd
thet_pred_mean=thet_pred_mean*ss+a0thet(it)
C Derivatives of the "mean" values in gamma1 and gamma2.
- dthetg1=(-athet(1,it)*y(2)+athet(2,it)*y(1))*ss
- dthetg2=(-bthet(1,it)*z(2)+bthet(2,it)*z(1))*ss
+ dthetg1=(-athet(1,it,ichir1,ichir2)*y(2)
+ &+athet(2,it,ichir1,ichir2)*y(1))*ss
+ dthetg2=(-bthet(1,it,ichir1,ichir2)*z(2)
+ & +bthet(2,it,ichir1,ichir2)*z(1))*ss
+ if (it.eq.10) then
+ dthetg1=(-athet(1,itype1,ichir11,ichir12)*y(2)
+ &+athet(2,itype1,ichir11,ichir12)*y(1))*ss
+ dthetg2=(-bthet(1,itype2,ichir21,ichir22)*z(2)
+ & +bthet(2,itype2,ichir21,ichir22)*z(1))*ss
+ endif
if (theta(i).gt.pi-delta) then
call theteng(pi-delta,thet_pred_mean,theta0(it),f0,fprim0,
& E_tc0)
logical lprn /.false./, lprn1 /.false./
etheta=0.0D0
do i=ithet_start,ithet_end
- if (itype(i-1).eq.21) cycle
+ if (itype(i-1).eq.ntyp1) cycle
+ if (iabs(itype(i+1)).eq.20) iblock=2
+ if (iabs(itype(i+1)).ne.20) iblock=1
dethetai=0.0d0
dephii=0.0d0
dephii1=0.0d0
theti2=0.5d0*theta(i)
- ityp2=ithetyp(itype(i-1))
+ ityp2=ithetyp((itype(i-1)))
do k=1,nntheterm
coskt(k)=dcos(k*theti2)
sinkt(k)=dsin(k*theti2)
enddo
- if (i.gt.3 .and. itype(i-2).ne.21) then
+ if (i.gt.3 .and. itype(i-2).ne.ntyp1) then
#ifdef OSF
phii=phi(i)
if (phii.ne.phii) phii=150.0
#else
phii=phi(i)
#endif
- ityp1=ithetyp(itype(i-2))
+ ityp1=ithetyp((itype(i-2)))
+C propagation of chirality for glycine type
do k=1,nsingle
cosph1(k)=dcos(k*phii)
sinph1(k)=dsin(k*phii)
sinph1(k)=0.0d0
enddo
endif
- if (i.lt.nres .and. itype(i).ne.21) then
+ if (i.lt.nres .and. itype(i).ne.ntyp1) then
#ifdef OSF
phii1=phi(i+1)
if (phii1.ne.phii1) phii1=150.0
#else
phii1=phi(i+1)
#endif
- ityp3=ithetyp(itype(i))
+ ityp3=ithetyp((itype(i)))
do k=1,nsingle
cosph2(k)=dcos(k*phii1)
sinph2(k)=dsin(k*phii1)
sinph2(k)=0.0d0
enddo
endif
- ethetai=aa0thet(ityp1,ityp2,ityp3)
+ ethetai=aa0thet(ityp1,ityp2,ityp3,iblock)
do k=1,ndouble
do l=1,k-1
ccl=cosph1(l)*cosph2(k-l)
enddo
endif
do k=1,ntheterm
- ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3)*sinkt(k)
- dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3)
+ ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3,iblock)*sinkt(k)
+ dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3,iblock)
& *coskt(k)
if (lprn)
- & write (iout,*) "k",k," aathet",aathet(k,ityp1,ityp2,ityp3),
+ & write (iout,*) "k",k,"
+ & aathet",aathet(k,ityp1,ityp2,ityp3,iblock),
& " ethetai",ethetai
enddo
if (lprn) then
endif
do m=1,ntheterm2
do k=1,nsingle
- aux=bbthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)
- & +ccthet(k,m,ityp1,ityp2,ityp3)*sinph1(k)
- & +ddthet(k,m,ityp1,ityp2,ityp3)*cosph2(k)
- & +eethet(k,m,ityp1,ityp2,ityp3)*sinph2(k)
+ aux=bbthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)
+ & +ccthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k)
+ & +ddthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)
+ & +eethet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k)
ethetai=ethetai+sinkt(m)*aux
dethetai=dethetai+0.5d0*m*aux*coskt(m)
dephii=dephii+k*sinkt(m)*(
- & ccthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)-
- & bbthet(k,m,ityp1,ityp2,ityp3)*sinph1(k))
+ & ccthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)-
+ & bbthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k))
dephii1=dephii1+k*sinkt(m)*(
- & eethet(k,m,ityp1,ityp2,ityp3)*cosph2(k)-
- & ddthet(k,m,ityp1,ityp2,ityp3)*sinph2(k))
+ & eethet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)-
+ & ddthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k))
if (lprn)
& write (iout,*) "m",m," k",k," bbthet",
- & bbthet(k,m,ityp1,ityp2,ityp3)," ccthet",
- & ccthet(k,m,ityp1,ityp2,ityp3)," ddthet",
- & ddthet(k,m,ityp1,ityp2,ityp3)," eethet",
- & eethet(k,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ & bbthet(k,m,ityp1,ityp2,ityp3,iblock)," ccthet",
+ & 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
enddo
enddo
if (lprn)
do m=1,ntheterm3
do k=2,ndouble
do l=1,k-1
- aux=ffthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)
+ aux=ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)
ethetai=ethetai+sinkt(m)*aux
dethetai=dethetai+0.5d0*m*coskt(m)*aux
dephii=dephii+l*sinkt(m)*(
- & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)-
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)-
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
dephii1=dephii1+(k-l)*sinkt(m)*(
- & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)-
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)-
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
if (lprn) then
write (iout,*) "m",m," k",k," l",l," ffthet",
- & ffthet(l,k,m,ityp1,ityp2,ityp3),
- & ffthet(k,l,m,ityp1,ityp2,ityp3)," ggthet",
- & ggthet(l,k,m,ityp1,ityp2,ityp3),
- & ggthet(k,l,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ & ffthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)," ggthet",
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock),
+ & " ethetai",ethetai
write (iout,*) cosph1ph2(l,k)*sinkt(m),
& cosph1ph2(k,l)*sinkt(m),
& sinph1ph2(l,k)*sinkt(m),sinph1ph2(k,l)*sinkt(m)
enddo
enddo
10 continue
- if (lprn1) write (iout,'(i2,3f8.1,9h ethetai ,f10.5)')
+c lprn1=.true.
+ if (lprn1)
+ & write (iout,'(i2,3f8.1,9h ethetai ,f10.5)')
& i,theta(i)*rad2deg,phii*rad2deg,
& phii1*rad2deg,ethetai
+c lprn1=.false.
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
c write (iout,'(a)') 'ESC'
do i=loc_start,loc_end
it=itype(i)
- if (it.eq.21) cycle
+ if (it.eq.ntyp1) cycle
if (it.eq.10) goto 1
- nlobit=nlob(it)
+ nlobit=nlob(iabs(it))
c print *,'i=',i,' it=',it,' nlobit=',nlobit
c write (iout,*) 'i=',i,' ssa=',ssa,' ssad=',ssad
theti=theta(i+1)-pipol
do j=1,nlobit
#ifdef OSF
- adexp=bsc(j,it)-0.5D0*contr(j,iii)+emin
+ adexp=bsc(j,iabs(it))-0.5D0*contr(j,iii)+emin
if(adexp.ne.adexp) adexp=1.0
expfac=dexp(adexp)
#else
- expfac=dexp(bsc(j,it)-0.5D0*contr(j,iii)+emin)
+ expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j,iii)+emin)
#endif
cd print *,'j=',j,' expfac=',expfac
escloc_i=escloc_i+expfac
dersc12=0.0d0
do j=1,nlobit
- expfac=dexp(bsc(j,it)-0.5D0*contr(j)+emin)
+ expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j)+emin)
escloc_i=escloc_i+expfac
do k=1,2
dersc(k)=dersc(k)+Ax(k,j)*expfac
delta=0.02d0*pi
escloc=0.0D0
do i=loc_start,loc_end
- if (itype(i).eq.21) cycle
+ if (itype(i).eq.ntyp1) cycle
costtab(i+1) =dcos(theta(i+1))
sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
cosfac=dsqrt(cosfac2)
sinfac2=0.5d0/(1.0d0-costtab(i+1))
sinfac=dsqrt(sinfac2)
- it=itype(i)
+ it=iabs(itype(i))
if (it.eq.10) goto 1
c
C Compute the axes of tghe local cartesian coordinates system; store in
y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
enddo
do j = 1,3
- z_prime(j) = -uz(j,i-1)
+ z_prime(j) = -uz(j,i-1)*dsign(1.0d0,dfloat(itype(i)))
enddo
c write (2,*) "i",i
c write (2,*) "x_prime",(x_prime(j),j=1,3)
C Compute the energy of the ith side cbain
C
c write (2,*) "xx",xx," yy",yy," zz",zz
- it=itype(i)
+ it=iabs(itype(i))
do j = 1,65
x(j) = sc_parmin(j,it)
enddo
Cc diagnostics - remove later
xx1 = dcos(alph(2))
yy1 = dsin(alph(2))*dcos(omeg(2))
- zz1 = -dsin(alph(2))*dsin(omeg(2))
+ zz1 = -dsign(1.0,dfloat(itype(i)))*dsin(alph(2))*dsin(omeg(2))
write(2,'(3f8.1,3f9.3,1x,3f9.3)')
& alph(2)*rad2deg,omeg(2)*rad2deg,theta(3)*rad2deg,xx,yy,zz,
& xx1,yy1,zz1
c & dscp1,dscp2,sumene
c sumene = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
escloc = escloc + sumene
-c write (2,*) "i",i," escloc",sumene,escloc
+c write (2,*) "i",i," escloc",sumene,escloc,it,itype(i)
+c & ,zz,xx,yy
+c#define DEBUG
#ifdef DEBUG
C
C This section to check the numerical derivatives of the energy of ith side
C
C Compute the gradient of esc
C
+c zz=zz*dsign(1.0,dfloat(itype(i)))
pom_s1=(1.0d0+x(63))/(0.1d0 + dscp1)**2
pom_s16=6*(1.0d0+x(64))/(0.1d0 + dscp1**6)**2
pom_s2=(1.0d0+x(65))/(0.1d0 + dscp2)**2
& +(sumene2x+sumene4x*cost2tab(i+1))*(s2+s2_6)
& +(pom1+pom2)*pom_dx
#ifdef DEBUG
- write(2,*), "de_dxx = ", de_dxx,de_dxx_num
+ write(2,*), "de_dxx = ", de_dxx,de_dxx_num,itype(i)
#endif
C
sumene1y=x(3) + 2*x(6)*yy + x(9)*xx + x(10)*zz
& +(sumene2y+sumene4y*cost2tab(i+1))*(s2+s2_6)
& +(pom1-pom2)*pom_dy
#ifdef DEBUG
- write(2,*), "de_dyy = ", de_dyy,de_dyy_num
+ write(2,*), "de_dyy = ", de_dyy,de_dyy_num,itype(i)
#endif
C
de_dzz =(x(24) +2*x(27)*zz +x(28)*xx +x(30)*yy
& +x(60)*xx*yy)*cost2tab(i+1)*(s2+s2_6)
& + ( x(14) + 2*x(17)*zz+ x(18)*xx + x(20)*yy)*(s2+s2_6)
#ifdef DEBUG
- write(2,*), "de_dzz = ", de_dzz,de_dzz_num
+ write(2,*), "de_dzz = ", de_dzz,de_dzz_num,itype(i)
#endif
C
de_dt = 0.5d0*sumene3*cost2tab(i+1)*(s1+s1_6)
& -0.5d0*sumene4*sint2tab(i+1)*(s2+s2_6)
& +pom1*pom_dt1+pom2*pom_dt2
#ifdef DEBUG
- write(2,*), "de_dt = ", de_dt,de_dt_num
+ write(2,*), "de_dt = ", de_dt,de_dt_num,itype(i)
#endif
+c#undef DEBUG
c
C
cossc=scalar(dc_norm(1,i),dc_norm(1,i+nres))
dZZ_Ci1(k)=0.0d0
dZZ_Ci(k)=0.0d0
do j=1,3
- dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)*dC_norm(j,i+nres)
- dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)*dC_norm(j,i+nres)
+ dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)
+ & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
+ dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)
+ & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
enddo
dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres))
dYY_XYZ(k)=vbld_inv(i+nres)*(y_prime(k)-yy*dC_norm(k,i+nres))
- dZZ_XYZ(k)=vbld_inv(i+nres)*(z_prime(k)-zz*dC_norm(k,i+nres))
+ dZZ_XYZ(k)=vbld_inv(i+nres)*
+ & (z_prime(k)-zz*dC_norm(k,i+nres))
c
dt_dCi(k) = -dt_dCi(k)/sinttab(i+1)
dt_dCi1(k)= -dt_dCi1(k)/sinttab(i+1)
etors=0.0D0
do i=iphi_start,iphi_end
etors_ii=0.0D0
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21
- & .or. itype(i).eq.21) cycle
+ if (itype(i-2).eq.ntyp1.or. itype(i-1).eq.ntyp1
+ & .or. itype(i).eq.ntyp1) cycle
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
phii=phi(i)
c lprn=.true.
etors=0.0D0
do i=iphi_start,iphi_end
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21
- & .or. itype(i).eq.21) cycle
- etors_ii=0.0D0
+ if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1
+ & .or. itype(i).eq.ntyp1) cycle
+ etors_ii=0.0D0
+ if (iabs(itype(i)).eq.20) then
+ iblock=2
+ else
+ iblock=1
+ endif
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
phii=phi(i)
gloci=0.0D0
C Regular cosine and sine terms
- do j=1,nterm(itori,itori1)
- v1ij=v1(j,itori,itori1)
- v2ij=v2(j,itori,itori1)
+ do j=1,nterm(itori,itori1,iblock)
+ v1ij=v1(j,itori,itori1,iblock)
+ v2ij=v2(j,itori,itori1,iblock)
cosphi=dcos(j*phii)
sinphi=dsin(j*phii)
etors=etors+v1ij*cosphi+v2ij*sinphi
C
cosphi=dcos(0.5d0*phii)
sinphi=dsin(0.5d0*phii)
- do j=1,nlor(itori,itori1)
+ do j=1,nlor(itori,itori1,iblock)
vl1ij=vlor1(j,itori,itori1)
vl2ij=vlor2(j,itori,itori1)
vl3ij=vlor3(j,itori,itori1)
gloci=gloci+vl1ij*(vl3ij*cosphi-vl2ij*sinphi)*pom
enddo
C Subtract the constant term
- etors=etors-v0(itori,itori1)
+ etors=etors-v0(itori,itori1,iblock)
if (energy_dec) write (iout,'(a6,i5,0pf7.3)')
- & 'etor',i,etors_ii-v0(itori,itori1)
+ & 'etor',i,etors_ii-v0(itori,itori1,iblock)
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,
- & (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6)
+ & (v1(j,itori,itori1,iblock),j=1,6),
+ & (v2(j,itori,itori1,iblock),j=1,6)
gloc(i-3,icg)=gloc(i-3,icg)+wtor*gloci
c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
enddo
lprn=.false.
c lprn=.true.
etors_d=0.0D0
+c write(iout,*) "a tu??"
do i=iphid_start,iphid_end
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21
- & .or. itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1
+ & .or. itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
itori2=itortyp(itype(i))
phii1=phi(i+1)
gloci1=0.0D0
gloci2=0.0D0
+ iblock=1
+ if (iabs(itype(i+1)).eq.20) iblock=2
+
C Regular cosine and sine terms
- do j=1,ntermd_1(itori,itori1,itori2)
- v1cij=v1c(1,j,itori,itori1,itori2)
- v1sij=v1s(1,j,itori,itori1,itori2)
- v2cij=v1c(2,j,itori,itori1,itori2)
- v2sij=v1s(2,j,itori,itori1,itori2)
+ do j=1,ntermd_1(itori,itori1,itori2,iblock)
+ v1cij=v1c(1,j,itori,itori1,itori2,iblock)
+ v1sij=v1s(1,j,itori,itori1,itori2,iblock)
+ v2cij=v1c(2,j,itori,itori1,itori2,iblock)
+ v2sij=v1s(2,j,itori,itori1,itori2,iblock)
cosphi1=dcos(j*phii)
sinphi1=dsin(j*phii)
cosphi2=dcos(j*phii1)
gloci1=gloci1+j*(v1sij*cosphi1-v1cij*sinphi1)
gloci2=gloci2+j*(v2sij*cosphi2-v2cij*sinphi2)
enddo
- do k=2,ntermd_2(itori,itori1,itori2)
+ do k=2,ntermd_2(itori,itori1,itori2,iblock)
do l=1,k-1
- v1cdij = v2c(k,l,itori,itori1,itori2)
- v2cdij = v2c(l,k,itori,itori1,itori2)
- v1sdij = v2s(k,l,itori,itori1,itori2)
- v2sdij = v2s(l,k,itori,itori1,itori2)
+ v1cdij = v2c(k,l,itori,itori1,itori2,iblock)
+ v2cdij = v2c(l,k,itori,itori1,itori2,iblock)
+ v1sdij = v2s(k,l,itori,itori1,itori2,iblock)
+ v2sdij = v2s(l,k,itori,itori1,itori2,iblock)
cosphi1p2=dcos(l*phii+(k-l)*phii1)
cosphi1m2=dcos(l*phii-(k-l)*phii1)
sinphi1p2=dsin(l*phii+(k-l)*phii1)
C Set lprn=.true. for debugging
lprn=.false.
c lprn=.true.
-c write (iout,*) "EBACK_SC_COR",iphi_start,iphi_end,nterm_sccor
+c write (iout,*) "EBACK_SC_COR",itau_start,itau_end
esccor=0.0D0
- do i=iphi_start,iphi_end
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21) cycle
+ do i=itau_start,itau_end
+ if ((itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)) cycle
esccor_ii=0.0D0
- itori=itype(i-2)
- itori1=itype(i-1)
+ isccori=isccortyp(itype(i-2))
+ isccori1=isccortyp(itype(i-1))
+c write (iout,*) "EBACK_SC_COR",i,nterm_sccor(isccori,isccori1)
phii=phi(i)
+ do intertyp=1,3 !intertyp
+cc Added 09 May 2012 (Adasko)
+cc Intertyp means interaction type of backbone mainchain correlation:
+c 1 = SC...Ca...Ca...Ca
+c 2 = Ca...Ca...Ca...SC
+c 3 = SC...Ca...Ca...SCi
gloci=0.0D0
- do j=1,nterm_sccor
- v1ij=v1sccor(j,itori,itori1)
- v2ij=v2sccor(j,itori,itori1)
- cosphi=dcos(j*phii)
- sinphi=dsin(j*phii)
+ if (((intertyp.eq.3).and.((itype(i-2).eq.10).or.
+ & (itype(i-1).eq.10).or.(itype(i-2).eq.ntyp1).or.
+ & (itype(i-1).eq.ntyp1)))
+ & .or. ((intertyp.eq.1).and.((itype(i-2).eq.10)
+ & .or.(itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)
+ & .or.(itype(i).eq.ntyp1)))
+ & .or.((intertyp.eq.2).and.((itype(i-1).eq.10).or.
+ & (itype(i-1).eq.ntyp1).or.(itype(i-2).eq.ntyp1).or.
+ & (itype(i-3).eq.ntyp1)))) cycle
+ if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.ntyp1)) cycle
+ if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.ntyp1))
+ & cycle
+ 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
gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
enddo
+c write (iout,*) "EBACK_SC_COR",i,v1ij*cosphi+v2ij*sinphi,intertyp
+ gloc_sc(intertyp,i-3,icg)=gloc_sc(intertyp,i-3,icg)+wsccor*gloci
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,itori,itori1),j=1,6),(v2sccor(j,itori,itori1),j=1,6)
+ & 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)
gsccor_loc(i-3)=gsccor_loc(i-3)+gloci
+ enddo !intertyp
enddo
+
return
end
c----------------------------------------------------------------------------
C o o C
C \ /l\ /j\ / C
C \ / \ / \ / C
- C o| o | | o |o C
+ C o| o | | o |o C
C \ j|/k\| \ |/k\|l C
C \ / \ \ / \ C
C o o C
- C i i C
- C C
+ C i i C
+ C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
cd write (2,*) 'eello6_graph2: i,',i,' j',j,' k',k,' l',l
C AL 7/4/01 s1 would occur in the sixth-order moment,
double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2)
logical swap
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
- C C
+ C C
C Parallel Antiparallel C
C C
- C o o C
+ C o o C
C /l\ / \ /j\ C
C / \ / \ / \ C
C /| o |o o| o |\ C
& auxvec1(2),auxmat1(2,2)
logical swap
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
- C C
+ C C
C Parallel Antiparallel C
C C
C o o C
C / \ / \ / \ C
C /| o |o o| o |\ C
C \ j|/k\| \ |/k\|l C
- C \ / \ \ / \ C
+ C \ / \ \ / \ C
C o \ o \ C
C i i C
- C C
+ C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
C
C 4/7/01 AL Component s1 was removed, because it pertains to the respective
do i=1,nrep
iremd_m_total=iremd_m_total+remd_m(i)
enddo
- write (iout,*) 'Total number of replicas ',iremd_m_total
+ write (iout,*) 'Total number of replicas ',iremd_m_total
+ endif
endif
- endif
if(me.eq.king.or..not.out1file)
- & write (iout,'(/30(1h=),a,29(1h=)/)') " End of REMD run setup "
+ & write (iout,'(/30(1h=),a,29(1h=)/)') " End of REMD run setup "
return
end
c--------------------------------------------------------------------------
rest = index(controlcard,"REST").gt.0
tbf = index(controlcard,"TBF").gt.0
usampl = index(controlcard,"USAMPL").gt.0
+
mdpdb = index(controlcard,"MDPDB").gt.0
call reada(controlcard,"T_BATH",t_bath,300.0d0)
call reada(controlcard,"TAU_BATH",tau_bath,1.0d-1)
C Body
C
C Read weights of the subsequent energy terms.
- call card_concat(weightcard)
- call reada(weightcard,'WLONG',wlong,1.0D0)
- call reada(weightcard,'WSC',wsc,wlong)
- call reada(weightcard,'WSCP',wscp,wlong)
- call reada(weightcard,'WELEC',welec,1.0D0)
- call reada(weightcard,'WVDWPP',wvdwpp,welec)
- call reada(weightcard,'WEL_LOC',wel_loc,1.0D0)
- call reada(weightcard,'WCORR4',wcorr4,0.0D0)
- call reada(weightcard,'WCORR5',wcorr5,0.0D0)
- call reada(weightcard,'WCORR6',wcorr6,0.0D0)
- call reada(weightcard,'WTURN3',wturn3,1.0D0)
- call reada(weightcard,'WTURN4',wturn4,1.0D0)
- call reada(weightcard,'WTURN6',wturn6,1.0D0)
- call reada(weightcard,'WSCCOR',wsccor,1.0D0)
- call reada(weightcard,'WSTRAIN',wstrain,1.0D0)
- call reada(weightcard,'WBOND',wbond,1.0D0)
- call reada(weightcard,'WTOR',wtor,1.0D0)
- call reada(weightcard,'WTORD',wtor_d,1.0D0)
- call reada(weightcard,'WANG',wang,1.0D0)
- call reada(weightcard,'WSCLOC',wscloc,1.0D0)
- call reada(weightcard,'SCAL14',scal14,0.4D0)
- call reada(weightcard,'SCALSCP',scalscp,1.0d0)
- call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
- call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
- call reada(weightcard,'TEMP0',temp0,300.0d0)
- if (index(weightcard,'SOFT').gt.0) ipot=6
+ call card_concat(weightcard)
+ call reada(weightcard,'WLONG',wlong,1.0D0)
+ call reada(weightcard,'WSC',wsc,wlong)
+ call reada(weightcard,'WSCP',wscp,wlong)
+ call reada(weightcard,'WELEC',welec,1.0D0)
+ call reada(weightcard,'WVDWPP',wvdwpp,welec)
+ call reada(weightcard,'WEL_LOC',wel_loc,1.0D0)
+ call reada(weightcard,'WCORR4',wcorr4,0.0D0)
+ call reada(weightcard,'WCORR5',wcorr5,0.0D0)
+ call reada(weightcard,'WCORR6',wcorr6,0.0D0)
+ call reada(weightcard,'WTURN3',wturn3,1.0D0)
+ call reada(weightcard,'WTURN4',wturn4,1.0D0)
+ call reada(weightcard,'WTURN6',wturn6,1.0D0)
+ call reada(weightcard,'WSCCOR',wsccor,1.0D0)
+ call reada(weightcard,'WSTRAIN',wstrain,1.0D0)
+ call reada(weightcard,'WBOND',wbond,1.0D0)
+ call reada(weightcard,'WTOR',wtor,1.0D0)
+ call reada(weightcard,'WTORD',wtor_d,1.0D0)
+ call reada(weightcard,'WANG',wang,1.0D0)
+ call reada(weightcard,'WSCLOC',wscloc,1.0D0)
+ call reada(weightcard,'SCAL14',scal14,0.4D0)
+ call reada(weightcard,'SCALSCP',scalscp,1.0d0)
+ call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
+ call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
+ call reada(weightcard,'TEMP0',temp0,300.0d0)
+ if (index(weightcard,'SOFT').gt.0) ipot=6
C 12/1/95 Added weight for the multi-body term WCORR
- call reada(weightcard,'WCORRH',wcorr,1.0D0)
- if (wcorr4.gt.0.0d0) wcorr=wcorr4
- weights(1)=wsc
- weights(2)=wscp
- weights(3)=welec
- weights(4)=wcorr
- weights(5)=wcorr5
- weights(6)=wcorr6
- weights(7)=wel_loc
- weights(8)=wturn3
- weights(9)=wturn4
- weights(10)=wturn6
- weights(11)=wang
- weights(12)=wscloc
- weights(13)=wtor
- weights(14)=wtor_d
- weights(15)=wstrain
- weights(16)=wvdwpp
- weights(17)=wbond
- weights(18)=scal14
- weights(21)=wsccor
+ call reada(weightcard,'WCORRH',wcorr,1.0D0)
+ if (wcorr4.gt.0.0d0) wcorr=wcorr4
+ weights(1)=wsc
+ weights(2)=wscp
+ weights(3)=welec
+ weights(4)=wcorr
+ weights(5)=wcorr5
+ weights(6)=wcorr6
+ weights(7)=wel_loc
+ weights(8)=wturn3
+ weights(9)=wturn4
+ weights(10)=wturn6
+ weights(11)=wang
+ weights(12)=wscloc
+ weights(13)=wtor
+ weights(14)=wtor_d
+ weights(15)=wstrain
+ weights(16)=wvdwpp
+ weights(17)=wbond
+ weights(18)=scal14
+ weights(21)=wsccor
if(me.eq.king.or..not.out1file)
& write (iout,10) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,
& wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,
& 'General scaling factor of SC-p interactions:',scalscp
endif
r0_corr=cutoff_corr-delt_corr
- do i=1,20
+ do i=1,ntyp
aad(i,1)=scalscp*aad(i,1)
aad(i,2)=scalscp*aad(i,2)
bad(i,1)=scalscp*bad(i,1)
maxsi=1000
do i=2,nres-1
iti=itype(i)
- if (iti.ne.10 .and. itype(i).ne.21) then
+ if (iti.ne.10 .and. itype(i).ne.ntyp1) then
nsi=0
fail=.true.
do while (fail.and.nsi.le.maxsi)
vbld_inv(i)=vblinv
enddo
do i=2,nres-1
- vbld(i+nres)=dsc(itype(i))
- vbld_inv(i+nres)=dsc_inv(itype(i))
+ vbld(i+nres)=dsc(iabs(itype(i)))
+ vbld_inv(i+nres)=dsc_inv(iabs(itype(i)))
c write (iout,*) "i",i," itype",itype(i),
c & " dsc",dsc(itype(i))," vbld",vbld(i),vbld(i+nres)
enddo
c print '(20i4)',(itype(i),i=1,nres)
do i=1,nres
#ifdef PROCOR
- if (itype(i).eq.21 .or. itype(i+1).eq.21) then
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) then
#else
- if (itype(i).eq.21) then
+ if (itype(i).eq.ntyp1) then
#endif
itel(i)=0
#ifdef PROCOR
- else if (itype(i+1).ne.20) then
+ else if (iabs(itype(i+1)).ne.20) then
#else
- else if (itype(i).ne.20) then
+ else if (iabs(itype(i)).ne.20) then
#endif
itel(i)=1
else
#endif
nct=nres
cd print *,'NNT=',NNT,' NCT=',NCT
- if (itype(1).eq.21) nnt=2
- if (itype(nres).eq.21) nct=nct-1
+ if (itype(1).eq.ntyp1) nnt=2
+ if (itype(nres).eq.ntyp1) nct=nct-1
if (pdbref) then
if(me.eq.king.or..not.out1file)
& write (iout,'(a,i3)') 'nsup=',nsup
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
do j=1,3
dc(j,i+nres)=c(j,i+nres)-c(j,i)
dc_norm(j,i+nres)=dc_norm(j,i+nres)*vbld_inv(i+nres)
enddo
do i=2,nres-1
omeg(i)=-120d0*deg2rad
+ if (itype(i).le.0) omeg(i)=-omeg(i)
enddo
else
if(me.eq.king.or..not.out1file)
i2=jhpb(i)-nres
it1=itype(i1)
it2=itype(i2)
- if (me.eq.king.or..not.out1file)
- & write (iout,'(2a,i3,3a,i3,a,3f10.3)')
+ write (iout,'(2a,i3,3a,i3,a,3f10.3)')
& restyp(it1),'(',i1,') -- ',restyp(it2),'(',i2,')',dhpb(i),
& ebr,forcon(i)
enddo
include 'COMMON.SETUP'
C Read bridging residues.
read (inp,*) ns,(iss(i),i=1,ns)
- c print *,'ns=',ns
+ print *,'ns=',ns
if(me.eq.king.or..not.out1file)
& write (iout,*) 'ns=',ns,' iss:',(iss(i),i=1,ns)
C Check whether the specified bridging residues are cystines.
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
do j=1,3
dc(j,i+nres)=c(j,i+nres)-c(j,i)
dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
nvar=ntheta+nphi
nside=0
do i=2,nres-1
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
nside=nside+1
ialph(i,1)=nvar+nside
ialph(nside,2)=i
open (itordp,file=tordname,status='old',readonly)
call getenv_loc('SCCORPAR',sccorname)
open (isccor,file=sccorname,status='old',readonly)
+#ifndef CRYST_THETA
+ call getenv_loc('THETPARPDB',thetname_pdb)
+ print *,"thetname_pdb ",thetname_pdb
+ open (ithep_pdb,file=thetname_pdb,status='old',action='read')
+ print *,ithep_pdb," opened"
+#endif
call getenv_loc('FOURIER',fouriername)
open (ifourier,file=fouriername,status='old',readonly)
call getenv_loc('ELEPAR',elename)
open (ielep,file=elename,status='old',readonly)
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old',readonly)
+#ifndef CRYST_SC
+ call getenv_loc('ROTPARPDB',rotname_pdb)
+ open (irotam_pdb,file=rotname_pdb,status='old',action='read')
+#endif
#endif
#ifndef OLDSCP
C
& thetname(:ilen(thetname))
write (iout,*) "Rotamer parameter file : ",
& rotname(:ilen(rotname))
+ write (iout,*) "Thetpdb parameter file : ",
+ & thetname_pdb(:ilen(thetname_pdb))
write (iout,*) "Threading database : ",
& patname(:ilen(patname))
if (lentmp.ne.0)
c write (iout,*) "j",j," k",k
ddjk=dist(j,k)
if (constr_dist.eq.1) then
- nhpb=nhpb+1
- ihpb(nhpb)=j
- jhpb(nhpb)=k
+ nhpb=nhpb+1
+ ihpb(nhpb)=j
+ jhpb(nhpb)=k
dhpb(nhpb)=ddjk
- forcon(nhpb)=wfrag_(i)
+ forcon(nhpb)=wfrag_(i)
else if (constr_dist.eq.2) then
if (ddjk.le.dist_cut) then
nhpb=nhpb+1
#endif
if (OKRandom) then
c r1 = prng_next(me)
- r1=ran_number(0.0D0,1.0D0)
+ r1=ran_number(0.0D0,1.0D0)
if(me.eq.king)
& write (iout,*) 'ran_num',r1
if (r1.lt.0.0d0) OKRandom=.false.
parmread.F
pinorm.f
printmat.f
+ prng_32.F
q_measure.F
randgens.f
rattle.F
ssMD.F
)
- if(Fortran_COMPILER_NAME STREQUAL "ifort")
- set(UNRES_MD_SRC0 ${UNRES_MD_SRC0} prng.f )
- elseif(Fortran_COMPILER_NAME STREQUAL "mpif90")
- set(UNRES_MD_SRC0 ${UNRES_MD_SRC0} prng.f )
- elseif(Fortran_COMPILER_NAME STREQUAL "f95")
- set(UNRES_MD_SRC0 ${UNRES_MD_SRC0} prng.f )
- elseif(Fortran_COMPILER_NAME STREQUAL "gfortran")
- set(UNRES_MD_SRC0 ${UNRES_MD_SRC0} prng.f )
- else()
- set(UNRES_MD_SRC0 ${UNRES_MD_SRC0} prng_32.F )
- endif (Fortran_COMPILER_NAME STREQUAL "ifort")
-
-
set(UNRES_MD_SRC3
energy_p_new_barrier.F
energy_p_new-sep_barrier.F
MP.F
MREMD.F
parmread.F
+ prng_32.F
q_measure1.F
q_measure3.F
q_measure.F
proc_proc.c
)
-
- if(NOT Fortran_COMPILER_NAME STREQUAL "ifort")
- set(UNRES_MD_PP_SRC ${UNRES_MD_PP_SRC} prng_32.F)
- endif(NOT Fortran_COMPILER_NAME STREQUAL "ifort")
-
#================================================
# Set comipiler flags for different sourcefiles
#================================================
set(FFLAGS2 "-std=legacy -I. ")
#set(FFLAGS3 "-c -w -O3 -ipo -ipo_obj -opt_report" )
set(FFLAGS3 "-std=legacy -I. " )
+elseif (Fortran_COMPILER_NAME STREQUAL "g77")
+ set(FFLAGS0 "-I ${CMAKE_CURRENT_SOURCE_DIR} " )
+ set(FFLAGS1 "-g -I ${CMAKE_CURRENT_SOURCE_DIR} " )
+ set(FFLAGS2 "-I ${CMAKE_CURRENT_SOURCE_DIR} ")
+ set(FFLAGS3 "-I ${CMAKE_CURRENT_SOURCE_DIR} " )
endif (Fortran_COMPILER_NAME STREQUAL "ifort")
#=========================================
if(UNRES_MD_FF STREQUAL "GAB" )
# set preprocesor flags
- set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC" )
+ set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DSCCORPDB" )
#=========================================
# Settings for E0LL2Y force field
#=========================================
elseif(UNRES_MD_FF STREQUAL "E0LL2Y")
# set preprocesor flags
- set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0" )
+ set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0 -DSCCORPDB" )
endif(UNRES_MD_FF STREQUAL "GAB")
#=========================================
elseif (Fortran_COMPILER_NAME STREQUAL "gfortran")
# Add old gfortran flags
set(CPPFLAGS "${CPPFLAGS} -DG77")
+elseif (Fortran_COMPILER_NAME STREQUAL "g77")
+ # Add old gfortran flags
+ set(CPPFLAGS "${CPPFLAGS} -DG77")
+else(Fortran_COMPILER_NAME STREQUAL "ifort")
+ # Default preprocessor flag
+ set(CPPFLAGS "${CPPFLAGS} -DPGI")
endif (Fortran_COMPILER_NAME STREQUAL "ifort")
#=========================================
endif(UNRES_WITH_MPI)
#=========================================
+ # Add 64-bit specific preprocessor flags
+ #=========================================
+ if (architektura STREQUAL "64")
+ set(CPPFLAGS "${CPPFLAGS} -DAMD64")
+ endif (architektura STREQUAL "64")
+
+ #=========================================
# Apply preprocesor flags to *.F files
#=========================================
set_property(SOURCE ${UNRES_MD_PP_SRC} PROPERTY COMPILE_DEFINITIONS ${CPPFLAGS} )
#========================================
if(UNRES_WITH_MPI)
# binary with mpi
- set(UNRES_BIN "unres_${Fortran_COMPILER_NAME}_MPICH_${UNRES_MD_FF}.exe")
+ set(UNRES_BIN "unresMD_${Fortran_COMPILER_NAME}_MPICH_${UNRES_MD_FF}.exe")
else(UNRES_WITH_MPI)
# binary without mpi
- set(UNRES_BIN "unres_${Fortran_COMPILER_NAME}_single_${UNRES_MD_FF}.exe")
+ set(UNRES_BIN "unresMD_${Fortran_COMPILER_NAME}_single_${UNRES_MD_FF}.exe")
endif(UNRES_WITH_MPI)
#=========================================
#=========================================
add_executable(UNRES_BIN-MD ${UNRES_MD_SRCS} )
set_target_properties(UNRES_BIN-MD PROPERTIES OUTPUT_NAME ${UNRES_BIN})
- #set_property(TARGET ${UNRES_BIN} PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin/unres/MD )
+ set_property(TARGET UNRES_BIN-MD PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin )
#add_dependencies (${UNRES_BIN} ${UNRES_XDRFLIB})
target_link_libraries( UNRES_BIN-MD xdrf )
#=========================================
- # INSTALL
+ # Install Path
#=========================================
-
- install(TARGETS UNRES_BIN-MD RUNTIME DESTINATION unrespack/bin)
+ install(TARGETS UNRES_BIN-MD DESTINATION ${CMAKE_INSTALL_PREFIX})
#=========================================
# TESTS
#=========================================
# test_single_ala.sh
#=========================================
+#
+# Set parmaeters depending on force field
+if(UNRES_MD_FF STREQUAL "GAB")
+ set(UNRES_BONDPAR "bond.parm")
+elseif(UNRES_MD_FF STREQUAL "E0LL2Y")
+ set(UNRES_BONDPAR "bond_AM1.parm")
+endif(UNRES_MD_FF STREQUAL "GAB")
FILE(WRITE ${CMAKE_CURRENT_BINARY_DIR}/scripts/test_single_ala.sh
"#!/bin/sh
export POT=GB
export PREFIX=ala10
#-----------------------------------------------------------------------------
- UNRES_BIN=./${UNRES_BIN}
+ UNRES_BIN=${CMAKE_BINARY_DIR}/bin/${UNRES_BIN}
#-----------------------------------------------------------------------------
DD=${CMAKE_SOURCE_DIR}/PARAM
-export BONDPAR=$DD/bond.parm
+export BONDPAR=$DD/${UNRES_BONDPAR}
export THETPAR=$DD/thetaml.5parm
export ROTPAR=$DD/scgauss.parm
export TORPAR=$DD/torsion_631Gdp.parm
double precision v1sccor,v2sccor,vlor1sccor,
& vlor2sccor,vlor3sccor,gloc_sc,
& dcostau,dsintau,dtauangle,dcosomicron,
- & domicron
+ & domicron,v0sccor
integer nterm_sccor,isccortyp,nsccortyp,nlor_sccor
- common/sccor/v1sccor(maxterm_sccor,3,20,20),
- & v2sccor(maxterm_sccor,3,20,20),
+ common/sccor/v1sccor(maxterm_sccor,3,-ntyp:ntyp,-ntyp:ntyp),
+ & v2sccor(maxterm_sccor,3,-ntyp:ntyp,-ntyp:ntyp),
+ & v0sccor(maxterm_sccor,-ntyp:ntyp,-ntyp:ntyp),
+ & nterm_sccor(-ntyp:ntyp,-ntyp:ntyp),isccortyp(-ntyp:ntyp),
+ & nsccortyp,
+ & nlor_sccor(-ntyp:ntyp,-ntyp:ntyp),
& vlor1sccor(maxterm_sccor,20,20),
& vlor2sccor(maxterm_sccor,20,20),
& vlor3sccor(maxterm_sccor,20,20),gloc_sc(3,0:maxres2,10),
- & v0sccor(ntyp,ntyp),
& dcostau(3,3,3,maxres2),dsintau(3,3,3,maxres2),
& dtauangle(3,3,3,maxres2),dcosomicron(3,3,3,maxres2),
- & domicron(3,3,3,maxres2),
- & nterm_sccor(ntyp,ntyp),isccortyp(ntyp),nsccortyp,
- & nlor_sccor(ntyp,ntyp)
+ & domicron(3,3,3,maxres2)
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
ind=ind+1
- itypj=itype(j)
+ itypj=iabs(itype(j))
c dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
chi1=chi(itypi,itypj)
C Zero the energy function and its derivative at 0 or pi.
call splinthet(theta(i),0.5d0*delta,ss,ssd)
it=itype(i-1)
+ ichir1=isign(1,itype(i-2))
+ ichir2=isign(1,itype(i))
+ if (itype(i-2).eq.10) ichir1=isign(1,itype(i-1))
+ if (itype(i).eq.10) ichir2=isign(1,itype(i-1))
+ if (itype(i-1).eq.10) then
+ itype1=isign(10,itype(i-2))
+ ichir11=isign(1,itype(i-2))
+ ichir12=isign(1,itype(i-2))
+ itype2=isign(10,itype(i))
+ ichir21=isign(1,itype(i))
+ ichir22=isign(1,itype(i))
+ endif
if (i.gt.3) then
#ifdef OSF
phii=phi(i)
C In following comments this theta will be referred to as t_c.
thet_pred_mean=0.0d0
do k=1,2
- athetk=athet(k,it)
- bthetk=bthet(k,it)
+ athetk=athet(k,it,ichir1,ichir2)
+ bthetk=bthet(k,it,ichir1,ichir2)
+ if (it.eq.10) then
+ athetk=athet(k,itype1,ichir11,ichir12)
+ bthetk=bthet(k,itype2,ichir21,ichir22)
+ endif
thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k)
enddo
dthett=thet_pred_mean*ssd
thet_pred_mean=thet_pred_mean*ss+a0thet(it)
C Derivatives of the "mean" values in gamma1 and gamma2.
- dthetg1=(-athet(1,it)*y(2)+athet(2,it)*y(1))*ss
- dthetg2=(-bthet(1,it)*z(2)+bthet(2,it)*z(1))*ss
+ dthetg1=(-athet(1,it,ichir1,ichir2)*y(2)
+ &+athet(2,it,ichir1,ichir2)*y(1))*ss
+ dthetg2=(-bthet(1,it,ichir1,ichir2)*z(2)
+ & +bthet(2,it,ichir1,ichir2)*z(1))*ss
+ if (it.eq.10) then
+ dthetg1=(-athet(1,itype1,ichir11,ichir12)*y(2)
+ &+athet(2,itype1,ichir11,ichir12)*y(1))*ss
+ dthetg2=(-bthet(1,itype2,ichir21,ichir22)*z(2)
+ & +bthet(2,itype2,ichir21,ichir22)*z(1))*ss
+ endif
if (theta(i).gt.pi-delta) then
call theteng(pi-delta,thet_pred_mean,theta0(it),f0,fprim0,
& E_tc0)
enddo
endif
if (i.lt.nres) then
+
+ if (iabs(itype(i+1)).eq.20) iblock=2
+ if (iabs(itype(i+1)).ne.20) iblock=1
#ifdef OSF
phii1=phi(i+1)
if (phii1.ne.phii1) phii1=150.0
sinph2(k)=0.0d0
enddo
endif
- ethetai=aa0thet(ityp1,ityp2,ityp3)
+ ethetai=aa0thet(ityp1,ityp2,ityp3,iblock)
do k=1,ndouble
do l=1,k-1
ccl=cosph1(l)*cosph2(k-l)
enddo
endif
do k=1,ntheterm
- ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3)*sinkt(k)
- dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3)
+ ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3,iblock)*sinkt(k)
+ dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3,iblock)
& *coskt(k)
if (lprn)
- & write (iout,*) "k",k," aathet",aathet(k,ityp1,ityp2,ityp3),
+ & write (iout,*) "k",k,
+ & "aathet",aathet(k,ityp1,ityp2,ityp3,iblock),
& " ethetai",ethetai
enddo
if (lprn) then
endif
do m=1,ntheterm2
do k=1,nsingle
- aux=bbthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)
- & +ccthet(k,m,ityp1,ityp2,ityp3)*sinph1(k)
- & +ddthet(k,m,ityp1,ityp2,ityp3)*cosph2(k)
- & +eethet(k,m,ityp1,ityp2,ityp3)*sinph2(k)
+ aux=bbthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)
+ & +ccthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k)
+ & +ddthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)
+ & +eethet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k)
ethetai=ethetai+sinkt(m)*aux
dethetai=dethetai+0.5d0*m*aux*coskt(m)
dephii=dephii+k*sinkt(m)*(
- & ccthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)-
- & bbthet(k,m,ityp1,ityp2,ityp3)*sinph1(k))
+ & ccthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)-
+ & bbthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k))
dephii1=dephii1+k*sinkt(m)*(
- & eethet(k,m,ityp1,ityp2,ityp3)*cosph2(k)-
- & ddthet(k,m,ityp1,ityp2,ityp3)*sinph2(k))
+ & eethet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)-
+ & ddthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k))
if (lprn)
& write (iout,*) "m",m," k",k," bbthet",
- & bbthet(k,m,ityp1,ityp2,ityp3)," ccthet",
- & ccthet(k,m,ityp1,ityp2,ityp3)," ddthet",
- & ddthet(k,m,ityp1,ityp2,ityp3)," eethet",
- & eethet(k,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ & bbthet(k,m,ityp1,ityp2,ityp3,iblock)," ccthet",
+ & 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
enddo
enddo
if (lprn)
do m=1,ntheterm3
do k=2,ndouble
do l=1,k-1
- aux=ffthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)
+ aux=ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)
+
ethetai=ethetai+sinkt(m)*aux
dethetai=dethetai+0.5d0*m*coskt(m)*aux
dephii=dephii+l*sinkt(m)*(
- & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)-
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)-
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
+
dephii1=dephii1+(k-l)*sinkt(m)*(
- & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)-
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ &-ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)-
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
+
if (lprn) then
write (iout,*) "m",m," k",k," l",l," ffthet",
- & ffthet(l,k,m,ityp1,ityp2,ityp3),
- & ffthet(k,l,m,ityp1,ityp2,ityp3)," ggthet",
- & ggthet(l,k,m,ityp1,ityp2,ityp3),
- & ggthet(k,l,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ & ffthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)," ggthet",
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock),
+ & " ethetai",ethetai
+
write (iout,*) cosph1ph2(l,k)*sinkt(m),
& cosph1ph2(k,l)*sinkt(m),
& sinph1ph2(l,k)*sinkt(m),sinph1ph2(k,l)*sinkt(m)
enddo
enddo
10 continue
- if (lprn1) write (iout,'(i2,3f8.1,9h ethetai ,f10.5)')
- & i,theta(i)*rad2deg,phii*rad2deg,
+ c lprn1=.true.
+ if (lprn1) write (iout,'(a4,i2,3f8.1,9h ethetai ,f10.5)')
+ & 'ebe', i,theta(i)*rad2deg,phii*rad2deg,
& phii1*rad2deg,ethetai
+ c lprn1=.false.
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
cosfac=dsqrt(cosfac2)
sinfac2=0.5d0/(1.0d0-costtab(i+1))
sinfac=dsqrt(sinfac2)
- it=itype(i)
+ it=iabs(itype(i))
if (it.eq.10) goto 1
c
C Compute the axes of tghe local cartesian coordinates system; store in
y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
enddo
do j = 1,3
- z_prime(j) = -uz(j,i-1)
+ z_prime(j) = -uz(j,i-1)*dsign(1.0d0,dfloat(itype(i)))
enddo
c write (2,*) "i",i
c write (2,*) "x_prime",(x_prime(j),j=1,3)
C Compute the energy of the ith side cbain
C
c write (2,*) "xx",xx," yy",yy," zz",zz
- it=itype(i)
+ it=iabs(itype(i))
do j = 1,65
x(j) = sc_parmin(j,it)
enddo
Cc diagnostics - remove later
xx1 = dcos(alph(2))
yy1 = dsin(alph(2))*dcos(omeg(2))
- zz1 = -dsin(alph(2))*dsin(omeg(2))
+ zz1 = -dsign(1.0, dfloat(itype(i)))*dsin(alph(2))*dsin(omeg(2))
write(2,'(3f8.1,3f9.3,1x,3f9.3)')
& alph(2)*rad2deg,omeg(2)*rad2deg,theta(3)*rad2deg,xx,yy,zz,
& xx1,yy1,zz1
dZZ_Ci1(k)=0.0d0
dZZ_Ci(k)=0.0d0
do j=1,3
- dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)*dC_norm(j,i+nres)
- dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)*dC_norm(j,i+nres)
+ dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)
+ & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
+ dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)
+ & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
enddo
dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres))
etors=0.0D0
do i=iphi_start,iphi_end
etors_ii=0.0D0
+c if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1
+c & .or. itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
phii=phi(i)
c lprn=.true.
etors_d=0.0D0
do i=iphid_start,iphid_end
+c if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1
+c & .or. itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
itori2=itortyp(itype(i))
C Set lprn=.true. for debugging
lprn=.false.
c lprn=.true.
-c write (iout,*) "EBACK_SC_COR",iphi_start,iphi_end,nterm_sccor
+c write (iout,*) "EBACK_SC_COR",itau_start,itau_end
esccor=0.0D0
do i=itau_start,itau_end
esccor_ii=0.0D0
+ if ((itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)) cycle
isccori=isccortyp(itype(i-2))
isccori1=isccortyp(itype(i-1))
phii=phi(i)
c 3 = SC...Ca...Ca...SCi
gloci=0.0D0
if (((intertyp.eq.3).and.((itype(i-2).eq.10).or.
- & (itype(i-1).eq.10).or.(itype(i-2).eq.21).or.
- & (itype(i-1).eq.21)))
+ & (itype(i-1).eq.10).or.(itype(i-2).eq.ntyp1).or.
+ & (itype(i-1).eq.ntyp1)))
& .or. ((intertyp.eq.1).and.((itype(i-2).eq.10)
- & .or.(itype(i-2).eq.21)))
+ & .or.(itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)
+ & .or.(itype(i).eq.ntyp1)))
& .or.((intertyp.eq.2).and.((itype(i-1).eq.10).or.
- & (itype(i-1).eq.21)))) cycle
- 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))
+ & (itype(i-1).eq.ntyp1).or.(itype(i-2).eq.ntyp1).or.
+ & (itype(i-3).eq.ntyp1)))) cycle
+ if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.ntyp1)) cycle
+ if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.ntyp1))
& cycle
do j=1,nterm_sccor(isccori,isccori1)
v1ij=v1sccor(j,intertyp,isccori,isccori1)
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)
+ & 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)
gsccor_loc(i-3)=gsccor_loc(i-3)+gloci
enddo !intertyp
enddo
printmat.f
randgens.f
readrtns_min.F
+ refsys.f
rescode.f
refsys.f
rmdd.f
#=========================================
# Build the binary
#=========================================
- add_executable(UNRES_BIN-MIN ${UNRES_MIN_SRCS} )
- set_target_properties(UNRES_BIN-MIN PROPERTIES OUTPUT_NAME ${UNRES_BIN})
+ add_executable(UNRES_MIN_BIN ${UNRES_MIN_SRCS} )
+ set_target_properties(UNRES_MIN_BIN PROPERTIES OUTPUT_NAME ${UNRES_BIN})
if (Fortran_COMPILER_NAME STREQUAL "ifort")
- target_link_libraries (UNRES_BIN-MIN ${CMAKE_THREAD_LIBS_INIT})
+ target_link_libraries (UNRES_MIN_BIN ${CMAKE_THREAD_LIBS_INIT})
endif (Fortran_COMPILER_NAME STREQUAL "ifort")
+ set_property(TARGET UNRES_MIN_BIN PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin )
- #set_property(TARGET ${UNRES_BIN} PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin/unres/MD )
#=========================================
- # INSTALL
+ # Install Path
#=========================================
+ install(TARGETS UNRES_MIN_BIN DESTINATION ${CMAKE_INSTALL_PREFIX})
- install(TARGETS UNRES_BIN-MIN RUNTIME DESTINATION unrespack/bin)
-
- #=========================================
- # TESTS
- #=========================================
-
- #-- Copy all the data files from the test directory into the source directory
- #SET(UNRES_TEST_FILES
- # ala10.inp
- # )
-
- #FOREACH (UNRES_TEST_FILE ${UNRES_TEST_FILES})
- # SET (unres_test_dest "${CMAKE_CURRENT_BINARY_DIR}/${UNRES_TEST_FILE}")
- # MESSAGE (STATUS " Copying ${UNRES_TEST_FILE} from ${CMAKE_SOURCE_DIR}/examples/unres/MD/ff_gab/${UNRES_TEST_FILE} to ${unres_test_dest}")
- # ADD_CUSTOM_COMMAND (
- # TARGET ${UNRES_BIN}
- # POST_BUILD
- # COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/examples/unres/MD/ff_gab/${UNRES_TEST_FILE} ${unres_test_dest}
- # )
- #ENDFOREACH (UNRES_TEST_FILE ${UNRES_TEST_FILES})
-
- #=========================================
- # Generate data test files
- #=========================================
-
- #if(NOT UNRES_WITH_MPI)
-
- # add_test(NAME UNRES_MD_Ala10 COMMAND sh ${CMAKE_CURRENT_BINARY_DIR}/test_single_ala.sh )
-
- #endif(NOT UNRES_WITH_MPI)
-
# Set comipiler flags for different sourcefiles
#================================================
if (Fortran_COMPILER_NAME STREQUAL "ifort")
- set(FFLAGS0 "-g -CB -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres -I${MPIF_INCLUDE_DIRECTORIES}" )
+ set(FFLAGS0 "-g -CB -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" )
elseif (Fortran_COMPILER_NAME STREQUAL "gfortran")
- set(FFLAGS0 "-std=legacy -g -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres -I${MPIF_INCLUDE_DIRECTORIES}" )
+ set(FFLAGS0 "-std=legacy -g -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" )
+ else ()
+ set(FFLAGS0 "-g -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" )
endif (Fortran_COMPILER_NAME STREQUAL "ifort")
# set preprocesor flags
set(CPPFLAGS "PROCOR -DSPLITELE -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DSCCORPDB" )
+
#=========================================
# Settings for E0LL2Y force field
#=========================================
elseif (Fortran_COMPILER_NAME STREQUAL "gfortran")
# Add old gfortran flags
set(CPPFLAGS "${CPPFLAGS} -DG77")
+else (Fortran_COMPILER_NAME STREQUAL "ifort")
+ # Default preprocessor flags
+ set(CPPFLAGS "${CPPFLAGS} -DPGI")
endif (Fortran_COMPILER_NAME STREQUAL "ifort")
#=========================================
#========================================
# Setting binary name
#========================================
- set(UNRES_WHAM_M_BIN "wham_${Fortran_COMPILER_NAME}.exe")
+ set(UNRES_WHAM_M_BIN "wham_M_${Fortran_COMPILER_NAME}.exe")
#=========================================
# cinfo.f workaround for CMake
#=========================================
add_executable(UNRES_WHAM_M_BIN ${UNRES_WHAM_M_SRCS} )
set_target_properties(UNRES_WHAM_M_BIN PROPERTIES OUTPUT_NAME ${UNRES_WHAM_M_BIN})
-
- #set_property(TARGET ${UNRES_BIN} PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin/unres/MD )
+ set_property(TARGET UNRES_WHAM_M_BIN PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin )
#add_dependencies (${UNRES_BIN} ${UNRES_XDRFLIB})
#=========================================
# link libxdrf.a
target_link_libraries( UNRES_WHAM_M_BIN xdrf )
+
+ #=========================================
+ # Install Path
+ #=========================================
+ install(TARGETS UNRES_WHAM_M_BIN DESTINATION ${CMAKE_INSTALL_PREFIX})
+
+
#=========================================
# TESTS
#=========================================
# Set comipiler flags for different sourcefiles
#================================================
if (Fortran_COMPILER_NAME STREQUAL "ifort")
- set(FFLAGS0 "-mcmodel=medium -g -CB -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" )
+ set(FFLAGS0 "-mcmodel=large -g -CB -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" )
elseif (Fortran_COMPILER_NAME STREQUAL "gfortran")
set(FFLAGS0 "-std=legacy -g -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" )
+ else ()
+ set(FFLAGS0 "-g -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" )
endif (Fortran_COMPILER_NAME STREQUAL "ifort")
elseif (Fortran_COMPILER_NAME STREQUAL "gfortran")
# Add old gfortran flags
set(CPPFLAGS "${CPPFLAGS} -DG77")
+else (Fortran_COMPILER_NAME STREQUAL "ifort")
+ # Default preprocessor flags
+ set(CPPFLAGS "${CPPFLAGS} -DPGI")
endif (Fortran_COMPILER_NAME STREQUAL "ifort")
#=========================================
#=========================================
add_executable(UNRES_WHAM_BIN ${UNRES_WHAM_SRCS} )
set_target_properties(UNRES_WHAM_BIN PROPERTIES OUTPUT_NAME ${UNRES_WHAM_BIN})
-
- #set_property(TARGET ${UNRES_BIN} PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin/unres/MD )
+ set_property(TARGET UNRES_WHAM_BIN PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin )
#add_dependencies (${UNRES_BIN} ${UNRES_XDRFLIB})
#=========================================
target_link_libraries( UNRES_WHAM_BIN xdrf )
#=========================================
+ # Install Path
+ #=========================================
+ install(TARGETS UNRES_WHAM_BIN DESTINATION ${CMAKE_INSTALL_PREFIX})
+
+
+ #=========================================
# TESTS
#=========================================
& +wturn3*fact(2)*gel_loc_turn3(i)
& +wturn6*fact(5)*gel_loc_turn6(i)
& +wel_loc*fact(2)*gel_loc_loc(i)
- & +wsccor*fact(1)*gsccor_loc(i)
+c & +wsccor*fact(1)*gsccor_loc(i)
enddo
endif
return
evdw=0.0D0
evdw_t=0.0d0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
cd write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
cd & 'iend=',iend(i,iint)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
evdw=0.0D0
evdw_t=0.0d0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
C
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
c endif
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
ind=ind+1
- itypj=itype(j)
+ itypj=iabs(itype(j))
dscj_inv=vbld_inv(j+nres)
chi1=chi(itypi,itypj)
chi2=chi(itypj,itypi)
c if (icall.gt.0) lprn=.true.
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
c & 'evdw',i,j,evdwij,' ss'
ELSE
ind=ind+1
- itypj=itype(j)
+ itypj=iabs(itype(j))
dscj_inv=vbld_inv(j+nres)
sig0ij=sigma(itypi,itypj)
chi1=chi(itypi,itypj)
c if (icall.gt.0) lprn=.true.
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
ind=ind+1
- itypj=itype(j)
+ itypj=iabs(itype(j))
dscj_inv=vbld_inv(j+nres)
sig0ij=sigma(itypi,itypj)
r0ij=r0(itypi,itypj)
do iint=1,nscp_gr(i)
do j=iscpstart(i,iint),iscpend(i,iint)
- itypj=itype(j)
+ itypj=iabs(itype(j))
C Uncomment following three lines for SC-p interactions
c xj=c(1,nres+j)-xi
c yj=c(2,nres+j)-yi
C distance and angle dependent SS bond potential.
if (.not.dyn_ss .and. i.le.nss) then
C 15/02/13 CC dynamic SSbond - additional check
- if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then
+ if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
+ & iabs(itype(jjj)).eq.1) then
call ssbond_ene(iii,jjj,eij)
ehpb=ehpb+2*eij
endif
include 'COMMON.VAR'
include 'COMMON.IOUNITS'
double precision erij(3),dcosom1(3),dcosom2(3),gg(3)
- itypi=itype(i)
+ itypi=iabs(itype(i))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,nres+i)
dsci_inv=dsc_inv(itypi)
- itypj=itype(j)
+ itypj=iabs(itype(j))
dscj_inv=dsc_inv(itypj)
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
c
do i=nnt,nct
- iti=itype(i)
+ iti=iabs(itype(i))
if (iti.ne.10) then
nbi=nbondterm(iti)
if (nbi.eq.1) then
C Zero the energy function and its derivative at 0 or pi.
call splinthet(theta(i),0.5d0*delta,ss,ssd)
it=itype(i-1)
+ ichir1=isign(1,itype(i-2))
+ ichir2=isign(1,itype(i))
+ if (itype(i-2).eq.10) ichir1=isign(1,itype(i-1))
+ if (itype(i).eq.10) ichir2=isign(1,itype(i-1))
+ if (itype(i-1).eq.10) then
+ itype1=isign(10,itype(i-2))
+ ichir11=isign(1,itype(i-2))
+ ichir12=isign(1,itype(i-2))
+ itype2=isign(10,itype(i))
+ ichir21=isign(1,itype(i))
+ ichir22=isign(1,itype(i))
+ endif
c if (i.gt.ithet_start .and.
c & (itel(i-1).eq.0 .or. itel(i-2).eq.0)) goto 1215
c if (i.gt.3 .and. (i.le.4 .or. itel(i-3).ne.0)) then
C In following comments this theta will be referred to as t_c.
thet_pred_mean=0.0d0
do k=1,2
- athetk=athet(k,it)
- bthetk=bthet(k,it)
+ athetk=athet(k,it,ichir1,ichir2)
+ bthetk=bthet(k,it,ichir1,ichir2)
+ if (it.eq.10) then
+ athetk=athet(k,itype1,ichir11,ichir12)
+ bthetk=bthet(k,itype2,ichir21,ichir22)
+ endif
thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k)
enddo
c write (iout,*) "thet_pred_mean",thet_pred_mean
thet_pred_mean=thet_pred_mean*ss+a0thet(it)
c write (iout,*) "thet_pred_mean",thet_pred_mean
C Derivatives of the "mean" values in gamma1 and gamma2.
- dthetg1=(-athet(1,it)*y(2)+athet(2,it)*y(1))*ss
- dthetg2=(-bthet(1,it)*z(2)+bthet(2,it)*z(1))*ss
+ dthetg1=(-athet(1,it,ichir1,ichir2)*y(2)
+ &+athet(2,it,ichir1,ichir2)*y(1))*ss
+ dthetg2=(-bthet(1,it,ichir1,ichir2)*z(2)
+ & +bthet(2,it,ichir1,ichir2)*z(1))*ss
+ if (it.eq.10) then
+ dthetg1=(-athet(1,itype1,ichir11,ichir12)*y(2)
+ &+athet(2,itype1,ichir11,ichir12)*y(1))*ss
+ dthetg2=(-bthet(1,itype2,ichir21,ichir22)*z(2)
+ & +bthet(2,itype2,ichir21,ichir22)*z(1))*ss
+ endif
if (theta(i).gt.pi-delta) then
call theteng(pi-delta,thet_pred_mean,theta0(it),f0,fprim0,
& E_tc0)
etheta=0.0D0
c write (iout,*) "ithetyp",(ithetyp(i),i=1,ntyp1)
do i=ithet_start,ithet_end
+ if (iabs(itype(i+1)).eq.20) iblock=2
+ if (iabs(itype(i+1)).ne.20) iblock=1
dethetai=0.0d0
dephii=0.0d0
dephii1=0.0d0
theti2=0.5d0*theta(i)
- ityp2=ithetyp(itype(i-1))
+ ityp2=ithetyp((itype(i-1)))
do k=1,nntheterm
coskt(k)=dcos(k*theti2)
sinkt(k)=dsin(k*theti2)
#else
phii=phi(i)
#endif
- ityp1=ithetyp(itype(i-2))
+ ityp1=ithetyp(iabs(itype(i-2)))
do k=1,nsingle
cosph1(k)=dcos(k*phii)
sinph1(k)=dsin(k*phii)
#else
phii1=phi(i+1)
#endif
- ityp3=ithetyp(itype(i))
+ ityp3=ithetyp((itype(i)))
do k=1,nsingle
cosph2(k)=dcos(k*phii1)
sinph2(k)=dsin(k*phii1)
c write (iout,*) "i",i," ityp1",itype(i-2),ityp1,
c & " ityp2",itype(i-1),ityp2," ityp3",itype(i),ityp3
c call flush(iout)
- ethetai=aa0thet(ityp1,ityp2,ityp3)
+ ethetai=aa0thet(ityp1,ityp2,ityp3,iblock)
do k=1,ndouble
do l=1,k-1
ccl=cosph1(l)*cosph2(k-l)
enddo
endif
do k=1,ntheterm
- ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3)*sinkt(k)
- dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3)
+ ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3,iblock)*sinkt(k)
+ dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3,iblock)
& *coskt(k)
if (lprn)
- & write (iout,*) "k",k," aathet",aathet(k,ityp1,ityp2,ityp3),
+ & write (iout,*) "k",k," aathet",aathet(k,ityp1,ityp2,ityp3,
+ & iblock),
& " ethetai",ethetai
enddo
if (lprn) then
endif
do m=1,ntheterm2
do k=1,nsingle
- aux=bbthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)
- & +ccthet(k,m,ityp1,ityp2,ityp3)*sinph1(k)
- & +ddthet(k,m,ityp1,ityp2,ityp3)*cosph2(k)
- & +eethet(k,m,ityp1,ityp2,ityp3)*sinph2(k)
+ aux=bbthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)
+ & +ccthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k)
+ & +ddthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)
+ & +eethet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k)
ethetai=ethetai+sinkt(m)*aux
dethetai=dethetai+0.5d0*m*aux*coskt(m)
dephii=dephii+k*sinkt(m)*(
- & ccthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)-
- & bbthet(k,m,ityp1,ityp2,ityp3)*sinph1(k))
+ & ccthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)-
+ & bbthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k))
dephii1=dephii1+k*sinkt(m)*(
- & eethet(k,m,ityp1,ityp2,ityp3)*cosph2(k)-
- & ddthet(k,m,ityp1,ityp2,ityp3)*sinph2(k))
+ & eethet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)-
+ & ddthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k))
if (lprn)
& write (iout,*) "m",m," k",k," bbthet",
- & bbthet(k,m,ityp1,ityp2,ityp3)," ccthet",
- & ccthet(k,m,ityp1,ityp2,ityp3)," ddthet",
- & ddthet(k,m,ityp1,ityp2,ityp3)," eethet",
- & eethet(k,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ & bbthet(k,m,ityp1,ityp2,ityp3,iblock)," ccthet",
+ & 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
enddo
enddo
if (lprn)
do m=1,ntheterm3
do k=2,ndouble
do l=1,k-1
- aux=ffthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)
+ aux=ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)
ethetai=ethetai+sinkt(m)*aux
dethetai=dethetai+0.5d0*m*coskt(m)*aux
dephii=dephii+l*sinkt(m)*(
- & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)-
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)-
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
dephii1=dephii1+(k-l)*sinkt(m)*(
- & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)-
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)-
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
if (lprn) then
write (iout,*) "m",m," k",k," l",l," ffthet",
- & ffthet(l,k,m,ityp1,ityp2,ityp3),
- & ffthet(k,l,m,ityp1,ityp2,ityp3)," ggthet",
- & ggthet(l,k,m,ityp1,ityp2,ityp3),
- & ggthet(k,l,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ & ffthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)," ggthet",
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)," ethetai",
+ & ethetai
write (iout,*) cosph1ph2(l,k)*sinkt(m),
& cosph1ph2(k,l)*sinkt(m),
& sinph1ph2(l,k)*sinkt(m),sinph1ph2(k,l)*sinkt(m)
enddo
enddo
10 continue
- if (lprn1) write (iout,'(i2,3f8.1,9h ethetai ,f10.5)')
- & i,theta(i)*rad2deg,phii*rad2deg,
+ c lprn1=.true.
+ if (lprn1) write (iout,'(a4,i2,3f8.1,9h ethetai ,f10.5)')
+ & 'ebe',i,theta(i)*rad2deg,phii*rad2deg,
& phii1*rad2deg,ethetai
+ c lprn1=.false.
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
do i=loc_start,loc_end
it=itype(i)
if (it.eq.10) goto 1
- nlobit=nlob(it)
+ nlobit=nlob(iabs(it))
c print *,'i=',i,' it=',it,' nlobit=',nlobit
c write (iout,*) 'i=',i,' ssa=',ssa,' ssad=',ssad
theti=theta(i+1)-pipol
do iii=-1,1
do j=1,nlobit
- expfac=dexp(bsc(j,it)-0.5D0*contr(j,iii)+emin)
+ expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j,iii)+emin)
cd print *,'j=',j,' expfac=',expfac
escloc_i=escloc_i+expfac
do k=1,3
dersc12=0.0d0
do j=1,nlobit
- expfac=dexp(bsc(j,it)-0.5D0*contr(j)+emin)
+ expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j)+emin)
escloc_i=escloc_i+expfac
do k=1,2
dersc(k)=dersc(k)+Ax(k,j)*expfac
cosfac=dsqrt(cosfac2)
sinfac2=0.5d0/(1.0d0-costtab(i+1))
sinfac=dsqrt(sinfac2)
- it=itype(i)
+ it=iabs(itype(i))
if (it.eq.10) goto 1
c
C Compute the axes of tghe local cartesian coordinates system; store in
y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
enddo
do j = 1,3
- z_prime(j) = -uz(j,i-1)
+ z_prime(j) = -uz(j,i-1)*dsign(1.0d0,dfloat(itype(i)))
enddo
c write (2,*) "i",i
c write (2,*) "x_prime",(x_prime(j),j=1,3)
C Compute the energy of the ith side cbain
C
c write (2,*) "xx",xx," yy",yy," zz",zz
- it=itype(i)
+ it=iabs(itype(i))
do j = 1,65
x(j) = sc_parmin(j,it)
enddo
Cc diagnostics - remove later
xx1 = dcos(alph(2))
yy1 = dsin(alph(2))*dcos(omeg(2))
- zz1 = -dsin(alph(2))*dsin(omeg(2))
+ zz1 = -dsign(1.0d0,itype(i))*dsin(alph(2))*dsin(omeg(2))
write(2,'(3f8.1,3f9.3,1x,3f9.3)')
& alph(2)*rad2deg,omeg(2)*rad2deg,theta(3)*rad2deg,xx,yy,zz,
& xx1,yy1,zz1
dZZ_Ci1(k)=0.0d0
dZZ_Ci(k)=0.0d0
do j=1,3
- dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)*dC_norm(j,i+nres)
- dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)*dC_norm(j,i+nres)
+ dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)
+ & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
+ dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)
+ & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
+
enddo
dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres))
etors=0.0D0
do i=iphi_start,iphi_end
if (itel(i-2).eq.0 .or. itel(i-1).eq.0) goto 1215
+ if (iabs(itype(i)).eq.20) then
+ iblock=2
+ else
+ iblock=1
+ endif
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
phii=phi(i)
gloci=0.0D0
C Regular cosine and sine terms
- do j=1,nterm(itori,itori1)
- v1ij=v1(j,itori,itori1)
- v2ij=v2(j,itori,itori1)
+ do j=1,nterm(itori,itori1,iblock)
+ v1ij=v1(j,itori,itori1,iblock)
+ v2ij=v2(j,itori,itori1,iblock)
cosphi=dcos(j*phii)
sinphi=dsin(j*phii)
etors=etors+v1ij*cosphi+v2ij*sinphi
C
cosphi=dcos(0.5d0*phii)
sinphi=dsin(0.5d0*phii)
- do j=1,nlor(itori,itori1)
+ do j=1,nlor(itori,itori1,iblock)
vl1ij=vlor1(j,itori,itori1)
vl2ij=vlor2(j,itori,itori1)
vl3ij=vlor3(j,itori,itori1)
gloci=gloci+vl1ij*(vl3ij*cosphi-vl2ij*sinphi)*pom
enddo
C Subtract the constant term
- etors=etors-v0(itori,itori1)
+ etors=etors-v0(itori,itori1,iblock)
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,
- & (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6)
+ & (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)
1215 continue
phii1=phi(i+1)
gloci1=0.0D0
gloci2=0.0D0
+ iblock=1
+ if (iabs(itype(i+1)).eq.20) iblock=2
C Regular cosine and sine terms
- do j=1,ntermd_1(itori,itori1,itori2)
- v1cij=v1c(1,j,itori,itori1,itori2)
- v1sij=v1s(1,j,itori,itori1,itori2)
- v2cij=v1c(2,j,itori,itori1,itori2)
- v2sij=v1s(2,j,itori,itori1,itori2)
+c c do j=1,ntermd_1(itori,itori1,itori2,iblock)
+c v1cij=v1c(1,j,itori,itori1,itori2,iblock)
+c v1sij=v1s(1,j,itori,itori1,itori2,iblock)
+c v2cij=v1c(2,j,itori,itori1,itori2,iblock)
+c v2sij=v1s(2,j,itori,itori1,itori2,iblock)
+ do j=1,ntermd_1(itori,itori1,itori2,iblock)
+ v1cij=v1c(1,j,itori,itori1,itori2,iblock)
+ v1sij=v1s(1,j,itori,itori1,itori2,iblock)
+ v2cij=v1c(2,j,itori,itori1,itori2,iblock)
+ v2sij=v1s(2,j,itori,itori1,itori2,iblock)
+
cosphi1=dcos(j*phii)
sinphi1=dsin(j*phii)
cosphi2=dcos(j*phii1)
gloci1=gloci1+j*(v1sij*cosphi1-v1cij*sinphi1)
gloci2=gloci2+j*(v2sij*cosphi2-v2cij*sinphi2)
enddo
- do k=2,ntermd_2(itori,itori1,itori2)
+ do k=2,ntermd_2(itori,itori1,itori2,iblock)
do l=1,k-1
- v1cdij = v2c(k,l,itori,itori1,itori2)
- v2cdij = v2c(l,k,itori,itori1,itori2)
- v1sdij = v2s(k,l,itori,itori1,itori2)
- v2sdij = v2s(l,k,itori,itori1,itori2)
+ v1cdij = v2c(k,l,itori,itori1,itori2,iblock)
+ v2cdij = v2c(l,k,itori,itori1,itori2,iblock)
+ v1sdij = v2s(k,l,itori,itori1,itori2,iblock)
+ v2sdij = v2s(l,k,itori,itori1,itori2,iblock)
cosphi1p2=dcos(l*phii+(k-l)*phii1)
cosphi1m2=dcos(l*phii-(k-l)*phii1)
sinphi1p2=dsin(l*phii+(k-l)*phii1)
esccor=0.0D0
do i=itau_start,itau_end
esccor_ii=0.0D0
- isccori=isccortyp(itype(i-2))
- isccori1=isccortyp(itype(i-1))
+ isccori=isccortyp((itype(i-2)))
+ isccori1=isccortyp((itype(i-1)))
phii=phi(i)
cccc Added 9 May 2012
cc Tauangle is torsional engle depending on the value of first digit
c 3 = SC...Ca...Ca...SCi
gloci=0.0D0
if (((intertyp.eq.3).and.((itype(i-2).eq.10).or.
- & (itype(i-1).eq.10).or.(itype(i-2).eq.21).or.
- & (itype(i-1).eq.21)))
+ & (itype(i-1).eq.10).or.(itype(i-2).eq.ntyp1).or.
+ & (itype(i-1).eq.ntyp1)))
& .or. ((intertyp.eq.1).and.((itype(i-2).eq.10)
- & .or.(itype(i-2).eq.21)))
+ & .or.(itype(i-2).eq.ntyp1)))
& .or.((intertyp.eq.2).and.((itype(i-1).eq.10).or.
- & (itype(i-1).eq.21)))) cycle
- 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))
+ & (itype(i-1).eq.ntyp1)))) cycle
+ if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.ntyp1)) cycle
+ if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.ntyp1))
& cycle
do j=1,nterm_sccor(isccori,isccori1)
v1ij=v1sccor(j,intertyp,isccori,isccori1)
& 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)
- gsccor_loc(i-3)=gsccor_loc(i-3)+gloci
+c gsccor_loc(i-3)=gsccor_loc(i-3)+gloci
enddo !intertyp
enddo
c do i=1,nres
integer dimen1,dimen2,atom,indx
double precision buffer(dimen1,dimen2)
double precision zapas
- common /contacts_hb/ zapas(3,20,maxres,7),
- & facont_hb(20,maxres),ees0p(20,maxres),ees0m(20,maxres),
- & num_cont_hb(maxres),jcont_hb(20,maxres)
+ common /contacts_hb/ zapas(3,ntyp,maxres,7),
+ & facont_hb(ntyp,maxres),ees0p(ntyp,maxres),ees0m(ntyp,maxres),
+ & num_cont_hb(maxres),jcont_hb(ntyp,maxres)
num_kont=num_cont_hb(atom)
do i=1,num_kont
do k=1,7
integer dimen1,dimen2,atom,indx
double precision buffer(dimen1,dimen2)
double precision zapas
- common /contacts_hb/ zapas(3,20,maxres,7),
- & facont_hb(20,maxres),ees0p(20,maxres),ees0m(20,maxres),
- & num_cont_hb(maxres),jcont_hb(20,maxres)
+ common /contacts_hb/ zapas(3,ntyp,maxres,7),
+ & facont_hb(ntyp,maxres),ees0p(ntyp,maxres),
+ & ees0m(ntyp,maxres),
+ & num_cont_hb(maxres),jcont_hb(ntyp,maxres)
num_kont=buffer(1,indx+26)
num_kont_old=num_cont_hb(atom)
num_cont_hb(atom)=num_kont+num_kont_old
#=========================================
-# Build the binaries
+# Build the binaries (used by "make")
#=========================================
add_executable(xdrf2pdb ${UNRES_XDRF_XDRF2PDB_SRC} )
+ set_property(TARGET xdrf2pdb PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin )
target_link_libraries( xdrf2pdb xdrf )
add_executable(xdrf2pdb-m ${UNRES_XDRF_XDRF2PDB-M_SRC} )
+ set_property(TARGET xdrf2pdb-m PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin )
target_link_libraries( xdrf2pdb-m xdrf )
add_executable(xdrf2x ${UNRES_XDRF_XDRF2X_SRC} )
+ set_property(TARGET xdrf2x PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin )
target_link_libraries( xdrf2x xdrf )
add_executable(xdrf2ang ${UNRES_XDRF_XDRF2XANG_SRC} )
+ set_property(TARGET xdrf2ang PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin )
target_link_libraries( xdrf2ang xdrf )
#=========================================
- # INSTALL (used by "make install")
+ # Install Path
#=========================================
- install(TARGETS xdrf2pdb RUNTIME DESTINATION unrespack/bin)
- install(TARGETS xdrf2pdb-m RUNTIME DESTINATION unrespack/bin)
- install(TARGETS xdrf2x RUNTIME DESTINATION unrespack/bin)
- install(TARGETS xdrf2ang RUNTIME DESTINATION unrespack/bin)
-install(TARGETS xdrf2pdb DESTINATION ${CMAKE_INSTALL_PREFIX})
-install(TARGETS xdrf2pdb-m DESTINATION ${CMAKE_INSTALL_PREFIX})
-install(TARGETS xdrf2x DESTINATION ${CMAKE_INSTALL_PREFIX})
-install(TARGETS xdrf2ang DESTINATION ${CMAKE_INSTALL_PREFIX})
++install(TARGETS xdrf2pdb DESTINATION ${CMAKE_INSTALL_PREFIX})
++install(TARGETS xdrf2pdb-m DESTINATION ${CMAKE_INSTALL_PREFIX})
++install(TARGETS xdrf2x DESTINATION ${CMAKE_INSTALL_PREFIX})
++install(TARGETS xdrf2ang DESTINATION ${CMAKE_INSTALL_PREFIX})
+
#=========================================
- # TESTS (used by "ctest")
+ # TESTS
#=========================================
projects / unres.git / commitdiff