From: Adam Sieradzan Date: Wed, 17 Dec 2014 09:48:55 +0000 (+0100) Subject: Merge branch 'master' of mmka:unres X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=commitdiff_plain;h=78c6b598700d2c701af6532afb20ebc905a0b8ef Merge branch 'master' of mmka:unres Conflicts: .gitignore bin/cluster/unres_clustMD-mult_MPICH-GAB.exe bin/unres/MD/unres_gfortran_single_GAB.exe bin/unres/MD/unres_ifort_single_GAB.exe bin/unres/MINIM/unres_ifort_MIN_single_E0LL2Y.exe bin/unres/MINIM/unres_ifort_MIN_single_GAB.exe bin/unres_clustMD_MPI-oldparm bin/wham/wham_multparm-ham_rep-oldparm source/cluster/wham/src/COMMON.SCCOR source/cluster/wham/src/Makefile source/unres/src_MD-M/Makefile source/unres/src_MD-M/energy_p_new_barrier.F source/unres/src_MD-M/stochfric.F source/unres/src_MD/cinfo.f source/wham/src-M/Makefile source/wham/src/DIMENSIONS.FREE --- 78c6b598700d2c701af6532afb20ebc905a0b8ef diff --cc .gitignore index 442c6c4,2d9541f..0604082 --- a/.gitignore +++ b/.gitignore @@@ -12,8 -12,7 +12,9 @@@ cinfo. # ignore build dir build/ build2/ +build_*/ +period_*/ + # latex files in documentation doc/*/*.aux doc/*/*.log diff --cc CMakeLists.txt index 9b6b6b8,5b824dd..89bd8ef --- a/CMakeLists.txt +++ b/CMakeLists.txt @@@ -207,10 -182,8 +180,9 @@@ if(UNRES_NA_MMCE # 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/cluster/wham/src) add_subdirectory(source/cluster/wham/src-M) endif (Fortran_COMPILER_NAME STREQUAL "ifort") @@@ -229,9 -202,7 +201,8 @@@ else( 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) add_subdirectory(source/wham/src-M) add_subdirectory(source/cluster/wham/src) diff --cc bin/unres/MINIM/unres_ifort_MIN_single_GAB.exe index 6e1ebca,8fbedcf..0000000 deleted file mode 100755,100755 Binary files differ diff --cc source/unres/src_MD-M/energy_p_new_barrier.F index 27c5f1d,2097265..6976071 --- a/source/unres/src_MD-M/energy_p_new_barrier.F +++ b/source/unres/src_MD-M/energy_p_new_barrier.F @@@ -296,10 -301,9 +301,11 @@@ 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 c print *," Processor",myrank," left SUM_ENERGY" #ifdef TIMING time_sumene=time_sumene+MPI_Wtime()-time00 @@@ -435,9 -439,9 +441,9 @@@ cMS$ATTRIBUTES C :: proc_pro #endif #ifdef MPI include 'mpif.h' + #endif 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.FFIELD' @@@ -1439,9 -1416,15 +1446,15 @@@ C Calculate SC interaction energy C do iint=1,nint_gr(i) do j=istart(i,iint),iend(i,iint) + IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN + call dyn_ssbond_ene(i,j,evdwij) + evdw=evdw+evdwij + if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') + & '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, @@@ -4280,13 -4035,19 +4294,19 @@@ C iii and jjj point to the residues fo iii=ii jjj=jj endif - cd write (iout,*) "i",i," ii",ii," iii",iii," jj",jj," jjj",jjj + c write (iout,*) "i",i," ii",ii," iii",iii," jj",jj," jjj",jjj, + c & dhpb(i),dhpb1(i),forcon(i) C 24/11/03 AL: SS bridges handled separately because of introducing a specific C distance and angle dependent SS bond potential. + if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and. + & iabs(itype(jjj)).eq.1) then + cmc if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then + 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 - if (ii.gt.nres - & .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then call ssbond_ene(iii,jjj,eij) ehpb=ehpb+2*eij + endif cd write (iout,*) "eij",eij else C Calculate the distance between the two points and its difference from the diff --cc source/unres/src_MD/COMMON.SCCOR index 154de36,8de6d3c..7952bd1 --- a/source/unres/src_MD/COMMON.SCCOR +++ b/source/unres/src_MD/COMMON.SCCOR @@@ -2,14 -2,10 +2,14 @@@ cc Parameters of the SCCOR ter 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),