dynamic dissulfides with finegrain parallelization

diff --git a/bin/unres/MD/unres_gfortran_single_E0LL2Y.exe b/bin/unres/MD/unres_gfortran_single_E0LL2Y.exe
index 4e086ce..98d46b9 100755 (executable)
Binary files a/bin/unres/MD/unres_gfortran_single_E0LL2Y.exe and b/bin/unres/MD/unres_gfortran_single_E0LL2Y.exe differ

diff --git a/bin/unres/MD/unres_gfortran_single_GAB.exe b/bin/unres/MD/unres_gfortran_single_GAB.exe
index fbdcabb..9259f78 100755 (executable)
Binary files a/bin/unres/MD/unres_gfortran_single_GAB.exe and b/bin/unres/MD/unres_gfortran_single_GAB.exe differ

diff --git a/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe b/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe
new file mode 100755 (executable)
index 0000000..c9769dd
Binary files /dev/null and b/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe differ

diff --git a/bin/unres/MD/unres_ifort_MPICH_GAB.exe b/bin/unres/MD/unres_ifort_MPICH_GAB.exe
new file mode 100755 (executable)
index 0000000..c8defa0
Binary files /dev/null and b/bin/unres/MD/unres_ifort_MPICH_GAB.exe differ

diff --git a/bin/unres/MD/unres_ifort_single_E0LL2Y.exe b/bin/unres/MD/unres_ifort_single_E0LL2Y.exe
index 651864e..6b3cf7c 100755 (executable)
Binary files a/bin/unres/MD/unres_ifort_single_E0LL2Y.exe and b/bin/unres/MD/unres_ifort_single_E0LL2Y.exe differ

diff --git a/bin/unres/MD/unres_ifort_single_GAB.exe b/bin/unres/MD/unres_ifort_single_GAB.exe
new file mode 100755 (executable)
index 0000000..93d0028
Binary files /dev/null and b/bin/unres/MD/unres_ifort_single_GAB.exe differ

diff --git a/source/unres/src_MD/Makefile_lnx_ifc10_opteron b/source/unres/src_MD/Makefile_lnx_ifc10_opteron
deleted file mode 100644 (file)
index 13c3249..0000000
--- a/source/unres/src_MD/Makefile_lnx_ifc10_opteron
+++ /dev/null
@@ -1,143 +0,0 @@
-CPPFLAGS = -DPROCOR -DLINUX -DUNRES -DMP -DMPI -DPGI -DISNAN \
-           -DSPLITELE -DAMD64 -DLANG0 
-#           -DCRYST_BOND -DCRYST_THETA -DCRYST_SC 
-#-DCRYST_TOR
-# -DPROCOR
-#           -DTSCSC
-#-DTIMING \
-# -DCRYST_BOND -DCRYST_THETA -DCRYST_SC 
-# -DMOMENT
-#-DPARVEC 
-#-DPARINT -DPARINTDER  
-
-INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh
-
-
-FC= ifort
-
-OPT =  -O3 -ip -w 
-
-FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include 
-FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)/include 
-FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include  
-FFLAGSE = -c -w -O3 -ipo -ipo_obj  -opt_report -I$(INSTALL_DIR)/include
-
-
-BIN = ../bin/unres_Tc_procor_new_em64_nh_hremd_92110.exe
-LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf_em64/libxdrf.a -lpthread 
-
-ARCH = LINUX
-PP = /lib/cpp -P
-
-
-all: unres
-
-.SUFFIXES: .F
-.F.o:
-       ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
-
-
-object = unres.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \
-        matmult.o readrtns_CSA.o parmread.o gen_rand_conf.o printmat.o map.o \
-        pinorm.o randgens.o rescode.o intcor.o timing.o misc.o intlocal.o \
-        cartder.o checkder_p.o econstr_local.o energy_p_new_barrier.o \
-       energy_p_new-sep_barrier.o gradient_p.o minimize_p.o sumsld.o \
-        cored.o rmdd.o geomout.o readpdb.o regularize.o thread.o fitsq.o mcm.o \
-        mc.o bond_move.o refsys.o check_sc_distr.o check_bond.o contact.o djacob.o \
-        eigen.o blas.o add.o entmcm.o minim_mcmf.o \
-        together.o csa.o minim_jlee.o shift.o diff12.o bank.o newconf.o ran.o \
-        indexx.o MP.o compare_s1.o prng_32.o \
-        test.o banach.o distfit.o rmsd.o elecont.o dihed_cons.o \
-        sc_move.o local_move.o \
-        intcartderiv.o lagrangian_lesyng.o\
-       stochfric.o kinetic_lesyng.o MD_A-MTS.o moments.o int_to_cart.o \
-        surfatom.o sort.o muca_md.o MREMD.o rattle.o gauss.o energy_split-sep.o \
-        q_measure.o gnmr1.o
-
-unres: ${object} 
-       cc -o compinfo compinfo.c
-       ./compinfo | true
-       ${FC} ${FFLAGS} cinfo.f
-       ${FC} ${OPT} ${object} cinfo.o ${LIBS}  -o ${BIN}
-
-
-clean:
-       /bin/rm *.o *.il
-
-newconf.o: newconf.f
-       ${FC} ${FFLAGS} ${CPPFLAGS} newconf.f
-
-bank.o: bank.F
-       ${FC} ${FFLAGS} ${CPPFLAGS} bank.F
-
-diff12.o: diff12.f
-       ${FC} ${FFLAGS} ${CPPFLAGS} diff12.f
-
-csa.o: csa.f
-       ${FC} ${FFLAGS} ${CPPFLAGS} csa.f
-
-shift.o: shift.F
-       ${FC} ${FFLAGS} ${CPPFLAGS} shift.F
-
-ran.o: ran.f
-       ${FC} ${FFLAGS} ${CPPFLAGS} ran.f
-
-together.o: together.F
-       ${FC} ${FFLAGS} ${CPPFLAGS} together.F
-
-test.o: test.F
-       ${FC} ${FFLAGS} ${CPPFLAGS} test.F
-
-chainbuild.o: chainbuild.F
-       ${FC} ${FFLAGS} ${CPPFLAGS} chainbuild.F
-
-matmult.o: matmult.f
-       ${FC} ${FFLAGS} ${CPPFLAGS} matmult.f
-
-parmread.o : parmread.F
-       ${FC} ${FFLAGS} ${CPPFLAGS} parmread.F
-
-intcor.o : intcor.f
-       ${FC} ${FFLAGS} ${CPPFLAGS} intcor.f
-
-cartder.o : cartder.F
-       ${FC} ${FFLAGS} ${CPPFLAGS} cartder.F
-
-readpdb.o : readpdb.F
-       ${FC} ${FFLAGS2} ${CPPFLAGS} readpdb.F
-
-sumsld.o : sumsld.f
-       ${FC} ${FFLAGS} ${CPPFLAGS} sumsld.f
-        
-cored.o : cored.f
-       ${FC} ${FFLAGS1} ${CPPFLAGS} cored.f
- 
-rmdd.o : rmdd.f
-       ${FC} ${FFLAGS} ${CPPFLAGS} rmdd.f
-
-energy_p_new_barrier.o : energy_p_new_barrier.F
-       ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new_barrier.F
-
-gradient_p.o : gradient_p.F
-       ${FC} ${FFLAGSE} ${CPPFLAGS} gradient_p.F
-
-energy_p_new-sep_barrier.o : energy_p_new-sep_barrier.F
-       ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new-sep_barrier.F
-
-lagrangian_lesyng.o : lagrangian_lesyng.F
-       ${FC} ${FFLAGSE} ${CPPFLAGS} lagrangian_lesyng.F
-
-MD_A-MTS.o : MD_A-MTS.F
-       ${FC} ${FFLAGSE} ${CPPFLAGS} MD_A-MTS.F
-
-blas.o : blas.f
-       ${FC} ${FFLAGS1} blas.f
-
-add.o : add.f
-       ${FC} ${FFLAGS1} add.f
-
-eigen.o : eigen.f
-       ${FC} ${FFLAGS2} eigen.f
-
-proc_proc.o: proc_proc.c
-       ${CC} ${CFLAGS} proc_proc.c

diff --git a/source/unres/src_MD/Makefile_lnx_ifc10_opteron_oldparm b/source/unres/src_MD/Makefile_lnx_ifc10_opteron_oldparm
deleted file mode 100644 (file)
index d155fa2..0000000
--- a/source/unres/src_MD/Makefile_lnx_ifc10_opteron_oldparm
+++ /dev/null
@@ -1,143 +0,0 @@
-CPPFLAGS = -DPROCOR -DLINUX -DUNRES -DMP -DMPI -DPGI -DISNAN \
-           -DSPLITELE -DAMD64 -DLANG0 \
-       -DCRYST_BOND -DCRYST_THETA -DCRYST_SC 
-#-DCRYST_TOR
-# -DPROCOR
-#           -DTSCSC
-#-DTIMING \
-# -DCRYST_BOND -DCRYST_THETA -DCRYST_SC 
-# -DMOMENT
-#-DPARVEC 
-#-DPARINT -DPARINTDER  
-
-INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh
-
-
-FC= ifort
-
-OPT =  -O3 -ip -w 
-
-FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include 
-FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)/include 
-FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include  
-FFLAGSE = -c -w -O3 -ipo -ipo_obj  -opt_report -I$(INSTALL_DIR)/include
-
-
-BIN = ../bin/unres_Tc_procor_old_em64_nh_hremd_92110.exe
-LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf_em64/libxdrf.a -lpthread 
-
-ARCH = LINUX
-PP = /lib/cpp -P
-
-
-all: unres
-
-.SUFFIXES: .F
-.F.o:
-       ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
-
-
-object = unres.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \
-        matmult.o readrtns_CSA.o parmread.o gen_rand_conf.o printmat.o map.o \
-        pinorm.o randgens.o rescode.o intcor.o timing.o misc.o intlocal.o \
-        cartder.o checkder_p.o econstr_local.o energy_p_new_barrier.o \
-       energy_p_new-sep_barrier.o gradient_p.o minimize_p.o sumsld.o \
-        cored.o rmdd.o geomout.o readpdb.o regularize.o thread.o fitsq.o mcm.o \
-        mc.o bond_move.o refsys.o check_sc_distr.o check_bond.o contact.o djacob.o \
-        eigen.o blas.o add.o entmcm.o minim_mcmf.o \
-        together.o csa.o minim_jlee.o shift.o diff12.o bank.o newconf.o ran.o \
-        indexx.o MP.o compare_s1.o prng_32.o \
-        test.o banach.o distfit.o rmsd.o elecont.o dihed_cons.o \
-        sc_move.o local_move.o \
-        intcartderiv.o lagrangian_lesyng.o\
-       stochfric.o kinetic_lesyng.o MD_A-MTS.o moments.o int_to_cart.o \
-        surfatom.o sort.o muca_md.o MREMD.o rattle.o gauss.o energy_split-sep.o \
-        q_measure.o gnmr1.o
-
-unres: ${object} 
-       cc -o compinfo compinfo.c
-       ./compinfo | true
-       ${FC} ${FFLAGS} cinfo.f
-       ${FC} ${OPT} ${object} cinfo.o ${LIBS}  -o ${BIN}
-
-
-clean:
-       /bin/rm *.o *.il
-
-newconf.o: newconf.f
-       ${FC} ${FFLAGS} ${CPPFLAGS} newconf.f
-
-bank.o: bank.F
-       ${FC} ${FFLAGS} ${CPPFLAGS} bank.F
-
-diff12.o: diff12.f
-       ${FC} ${FFLAGS} ${CPPFLAGS} diff12.f
-
-csa.o: csa.f
-       ${FC} ${FFLAGS} ${CPPFLAGS} csa.f
-
-shift.o: shift.F
-       ${FC} ${FFLAGS} ${CPPFLAGS} shift.F
-
-ran.o: ran.f
-       ${FC} ${FFLAGS} ${CPPFLAGS} ran.f
-
-together.o: together.F
-       ${FC} ${FFLAGS} ${CPPFLAGS} together.F
-
-test.o: test.F
-       ${FC} ${FFLAGS} ${CPPFLAGS} test.F
-
-chainbuild.o: chainbuild.F
-       ${FC} ${FFLAGS} ${CPPFLAGS} chainbuild.F
-
-matmult.o: matmult.f
-       ${FC} ${FFLAGS} ${CPPFLAGS} matmult.f
-
-parmread.o : parmread.F
-       ${FC} ${FFLAGS} ${CPPFLAGS} parmread.F
-
-intcor.o : intcor.f
-       ${FC} ${FFLAGS} ${CPPFLAGS} intcor.f
-
-cartder.o : cartder.F
-       ${FC} ${FFLAGS} ${CPPFLAGS} cartder.F
-
-readpdb.o : readpdb.F
-       ${FC} ${FFLAGS2} ${CPPFLAGS} readpdb.F
-
-sumsld.o : sumsld.f
-       ${FC} ${FFLAGS} ${CPPFLAGS} sumsld.f
-        
-cored.o : cored.f
-       ${FC} ${FFLAGS1} ${CPPFLAGS} cored.f
- 
-rmdd.o : rmdd.f
-       ${FC} ${FFLAGS} ${CPPFLAGS} rmdd.f
-
-energy_p_new_barrier.o : energy_p_new_barrier.F
-       ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new_barrier.F
-
-gradient_p.o : gradient_p.F
-       ${FC} ${FFLAGSE} ${CPPFLAGS} gradient_p.F
-
-energy_p_new-sep_barrier.o : energy_p_new-sep_barrier.F
-       ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new-sep_barrier.F
-
-lagrangian_lesyng.o : lagrangian_lesyng.F
-       ${FC} ${FFLAGSE} ${CPPFLAGS} lagrangian_lesyng.F
-
-MD_A-MTS.o : MD_A-MTS.F
-       ${FC} ${FFLAGSE} ${CPPFLAGS} MD_A-MTS.F
-
-blas.o : blas.f
-       ${FC} ${FFLAGS1} blas.f
-
-add.o : add.f
-       ${FC} ${FFLAGS1} add.f
-
-eigen.o : eigen.f
-       ${FC} ${FFLAGS2} eigen.f
-
-proc_proc.o: proc_proc.c
-       ${CC} ${CFLAGS} proc_proc.c

diff --git a/source/unres/src_MD/Makefile_single_ifort b/source/unres/src_MD/Makefile_single_ifort
index 245206b..c651e39 100644 (file)
--- a/source/unres/src_MD/Makefile_single_ifort
+++ b/source/unres/src_MD/Makefile_single_ifort
@@ -43,7 +43,7 @@ object = unres.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \
         intcartderiv.o lagrangian_lesyng.o\
        stochfric.o kinetic_lesyng.o MD_A-MTS.o moments.o int_to_cart.o \
         surfatom.o sort.o muca_md.o MREMD.o rattle.o gauss.o energy_split-sep.o \
-        q_measure.o gnmr1.o test.o
+        q_measure.o gnmr1.o test.o ssMD.o
 
 GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES -DISNAN \
        -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC

diff --git a/source/unres/src_MD/cinfo.f b/source/unres/src_MD/cinfo.f
index 26b5cab..5d23d6b 100644 (file)
--- a/source/unres/src_MD/cinfo.f
+++ b/source/unres/src_MD/cinfo.f
@@ -1,10 +1,10 @@
 C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
-C 3 1 79
+C 3 1 92
       subroutine cinfo
       include 'COMMON.IOUNITS'
       write(iout,*)'++++ Compile info ++++'
-      write(iout,*)'Version 3.1 build 79'
-      write(iout,*)'compiled Sun Feb 17 14:00:16 2013'
+      write(iout,*)'Version 3.1 build 92'
+      write(iout,*)'compiled Mon Feb 18 04:11:12 2013'
       write(iout,*)'compiled by czarek@piasek3'
       write(iout,*)'OS name:    Linux '
       write(iout,*)'OS release: 2.6.32-42-generic '

diff --git a/source/unres/src_MD/energy_p_new_barrier.F b/source/unres/src_MD/energy_p_new_barrier.F
index 8a9a3eb..2557051 100644 (file)
--- a/source/unres/src_MD/energy_p_new_barrier.F
+++ b/source/unres/src_MD/energy_p_new_barrier.F
@@ -1589,6 +1589,8 @@ C
             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)

diff --git a/source/unres/src_MD/parmread.F b/source/unres/src_MD/parmread.F
index 62a0ddf..030d64e 100644 (file)
--- a/source/unres/src_MD/parmread.F
+++ b/source/unres/src_MD/parmread.F
@@ -565,7 +565,8 @@ cc maxinter is maximum interaction sites
       do l=1,maxinter    
       do i=1,nsccortyp
        do j=1,nsccortyp
-         read (isccor,*,end=1113,err=1113) nterm_sccor(i,j),nlor_sccor(i,j)
+         read (isccor,*,end=1113,err=1113) nterm_sccor(i,j),
+     &             nlor_sccor(i,j)
           v0ijsccor=0.0d0
           si=-1.0d0
   

diff --git a/source/unres/src_MD/readrtns.F b/source/unres/src_MD/readrtns.F
index 10cde78..332a2f7 100644 (file)
--- a/source/unres/src_MD/readrtns.F
+++ b/source/unres/src_MD/readrtns.F
@@ -1251,18 +1251,6 @@ C Generate distance constraints, if the PDB structure is to be regularized.
         write (iout,'(20i4)') (iss(i),i=1,ns)
        if (dyn_ss) then
           write(iout,*)"Running with dynamic disulfide-bond formation"
-          do i=nss+1,nhpb
-            ihpb(i-nss)=ihpb(i)
-            jhpb(i-nss)=jhpb(i)
-            forcon(i-nss)=forcon(i)
-            dhpb(i-nss)=dhpb(i)
-          enddo
-          nhpb=nhpb-nss
-          nss=0
-          call hpb_partition
-          do i=1,ns
-            dyn_ss_mask(iss(i))=.true.
-          enddo
        else
         write (iout,'(/a/)') 'Pre-formed links are:' 
        do i=1,nss
@@ -1270,14 +1258,27 @@ C Generate distance constraints, if the PDB structure is to be regularized.
          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
        write (iout,'(a)')
        endif
       endif
+      if (ns.gt.0.and.dyn_ss) then
+          do i=nss+1,nhpb
+            ihpb(i-nss)=ihpb(i)
+            jhpb(i-nss)=jhpb(i)
+            forcon(i-nss)=forcon(i)
+            dhpb(i-nss)=dhpb(i)
+          enddo
+          nhpb=nhpb-nss
+          nss=0
+          call hpb_partition
+          do i=1,ns
+            dyn_ss_mask(iss(i))=.true.
+          enddo
+      endif
       if (i2ndstr.gt.0) call secstrp2dihc
 c      call geom_to_var(nvar,x)
 c      call etotal(energia(0))