Merge branch 'devel' of mmka:unres into devel

diff --git a/.gitignore b/.gitignore
index 7fe4126..8b33225 100644 (file)
--- a/.gitignore
+++ b/.gitignore
@@ -22,3 +22,5 @@ mapcheck/
 run/
 sympcheck/
 compinfo
+DIL/
+bin/unres/MD/unres_ifort_MPICH_GAB_czyt.exe

diff --git a/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe b/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe
deleted file mode 100755 (executable)
index 5a2cb0a..0000000
Binary files a/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe and /dev/null differ

diff --git a/bin/unres/MD/unres_ifort_MPICH_GAB.exe b/bin/unres/MD/unres_ifort_MPICH_GAB.exe
index 2ffec15..da4efff 100755 (executable)
Binary files a/bin/unres/MD/unres_ifort_MPICH_GAB.exe and b/bin/unres/MD/unres_ifort_MPICH_GAB.exe differ

diff --git a/bin/unres/MD/unres_ifort_single_GAB.exe b/bin/unres/MD/unres_ifort_single_GAB.exe
index 66109ea..228bcd7 100755 (executable)
Binary files a/bin/unres/MD/unres_ifort_single_GAB.exe and b/bin/unres/MD/unres_ifort_single_GAB.exe differ

diff --git a/bin/wham/wham_ifort_MPICH_E0LL2Y.exe b/bin/wham/wham_ifort_MPICH_E0LL2Y.exe
index 508b4f6..b26354a 100755 (executable)
Binary files a/bin/wham/wham_ifort_MPICH_E0LL2Y.exe and b/bin/wham/wham_ifort_MPICH_E0LL2Y.exe differ

diff --git a/bin/wham/wham_multparm-ham_rep-oldparm b/bin/wham/wham_multparm-ham_rep-oldparm
index 2ddc49d..6f60701 100755 (executable)
Binary files a/bin/wham/wham_multparm-ham_rep-oldparm and b/bin/wham/wham_multparm-ham_rep-oldparm differ

diff --git a/source/cluster/wham/src/COMMON.SCCOR b/source/cluster/wham/src/COMMON.SCCOR
index ca6210f..0857cd8 100644 (file)
--- a/source/cluster/wham/src/COMMON.SCCOR
+++ b/source/cluster/wham/src/COMMON.SCCOR
@@ -7,10 +7,11 @@ cc Parameters of the SCCOR term
       common/sccor/v1sccor(maxterm_sccor,3,20,20),
      &    v2sccor(maxterm_sccor,3,20,20),
      &    v0sccor(maxterm_sccor,20),
-     &    nterm_sccor(ntyp,ntyp),isccortyp(ntyp),nsccortyp,
-     &    nlor_sccor(ntyp,ntyp),vlor1sccor(maxterm_sccor,20,20),
+     &    vlor1sccor(maxterm_sccor,20,20),
      &    vlor2sccor(maxterm_sccor,20,20),
      &    vlor3sccor(maxterm_sccor,20,20),gloc_sc(3,0:maxres2,10),
      &    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)
+     &    domicron(3,3,3,maxres2),
+     &    nterm_sccor(ntyp,ntyp),isccortyp(ntyp),nsccortyp,
+     &    nlor_sccor(ntyp,ntyp)

diff --git a/source/cluster/wham/src/int_from_cart1.f b/source/cluster/wham/src/int_from_cart1.f
index 4f768e1..7d266de 100644 (file)
--- a/source/cluster/wham/src/int_from_cart1.f
+++ b/source/cluster/wham/src/int_from_cart1.f
@@ -24,6 +24,9 @@
         enddo
         be=0.0D0
         if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
+        if (i.gt.2) tauangle(3,i+1)=beta(i+nres-1,i-1,i,i+nres)
+        if (i.gt.2) tauangle(1,i+1)=beta(i-1+nres,i-1,i,i+1)
+        if (i.gt.2) tauangle(2,i+1)=beta(i-2,i-1,i,i+nres)
         omeg(i)=beta(nres+i,i,maxres2,i+1)
         theta(i+1)=alpha(i-1,i,i+1)
         alph(i)=alpha(nres+i,i,maxres2)

diff --git a/source/unres/src_MD/COMMON.SCCOR b/source/unres/src_MD/COMMON.SCCOR
index ca6210f..ccfe0c4 100644 (file)
--- a/source/unres/src_MD/COMMON.SCCOR
+++ b/source/unres/src_MD/COMMON.SCCOR
@@ -6,7 +6,7 @@ cc Parameters of the SCCOR term
       integer nterm_sccor,isccortyp,nsccortyp,nlor_sccor
       common/sccor/v1sccor(maxterm_sccor,3,20,20),
      &    v2sccor(maxterm_sccor,3,20,20),
-     &    v0sccor(maxterm_sccor,20),
+     &    v0sccor(ntyp,ntyp),
      &    nterm_sccor(ntyp,ntyp),isccortyp(ntyp),nsccortyp,
      &    nlor_sccor(ntyp,ntyp),vlor1sccor(maxterm_sccor,20,20),
      &    vlor2sccor(maxterm_sccor,20,20),

diff --git a/source/unres/src_MD/Makefile b/source/unres/src_MD/Makefile
deleted file mode 120000 (symlink)
index 6584c5e..0000000
--- a/source/unres/src_MD/Makefile
+++ /dev/null
@@ -1 +0,0 @@
-Makefile_single_ifort
\ No newline at end of file

diff --git a/source/unres/src_MD/Makefile_MPICH_ifort b/source/unres/src_MD/Makefile_MPICH_ifort
index ec1bcf3..4505541 100644 (file)
--- a/source/unres/src_MD/Makefile_MPICH_ifort
+++ b/source/unres/src_MD/Makefile_MPICH_ifort
@@ -1,3 +1,4 @@
+###################################################################
 INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh
 
 

diff --git a/source/unres/src_MD/cinfo.f b/source/unres/src_MD/cinfo.f
deleted file mode 100644 (file)
index afd4fb8..0000000
--- a/source/unres/src_MD/cinfo.f
+++ /dev/null
@@ -1,34 +0,0 @@
-C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
-C 2 5 297
-      subroutine cinfo
-      include 'COMMON.IOUNITS'
-      write(iout,*)'++++ Compile info ++++'
-      write(iout,*)'Version 2.5 build 297'
-      write(iout,*)'compiled Mon Jun 25 07:29:48 2012'
-      write(iout,*)'compiled by aks255@matrix.chem.cornell.edu'
-      write(iout,*)'OS name:    Linux '
-      write(iout,*)'OS release: 2.6.34.9-69.fc13.x86_64 '
-      write(iout,*)'OS version:',
-     & ' #1 SMP Tue May 3 09:23:03 UTC 2011 '
-      write(iout,*)'flags:'
-      write(iout,*)'INSTALL_DIR = /users/software/mpich-1.2.7p1_int...'
-      write(iout,*)'FC= ifort'
-      write(iout,*)'OPT =  -g -ip -w -CB '
-      write(iout,*)'FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include '
-      write(iout,*)'FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)...'
-      write(iout,*)'FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include'
-      write(iout,*)'FFLAGSE = -c -w -O3 -ipo -ipo_obj  -opt_report ...'
-      write(iout,*)'CC = cc'
-      write(iout,*)'CFLAGS = -DLINUX -DPGI -c'
-      write(iout,*)'OPT =  -O3 -ip -w'
-      write(iout,*)'LIBS = -Lxdrf -lxdrf'
-      write(iout,*)'ARCH = LINUX'
-      write(iout,*)'PP = /lib/cpp -P'
-      write(iout,*)'object = unres.o arcos.o cartprint.o chainbuild...'
-      write(iout,*)'GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES ...'
-      write(iout,*)'GAB: BIN = ../../../bin/unres/MD/unres_ifort_si...'
-      write(iout,*)'E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR...'
-      write(iout,*)'E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort...'
-      write(iout,*)'++++ End of compile info ++++'
-      return
-      end

diff --git a/source/unres/src_MD/tmptmp b/source/unres/src_MD/tmptmp
deleted file mode 100644 (file)
index fb6f043..0000000
--- a/source/unres/src_MD/tmptmp
+++ /dev/null
@@ -1 +0,0 @@
-aks255

diff --git a/source/unres/src_MD/xdrf b/source/unres/src_MD/xdrf
new file mode 120000 (symlink)
index 0000000..26825c5
--- /dev/null
+++ b/source/unres/src_MD/xdrf
@@ -0,0 +1 @@
+../../lib/xdrf
\ No newline at end of file

diff --git a/source/wham/src/Makefile b/source/wham/src/Makefile
deleted file mode 100644 (file)
index 15fcd21..0000000
--- a/source/wham/src/Makefile
+++ /dev/null
@@ -1,68 +0,0 @@
-INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh
-BIN = ../../../bin/wham/
-FC= ifort
-#OPT = -mcmodel=medium -O3 -ip -w
-OPT = -mcmodel=medium -g -CB
-FFLAGS = ${OPT} -c -I. -I./include_unres -I$(INSTALL_DIR)/include
-LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpmpich xdrf/libxdrf.a
-CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI -DISNAN -DAMD64 \
-       -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
-
-.f.o:
-       ${FC} ${FFLAGS} $*.f
-
-.F.o:
-       ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
-
-all: make_dbase
-
-objects = \
-       wham_multparm.o \
-       bxread.o \
-       xread.o \
-       cxread.o \
-       enecalc1.o \
-       energy_p_new.o \
-       initialize_p.o \
-       molread_zs.o \
-       openunits.o \
-       readrtns.o \
-       arcos.o \
-       cartder.o \
-       cartprint.o \
-       chainbuild.o \
-       geomout.o \
-       icant.o \
-       intcor.o \
-       int_from_cart.o \
-       make_ensemble1.o \
-       matmult.o \
-       misc.o \
-       mygetenv.o \
-       parmread.o \
-       pinorm.o \
-       printmat.o \
-       proc_proc.o \
-       rescode.o \
-       setup_var.o \
-       slices.o \
-       store_parm.o \
-       timing.o \
-       wham_calc1.o
-
-objects_compar = \
-        readrtns_compar.o \
-        readpdb.o fitsq.o contact.o \
-        elecont.o contfunc.o cont_frag.o conf_compar.o match_contact.o \
-        angnorm.o odlodc.o promienie.o qwolynes.o read_ref_str.o \
-        rmscalc.o secondary.o proc_cont.o define_pairs.o mysort.o
-
-make_dbase: ${objects} ${objects_compar}
-       cc -o compinfo compinfo.c
-       ./compinfo
-       ${FC} -c ${FFLAGS} cinfo.f
-       $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \
-       ${LIBS} -static-intel -o ${BIN}/wham_multparm-ham_rep-oldparm
-
-clean:
-       /bin/rm *.o

diff --git a/source/wham/src/cinfo.f b/source/wham/src/cinfo.f
deleted file mode 100644 (file)
index 97eabbe..0000000
--- a/source/wham/src/cinfo.f
+++ /dev/null
@@ -1,61 +0,0 @@
-C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
-C 0 0 565
-      subroutine cinfo
-      include 'COMMON.IOUNITS'
-      write(iout,*)'++++ Compile info ++++'
-      write(iout,*)'Version 0.0 build 565'
-      write(iout,*)'compiled Tue May 29 04:48:26 2012'
-      write(iout,*)'compiled by adam@matrix.chem.cornell.edu'
-      write(iout,*)'OS name:    Linux '
-      write(iout,*)'OS release: 2.6.34.9-69.fc13.x86_64 '
-      write(iout,*)'OS version: #1 SMP Tue May 3 09:23:03 UTC 2011 '
-      write(iout,*)'flags:'
-      write(iout,*)'INSTALL_DIR = /users/software/mpich-1.2.7p1_int...'
-      write(iout,*)'BIN = ../../../bin/wham'
-      write(iout,*)'FC= ifort'
-      write(iout,*)'OPT = -mcmodel=medium -O3 -ip -w'
-      write(iout,*)'FFLAGS = ${OPT} -c -I. -I./include_unres -I$(IN...'
-      write(iout,*)'LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpmpich xd...'
-      write(iout,*)'objects = \\'
-      write(iout,*)'   wham_multparm.o \\'
-      write(iout,*)'   bxread.o \\'
-      write(iout,*)'   xread.o \\'
-      write(iout,*)'   cxread.o \\'
-      write(iout,*)'   enecalc1.o \\'
-      write(iout,*)'   energy_p_new.o \\'
-      write(iout,*)'   gnmr1.o \\'
-      write(iout,*)'   initialize_p.o \\'
-      write(iout,*)'   molread_zs.o \\'
-      write(iout,*)'   openunits.o \\'
-      write(iout,*)'   readrtns.o \\'
-      write(iout,*)'   arcos.o \\'
-      write(iout,*)'   cartder.o \\'
-      write(iout,*)'   cartprint.o \\'
-      write(iout,*)'   chainbuild.o \\'
-      write(iout,*)'   geomout.o \\'
-      write(iout,*)'   icant.o \\'
-      write(iout,*)'   intcor.o \\'
-      write(iout,*)'   int_from_cart.o \\'
-      write(iout,*)'   make_ensemble1.o \\'
-      write(iout,*)'   matmult.o \\'
-      write(iout,*)'   misc.o \\'
-      write(iout,*)'   mygetenv.o \\'
-      write(iout,*)'   parmread.o \\'
-      write(iout,*)'   pinorm.o \\'
-      write(iout,*)'   printmat.o \\'
-      write(iout,*)'   proc_proc.o \\'
-      write(iout,*)'   rescode.o \\'
-      write(iout,*)'   setup_var.o \\'
-      write(iout,*)'   slices.o \\'
-      write(iout,*)'   store_parm.o \\'
-      write(iout,*)'   timing.o \\'
-      write(iout,*)'   wham_calc1.o'
-      write(iout,*)'objects_compar = \\'
-      write(iout,*)'        readrtns_compar.o \\'
-      write(iout,*)'        readpdb.o fitsq.o contact.o \\'
-      write(iout,*)'        elecont.o contfunc.o cont_frag.o conf_c...'
-      write(iout,*)'GAB: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITEL...'
-      write(iout,*)'E0LL2Y: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLI...'
-      write(iout,*)'++++ End of compile info ++++'
-      return
-      end

diff --git a/source/wham/src/cxread.F b/source/wham/src/cxread.F
index 7bb2f6a..65372e3 100644 (file)
--- a/source/wham/src/cxread.F
+++ b/source/wham/src/cxread.F
@@ -54,14 +54,21 @@ c      print *,"bumbum"
       do while (iret.gt.0) 
 
 #if (defined(AIX) && !defined(JUBL))
+#ifdef DEBUG
+      write (iout,*) "ii",ii," itraj",itraj," it",it
+#endif
       call xdrffloat_(ixdrf, rtime, iret)
-c      print *,"rtime",rtime," iret",iret
       call xdrffloat_(ixdrf, rpotE, iret)
-c      write (iout,*) "rpotE",rpotE," iret",iret
+#ifdef DEBUG
+      write (iout,*) "rtime",rtime," rpotE",rpotE," iret",iret
+#endif
       call flush(iout)
       call xdrffloat_(ixdrf, ruconst, iret)
       call xdrffloat_(ixdrf, rt_bath, iret)
       call xdrfint_(ixdrf, nss, iret)
+#ifdef DEBUG
+      write (iout,*) "ruconst",ruconst," rt_bath",rt_bath," nss",nss
+#endif
       do j=1,nss
         call xdrfint_(ixdrf, ihpb(j), iret)
         call xdrfint_(ixdrf, jhpb(j), iret)
@@ -73,13 +80,21 @@ c      write (iout,*) "rpotE",rpotE," iret",iret
         call xdrffloat_(ixdrf, rprop(i), iret)
       enddo
 #else
+#ifdef DEBUG
+      write (iout,*) "ii",ii," itraj",itraj," it",it
+#endif
       call xdrffloat(ixdrf, rtime, iret)
       call xdrffloat(ixdrf, rpotE, iret)
-c      write (iout,*) "rpotE",rpotE," iret",iret
+#ifdef DEBUG
+      write (iout,*) "rtime",rtime," rpotE",rpotE," iret",iret
+#endif
       call flush(iout)
       call xdrffloat(ixdrf, ruconst, iret)
       call xdrffloat(ixdrf, rt_bath, iret)
       call xdrfint(ixdrf, nss, iret)
+#ifdef DEBUG
+      write (iout,*) "ruconst",ruconst," rt_bath",rt_bath," nss",nss
+#endif
       do j=1,nss
         call xdrfint(ixdrf, ihpb(j), iret)
         call xdrfint(ixdrf, jhpb(j), iret)
@@ -102,9 +117,6 @@ c      write (iout,*) "nprop",nprop
 #endif
       if (iret.eq.0) exit
       itraj=mod(it,totraj(iR,iparm))
-#ifdef DEBUG
-      write (iout,*) "ii",ii," itraj",itraj," it",it
-#endif
       if (iset.eq.0) iset = 1
       call flush(iout)
       it=it+1

diff --git a/source/wham/src/energy_p_new.F b/source/wham/src/energy_p_new.F
index 27f9010..cb4b7b0 100644 (file)
--- a/source/wham/src/energy_p_new.F
+++ b/source/wham/src/energy_p_new.F
@@ -4534,7 +4534,7 @@ c        amino-acid residues.
 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,nterm_sccor
       esccor=0.0D0
       do i=itau_start,itau_end
         esccor_ii=0.0D0

diff --git a/source/wham/src/include_unres/COMMON.SCCOR b/source/wham/src/include_unres/COMMON.SCCOR
index efab24f..28d748a 100644 (file)
--- a/source/wham/src/include_unres/COMMON.SCCOR
+++ b/source/wham/src/include_unres/COMMON.SCCOR
@@ -6,7 +6,7 @@ cc Parameters of the SCCOR term
       integer nterm_sccor,isccortyp,nsccortyp,nlor_sccor
       common /sccor/ v1sccor(maxterm_sccor,3,20,20),
      &    v2sccor(maxterm_sccor,3,20,20),
-     &    v0sccor(maxterm_sccor,20),
+     &    v0sccor(ntyp,ntyp),
      &    vlor1sccor(maxterm_sccor,20,20),
      &    vlor2sccor(maxterm_sccor,20,20),
      &    vlor3sccor(maxterm_sccor,20,20),gloc_sc(3,0:maxres2,10),

diff --git a/source/wham/src/int_from_cart.f b/source/wham/src/int_from_cart.f
index 12d0c9c..c0cd6e7 100644 (file)
--- a/source/wham/src/int_from_cart.f
+++ b/source/wham/src/int_from_cart.f
@@ -26,6 +26,10 @@
         enddo
         be=0.0D0
         if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
+        if (i.gt.2) tauangle(3,i+1)=beta(i+nres-1,i-1,i,i+nres)
+        if (i.gt.2) tauangle(1,i+1)=beta(i-1+nres,i-1,i,i+1)
+        if (i.gt.2) tauangle(2,i+1)=beta(i-2,i-1,i,i+nres)
+
         omeg(i)=beta(nres+i,i,maxres2,i+1)
         theta(i+1)=alpha(i-1,i,i+1)
         alph(i)=alpha(nres+i,i,maxres2)

diff --git a/source/wham/src/xdrf b/source/wham/src/xdrf
new file mode 120000 (symlink)
index 0000000..26825c5
--- /dev/null
+++ b/source/wham/src/xdrf
@@ -0,0 +1 @@
+../../lib/xdrf
\ No newline at end of file