Merge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1

Conflicts:
	source/unres/src_MD-M/cinfo.f
	source/unres/src_MD-M/refsys.f

diff --git a/source/cluster/wham/src-M/energy_p_new.F b/source/cluster/wham/src-M/energy_p_new.F
index d6ea982..c7c2c2f 100644 (file)
--- a/source/cluster/wham/src-M/energy_p_new.F
+++ b/source/cluster/wham/src-M/energy_p_new.F
@@ -3045,7 +3045,7 @@ c          write (iout,*) i,vbld(i),vbldp0,diff,AKP*diff*diff
         endif
 
       enddo
-      estr=0.5d0*AKP*estr
+      estr=0.5d0*AKP*estr+estr1
 c
 c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
 c

diff --git a/source/unres/src_CSA/Makefile_MPICH_ifort b/source/unres/src_CSA/Makefile_MPICH_ifort
index 1720452..8a8aa2b 100644 (file)
--- a/source/unres/src_CSA/Makefile_MPICH_ifort
+++ b/source/unres/src_CSA/Makefile_MPICH_ifort
@@ -1,6 +1,6 @@
 ###################################################################
-INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh
-
+#INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh
+INSTALL_DIR = /users/software/mpich2-1.4.1p1_intel
 
 FC= ifort
 
@@ -11,8 +11,8 @@ FFLAGS1 = -c  -g -CA -CB -I$(INSTALL_DIR)/include
 FFLAGS2 = -c  -g -O0 -I$(INSTALL_DIR)/include  
 FFLAGSE = -c  -O3 -ipo  -opt_report -I$(INSTALL_DIR)/include
 
-
-LIBS = -L$(INSTALL_DIR)/lib -lmpich 
+# -lmpl only necessary for mpich2-1.4.1p1_intel
+LIBS = -L$(INSTALL_DIR)/lib -lmpich -lmpl
 
 ARCH = LINUX
 PP = /lib/cpp -P
@@ -45,7 +45,6 @@ no_option:
 GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
        -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
 GAB: BIN = ../../../bin/unres/CSA/unres_csa_ifort_MPICH_GAB.exe
-LIBS =  -lpthread -L$(INSTALL_DIR)/lib -lmpich
 GAB: ${object}
        cc -o compinfo compinfo.c
        ./compinfo | true

diff --git a/source/unres/src_MD-M/Makefile_MPICH_ifort b/source/unres/src_MD-M/Makefile_MPICH_ifort
index 0d2a6d4..96d91a2 100644 (file)
--- a/source/unres/src_MD-M/Makefile_MPICH_ifort
+++ b/source/unres/src_MD-M/Makefile_MPICH_ifort
@@ -1,6 +1,6 @@
 ###################################################################
-INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh
-
+#INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh
+INSTALL_DIR = /users/software/mpich2-1.4.1p1_intel
 
 FC= ifort
 
@@ -11,8 +11,8 @@ FFLAGS1 = -c  -g -CA -CB -I$(INSTALL_DIR)/include
 FFLAGS2 = -c  -g -O0 -I$(INSTALL_DIR)/include  
 FFLAGSE = -c  -O3 -ipo  -opt_report -I$(INSTALL_DIR)/include
 
-
-LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdrf.a
+# -lmpl only necessary for mpich2-1.4.1p1_intel
+LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdrf.a -lmpl
 
 ARCH = LINUX
 PP = /lib/cpp -P

diff --git a/source/unres/src_MD-M/cinfo.f b/source/unres/src_MD-M/cinfo.f
index c7b5141..db23899 100644 (file)
--- a/source/unres/src_MD-M/cinfo.f
+++ b/source/unres/src_MD-M/cinfo.f
@@ -1,4 +1,5 @@
 C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
+<<<<<<< HEAD
 C 0 40360 9
       subroutine cinfo
       include 'COMMON.IOUNITS'
@@ -6,12 +7,25 @@ C 0 40360 9
       write(iout,*)'Version 0.40360 build 9'
       write(iout,*)'compiled Fri Jan 23 21:00:08 2015'
       write(iout,*)'compiled by adam@mmka'
+=======
+C 0 40360 1
+      subroutine cinfo
+      include 'COMMON.IOUNITS'
+      write(iout,*)'++++ Compile info ++++'
+      write(iout,*)'Version 0.40360 build 1'
+      write(iout,*)'compiled Wed Jan  7 10:41:15 2015'
+      write(iout,*)'compiled by czarek@piasek4'
+>>>>>>> 9a082c1ab203120d8e865971546d473fb146fcdc
       write(iout,*)'OS name:    Linux '
       write(iout,*)'OS release: 3.2.0-72-generic '
       write(iout,*)'OS version:',
      & ' #107-Ubuntu SMP Thu Nov 6 14:24:01 UTC 2014 '
       write(iout,*)'flags:'
+<<<<<<< HEAD
       write(iout,*)'INSTALL_DIR = /users/software/mpich-1.2.7p1_int...'
+=======
+      write(iout,*)'INSTALL_DIR = /users/software/mpich2-1.4.1p1_in...'
+>>>>>>> 9a082c1ab203120d8e865971546d473fb146fcdc
       write(iout,*)'FC= ifort'
       write(iout,*)'OPT =  -O3 -ip '
       write(iout,*)'FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include '

diff --git a/source/unres/src_MD-M/energy_p_new_barrier.F b/source/unres/src_MD-M/energy_p_new_barrier.F
index eae81d8..539102b 100644 (file)
--- a/source/unres/src_MD-M/energy_p_new_barrier.F
+++ b/source/unres/src_MD-M/energy_p_new_barrier.F
@@ -5559,7 +5559,8 @@ 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
+     &       .or. itype(i).eq.21
+     &       .or. itype(i-3).eq.ntyp1) cycle
       etors_ii=0.0D0
         itori=itortyp(itype(i-2))
         itori1=itortyp(itype(i-1))
@@ -5655,7 +5656,8 @@ c     lprn=.true.
 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
+     &      .or. itype(i).eq.21 .or. itype(i+1).eq.21
+     &       .or. itype(i-3).eq.ntyp1) cycle
         itori=itortyp(itype(i-2))
         itori1=itortyp(itype(i-1))
         itori2=itortyp(itype(i))

diff --git a/source/unres/src_MD-M/refsys.f b/source/unres/src_MD-M/refsys.f
index b57c201..a6aa5e9 100644 (file)
--- a/source/unres/src_MD-M/refsys.f
+++ b/source/unres/src_MD-M/refsys.f
@@ -1,8 +1,13 @@
       subroutine refsys(i2,i3,i4,e1,e2,e3,fail)
+<<<<<<< HEAD
       implicit real*8 (a-h,o-z)
       include 'DIMENSIONS'
 c this subroutine calculates unity vectors of a local reference system
 c defined by atoms (i2), (i3), and (i4). the x axis is the axis from
+=======
+c This subroutine calculates unit vectors of a local reference system
+c defined by atoms (i2), (i3), and (i4). The x axis is the axis from
+>>>>>>> 9a082c1ab203120d8e865971546d473fb146fcdc
 c atom (i3) to atom (i2), and the xy plane is the plane defined by atoms
 c (i2), (i3), and (i4). z axis is directed according to the sign of the
 c vector product (i3)-(i2) and (i3)-(i4). sets fail to .true. if atoms

diff --git a/source/wham/src-M/enecalc1.F b/source/wham/src-M/enecalc1.F
index 5ce2fff..880664c 100644 (file)
--- a/source/wham/src-M/enecalc1.F
+++ b/source/wham/src-M/enecalc1.F
@@ -201,6 +201,10 @@ c        call pdbout(ii+1,beta_h(ib,ipar),efree,energia(0),0.0d0,rmsdev)
      &         " the value read in: ",energia(0),eini," point",
      &         iii+1,indstart(me1)+iii," T",
      &         1.0d0/(1.987D-3*beta_h(ib,ipar))
+              call pdbout(indstart(me1)+iii,
+     & 1.0d0/(1.987D-3*beta_h(ib,ipar)),
+     &energia(0),eini,0.0d0,0.0d0)
+              call enerprint(energia(0),fT)
               errmsg_count=errmsg_count+1
               if (errmsg_count.gt.maxerrmsg_count) 
      &          write (iout,*) "Too many warning messages"

diff --git a/source/wham/src-M/energy_p_new.F b/source/wham/src-M/energy_p_new.F
index b5e9340..af921d0 100644 (file)
--- a/source/wham/src-M/energy_p_new.F
+++ b/source/wham/src-M/energy_p_new.F
@@ -3095,7 +3095,7 @@ c          write (iout,*) i,vbld(i),vbldp0,diff,AKP*diff*diff
         endif
 
       enddo
-      estr=0.5d0*AKP*estr
+      estr=0.5d0*AKP*estr+estr1
 c
 c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
 c
@@ -4360,7 +4360,8 @@ 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
+     &       .or. itype(i).eq.21
+     &       .or. itype(i-3).eq.ntyp1) cycle
         if (itel(i-2).eq.0 .or. itel(i-1).eq.0) goto 1215
         itori=itortyp(itype(i-2))
         itori1=itortyp(itype(i-1))
@@ -4454,7 +4455,8 @@ c     lprn=.true.
       etors_d=0.0D0
       do i=iphi_start,iphi_end-1
         if (itype(i-2).eq.21 .or. itype(i-1).eq.21
-     &      .or. itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+     &      .or. itype(i).eq.21 .or. itype(i+1).eq.21
+     &       .or. itype(i-3).eq.ntyp1) cycle
         if (itel(i-2).eq.0 .or. itel(i-1).eq.0 .or. itel(i).eq.0) 
      &     goto 1215
         itori=itortyp(itype(i-2))

diff --git a/source/wham/src-M/readpdb.f b/source/wham/src-M/readpdb.f
index 93c9cbe..fa2d05d 100644 (file)
--- a/source/wham/src-M/readpdb.f
+++ b/source/wham/src-M/readpdb.f
@@ -173,17 +173,19 @@ c       write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
         do j=1,3
           cref(j,i,cou)=c(j,i)
           cref(j,i+nres,cou)=c(j,i+nres)
-          if (i.le.nres) then
+          if ((i.le.nres).and.(symetr.gt.1)) then
           chain_rep(j,lll,kkk)=c(j,i)
           chain_rep(j,lll+nres,kkk)=c(j,i+nres)
           endif
          enddo
       enddo
+      if (symetr.gt.1) then
       do j=1,3
       chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
       chain_rep(j,chain_length+nres,symetr)
      &=chain_rep(j,chain_length+nres,1)
       enddo
+      endif
 c diagnostic
 
 c diagnostic