Commit 10/1/12

diff --git a/bin/unres/MINIM/unres_ifort_MIN_single_GAB.exe b/bin/unres/MINIM/unres_ifort_MIN_single_GAB.exe
index 394eaac..cfd83ee 100755 (executable)
Binary files a/bin/unres/MINIM/unres_ifort_MIN_single_GAB.exe and b/bin/unres/MINIM/unres_ifort_MIN_single_GAB.exe differ

diff --git a/source/unres/src_MIN/Makefile_OLDPARM_ifort b/source/unres/src_MIN/Makefile_OLDPARM_ifort
deleted file mode 100644 (file)
index 598a89f..0000000
--- a/source/unres/src_MIN/Makefile_OLDPARM_ifort
+++ /dev/null
@@ -1,85 +0,0 @@
-CPPFLAGS = -DPROCOR -DLINUX -DPGI -DISNAN \
-           -DSPLITELE -DAMD64 -DLANG0 \
-           -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DPROCOR
-
-FC= ifort -g
-
-OPT =  -O3 -ip -w 
-
-FFLAGS = -c ${OPT} 
-FFLAGS1 = -c -w -g -d2 -CA -CB 
-FFLAGS2 = -c -w -g -O0 
-FFLAGSE = -c -w -O3 -ipo -ipo_obj  -opt_report 
-
-
-BIN = ../../../bin/unres/MINIM/unres_Tc_procor_new_em64_min_sumsl_old.exe
-LIBS =  -lpthread 
-
-ARCH = LINUX
-PP = /lib/cpp -P
-
-
-all: unres
-
-.SUFFIXES: .F.f
-.F.o:
-       ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
-.f.o:
-       ${FC} ${FFLAGS} ${CPPFLAGS} $*.f
-
-
-object = unres_min.o arcos.o cartprint.o chainbuild.o initialize_p.o \
-        matmult.o readrtns_min.o parmread.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 \
-       gradient_p.o minimize_p.o sumsld.o \
-        cored.o rmdd.o geomout_min.o readpdb.o \
-        intcartderiv.o \
-        MP.o printmat.o convert.o int_to_cart.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
-
-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
-
-
-
-

diff --git a/source/unres/src_MIN/Makefile_gfortran b/source/unres/src_MIN/Makefile_gfortran
deleted file mode 100644 (file)
index 0c85368..0000000
--- a/source/unres/src_MIN/Makefile_gfortran
+++ /dev/null
@@ -1,92 +0,0 @@
-CPPFLAGS = -DPROCOR -DLINUX -DG77 -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  
-
-FC= gfortran
-
-OPT =  -O 
-
-FFLAGS = -c ${OPT} 
-FFLAGS1 = -c -g -C
-FFLAGS2 = -c -g -O0 
-FFLAGSE = -c -O3 
-
-
-BIN = ../../../bin/unres/MIN/unres_min_gfortran.exe
-LIBS = 
-#LIBS =  -lpthread 
-
-ARCH = LINUX
-PP = /lib/cpp -P
-
-
-all: unres
-
-.SUFFIXES: .F
-.F.o:
-       ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
-
-
-object = unres_min.o arcos.o cartprint.o chainbuild.o initialize_p.o \
-        matmult.o readrtns_min.o parmread.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 \
-       gradient_p.o minimize_p.o sumsld.o \
-        cored.o rmdd.o geomout_min.o readpdb.o \
-        intcartderiv.o \
-        MP.o printmat.o convert.o int_to_cart.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
-
-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
-
-
-
-

diff --git a/source/unres/src_MIN/Makefile_ifort b/source/unres/src_MIN/Makefile_ifort
deleted file mode 100644 (file)
index 193d9e6..0000000
--- a/source/unres/src_MIN/Makefile_ifort
+++ /dev/null
@@ -1,91 +0,0 @@
-CPPFLAGS = -DPROCOR -DLINUX -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  
-
-FC= ifort -g
-
-OPT =  -O3 -ip -w 
-
-FFLAGS = -c ${OPT} 
-FFLAGS1 = -c -w -g -d2 -CA -CB 
-FFLAGS2 = -c -w -g -O0 
-FFLAGSE = -c -w -O3 -ipo -ipo_obj  -opt_report 
-
-
-BIN = ../bin/unres_Tc_procor_new_em64_nh_hremd_92110_min_sumsl.exe
-LIBS =  -lpthread 
-
-ARCH = LINUX
-PP = /lib/cpp -P
-
-
-all: unres
-
-.SUFFIXES: .F
-.F.o:
-       ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
-
-
-object = unres_min.o arcos.o cartprint.o chainbuild.o initialize_p.o \
-        matmult.o readrtns_min.o parmread.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 \
-       gradient_p.o minimize_p.o sumsld.o \
-        cored.o rmdd.o geomout_min.o readpdb.o \
-        intcartderiv.o \
-        MP.o printmat.o convert.o int_to_cart.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
-
-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
-
-
-
-

diff --git a/source/unres/src_MIN/minimize_p.F b/source/unres/src_MIN/minimize_p.F
index 1721510..72190e8 100644 (file)
--- a/source/unres/src_MIN/minimize_p.F
+++ b/source/unres/src_MIN/minimize_p.F
@@ -27,7 +27,10 @@
 c      common /przechowalnia/ v
 
       icall = 1
-c      print *,"liv",liv," lv",lv
+C Following 3 line for diagnostics; comment out if not needed
+      write(iout,*) "Enter MINIMIZE liv",liv," lv",lv
+      write (iout,*) "Coordinates before minimization"
+      call intout
       call deflt(2,iv,liv,lv,v)                                         
 * 12 means fresh start, dont call deflt                                 
       iv(1)=12                                                          

diff --git a/source/unres/src_MIN/readpdb.F b/source/unres/src_MIN/readpdb.F
index dacd12d..1d79870 100644 (file)
--- a/source/unres/src_MIN/readpdb.F
+++ b/source/unres/src_MIN/readpdb.F
@@ -258,6 +258,9 @@ c      endif
           enddo
           iti=itype(i)
           di=dist(i,nres+i)
+C 9/29/12 Adam: Correction for zero SC-SC bond length 
+          if (itype(i).ne.10 .and. itype(i).ne.21. and. di.eq.0.0d0) 
+     &     di=dsc(itype(i))
           vbld(i+nres)=di
           if (itype(i).ne.10) then
             vbld_inv(i+nres)=1.0d0/di

diff --git a/source/unres/src_MIN/readrtns_min.F b/source/unres/src_MIN/readrtns_min.F
index dee929a..9d444cf 100644 (file)
--- a/source/unres/src_MIN/readrtns_min.F
+++ b/source/unres/src_MIN/readrtns_min.F
@@ -422,6 +422,9 @@ c        print *,'Finished reading pdb data'
 c        call contact(.false.,ncont_ref,icont_ref,co)
 
         if (sideadd) then 
+C Following 2 lines for diagnostics; comment out if not needed
+         write (iout,*) "Before sideadd"
+         call intout
          if(me.eq.king.or..not.out1file)
      &    write(iout,*)'Adding sidechains'
          maxsi=1000
@@ -438,7 +441,12 @@ c        call contact(.false.,ncont_ref,icont_ref,co)
      &              i,' after ',nsi,' trials'
           endif
          enddo
+C 9/29/12 Adam: Recalculate coordinates with new side chain positions
+         call chainbuild
         endif  
+C Following 2 lines for diagnostics; comment out if not needed
+        write (iout,*) "After sideadd"
+        call intout
       endif
       if (indpdb.eq.0) then
 C Read sequence if not taken from the pdb file.