From: Adam Liwo <jal47@matrix.chem.cornell.edu>
Date: Wed, 17 Oct 2012 05:36:46 +0000 (-0400)
Subject: 10/17/2012 by Adam: Implemented sideadd correction in Bartek's DiL source (readrtns_C... 
X-Git-Tag: v.3.2~66
X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=commitdiff_plain;h=e3a8e8d61d7f6f11117e3b4b70e551f04f198b1c

10/17/2012 by Adam: Implemented sideadd correction in Bartek's DiL source (readrtns_CSA.F and readpdb.F)
---

diff --git a/bin/unres/CSA/unres_dfa_csa-Yi.exe b/bin/unres/CSA/unres_dfa_csa-Yi.exe
index 30642a1..528b3aa 100755
Binary files a/bin/unres/CSA/unres_dfa_csa-Yi.exe and b/bin/unres/CSA/unres_dfa_csa-Yi.exe differ
diff --git a/source/unres/src_CSA_DiL/Makefile b/source/unres/src_CSA_DiL/Makefile
index 74b5dd0..def0aff 120000
--- a/source/unres/src_CSA_DiL/Makefile
+++ b/source/unres/src_CSA_DiL/Makefile
@@ -1 +1 @@
-Makefile-DFA-NEWPARM.piasek
\ No newline at end of file
+Makefile-DFA-NEWPARM.matrix
\ No newline at end of file
diff --git a/source/unres/src_CSA_DiL/Makefile-DFA-NEWPARM.matrix b/source/unres/src_CSA_DiL/Makefile-DFA-NEWPARM.matrix
new file mode 100644
index 0000000..adcfcc0
--- /dev/null
+++ b/source/unres/src_CSA_DiL/Makefile-DFA-NEWPARM.matrix
@@ -0,0 +1,108 @@
+CPPFLAGS = -DPROCOR -DLINUX -DPGI -DISNAN -DMP -DMPI -DUNRES \
+           -DSPLITELE -DAMD64 -DLANG0 
+#           -DCRYST_BOND -DCRYST_THETA -DCRYST_SC 
+#-DCRYST_TOR
+# -DPROCOR
+#           -DTSCSC
+#-DTIMING \
+# -DMOMENT
+#-DPARVEC 
+#-DPARINT -DPARINTDER  
+
+#INSTALL_DIR = /usr/local/mpich-1.2.0
+INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh/
+#INSTALL_DIR = /opt/mpi/mvapich
+#INSTALL_DIR = /users/local/mpi64/mpich-1.2.7p1/
+#
+#FC= /usr/local/opt/intel/compiler60/ia32/bin/ifc
+FC= ifort
+#FCL = ${INSTALL_DIR}/bin/mpif77
+#CC = cc
+
+OPT =  -O3 -ip -w 
+
+FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
+FFLAGS1 = -c -w -g -O0 -d2 -CA -CB -I$(INSTALL_DIR)/include
+FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include
+FFLAGS3 = -c -w -O3 -mp
+FFLAGSE = -c -w -O3 -ipo -ipo_obj  -opt_report -I$(INSTALL_DIR)/include
+
+BIN = ../../../bin/unres/CSA/unres_dfa_csa-Yi.exe
+#BIN = ../../../bin/unres/CSA/unres_csa_ifort_mpich-1.2.7p1.exe
+#LIBS = -L$(INSTALL_DIR)/lib -lmpich 
+LIBS =  -lpthread -L$(INSTALL_DIR)/lib -lmpich
+
+ARCH = LINUX
+PP = /lib/cpp -P
+
+#all: unresCSA
+all: unres
+
+.SUFFIXES: .F
+.F.o:
+	${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+
+object = unres_csa.o arcos.o cartprint.o chainbuild.o initialize_p.o \
+        matmult.o readrtns_csa.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 \
+	dfa.o \
+        together.o csa.o minim_jlee.o shift.o diff12.o bank.o newconf.o ran.o \
+        indexx.o prng_32.o contact.o gen_rand_conf.o \
+        sc_move.o test.o local_move.o rmsd.o fitsq.o elecont.o djacob.o \
+        distfit.o banach.o TMscore_subroutine.o minim_mult.o
+
+#unresCSA: ${object}
+unres: ${object} 
+#	cc -o compinfo compinfo.c
+#	./compinfo
+	${FC} ${FFLAGS} cinfo.f
+#	${FCL} -static-libcxa ${OPT} ${object} cinfo.o ${LIBS}  -o ${BIN}
+	${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} ${FFLAGS3} ${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
+
+dfa.o : dfa.F
+	${FC} -mp  ${FFLAGS3} ${CPPFLAGS} dfa.F
+
+
+
diff --git a/source/unres/src_CSA_DiL/readpdb.F b/source/unres/src_CSA_DiL/readpdb.F
index dacd12d..69ec3e1 100644
--- a/source/unres/src_CSA_DiL/readpdb.F
+++ b/source/unres/src_CSA_DiL/readpdb.F
@@ -258,6 +258,9 @@ c      endif
           enddo
           iti=itype(i)
           di=dist(i,nres+i)
+C 10/03/12 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_CSA_DiL/readrtns_csa.F b/source/unres/src_CSA_DiL/readrtns_csa.F
index 4511d33..a6ed1f8 100644
--- a/source/unres/src_CSA_DiL/readrtns_csa.F
+++ b/source/unres/src_CSA_DiL/readrtns_csa.F
@@ -455,6 +455,9 @@ c        print *,'Finished reading pdb data'
         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
@@ -472,6 +475,11 @@ c              call gen_side(iti,theta(i+1),alph(i),omeg(i),fail)
           endif
          enddo
         endif  
+C 10/03/12 Adam: Recalculate coordinates with new side chain positions
+        call chainbuild
+C Following 2 lines for diagnostics; comment out if not needed
+        write (iout,*) "After sideadd"
+        call intout
       endif
 
       if (indpdb.eq.0) then