Added directory analysis to compute teperature-averaged number of contacts, etc.

Corrected electrostatic energy evaluation in cluster

diff --git a/source/cluster/wham/src-M/energy_p_new.F b/source/cluster/wham/src-M/energy_p_new.F
index d5ccc6d..2a02340 100644 (file)
--- a/source/cluster/wham/src-M/energy_p_new.F
+++ b/source/cluster/wham/src-M/energy_p_new.F
@@ -1922,7 +1922,7 @@ C End diagnostics
           if (yj.lt.0) yj=yj+boxysize
           zj=mod(zj,boxzsize)
           if (zj.lt.0) zj=zj+boxzsize
-      dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+      dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
       xj_safe=xj
       yj_safe=yj
       zj_safe=zj

diff --git a/source/wham/src-M/Makefile b/source/wham/src-M/Makefile
deleted file mode 100644 (file)
index 24b3056b7fe6513ea7bb239bb10acc91fe3ac205..0000000000000000000000000000000000000000
--- a/source/wham/src-M/Makefile
+++ /dev/null
@@ -1,76 +0,0 @@
-INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh
-BIN = ../../../bin
-CC = cc
-FC = ifort
-#OPT = -O3 -ip -w
-OPT = -g -CB
-FFLAGS = -c ${OPT} -I. -I./include_unres -I$(INSTALL_DIR)/include
-#FFLAGS = -c -g -C -I. -I./include_unres -I$(INSTALL_DIR)/include
-LIBS = -L$(INSTALL_DIR)/lib -lmpich ../../lib/xdrf/libxdrf.a 
-#LIBS = -L$(INSTALL_DIR)/lib_pgi -lmpich -lpmpich -Vaxlib
-#CPPFLAGS = -DMPI -DLINUX -DUNRES -DMOMENT -DCHECKGRAD -DPGI
-#CPPFLAGS = -DMPI -DLINUX -DUNRES -DCHECKGRAD -DPGI -DMYGETENV
-CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI -DCRYST_BOND -DCRYST_SC -DCRYST_THETA 
-#CPPFLAGS = -DMPI -DLINUX -DUNRES -DPGI
-#CPPFLAGS = -DMPI -DLINUX -DUNRES
-
-.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 \
-       gnmr1.o \
-       initialize_p.o \
-       molread_zs.o \
-       openunits.o \
-       readrtns.o \
-       read_dist_constr.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 permut.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} -o ${BIN}/wham_multparm-D-sccor-oldparm
-
-clean:
-       /bin/rm *.o

diff --git a/source/wham/src-M/Makefile b/source/wham/src-M/Makefile
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..8453cddeb7b08caf0a886e4bb11a3abc3a14980c
--- /dev/null
+++ b/source/wham/src-M/Makefile
@@ -0,0 +1 @@
+Makefile_MPICH_ifort
\ No newline at end of file

diff --git a/source/wham/src-M/Makefile_MPICH_ifort b/source/wham/src-M/Makefile_MPICH_ifort
index 07ffac6..e24003b 100644 (file)
--- a/source/wham/src-M/Makefile_MPICH_ifort
+++ b/source/wham/src-M/Makefile_MPICH_ifort
@@ -68,7 +68,7 @@ GAB: ${objects} ${objects_compar} xdrf/libxdrf.a
        ./compinfo
        ${FC} -c ${FFLAGS} cinfo.f
        $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \
-       ${LIBS} -static-intel -o ${BIN}/wham-mult_ifort_MPICH-GAB.exe
+       ${LIBS} -static-intel -o ${BIN}/wham-mult_ifort_MPICH-GAB-DEBUG.exe
 
 4P: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPGI -DISNAN -DAMD64 \
        -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DWHAM

diff --git a/source/wham/src-M/cinfo.f b/source/wham/src-M/cinfo.f
index 858334a..cdf079d 100644 (file)
--- a/source/wham/src-M/cinfo.f
+++ b/source/wham/src-M/cinfo.f
@@ -1,24 +1,22 @@
 C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
-C 0 0 703
+C 0 0 704
       subroutine cinfo
       include 'COMMON.IOUNITS'
       write(iout,*)'++++ Compile info ++++'
-      write(iout,*)'Version 0.0 build 703'
-      write(iout,*)'compiled Thu May 15 10:35:39 2014'
-      write(iout,*)'compiled by aks255@matrix.chem.cornell.edu'
+      write(iout,*)'Version 0.0 build 704'
+      write(iout,*)'compiled Sat Oct 31 12:18:25 2015'
+      write(iout,*)'compiled by adam@piasek4'
       write(iout,*)'OS name:    Linux '
-      write(iout,*)'OS release: 2.6.34.9-69.fc13.x86_64 '
+      write(iout,*)'OS release: 3.2.0-91-generic '
       write(iout,*)'OS version:',
-     & ' #1 SMP Tue May 3 09:23:03 UTC 2011 '
+     & ' #129-Ubuntu SMP Wed Sep 9 10:56:06 UTC 2015 '
       write(iout,*)'flags:'
       write(iout,*)'INSTALL_DIR = /users/software/mpich-1.2.7p1_int...'
-      write(iout,*)'BIN = ../../../bin'
-      write(iout,*)'CC = cc'
-      write(iout,*)'FC = ifort'
-      write(iout,*)'OPT = -g -CB'
-      write(iout,*)'FFLAGS = -c ${OPT} -I. -I./include_unres -I$(IN...'
-      write(iout,*)'LIBS = -L$(INSTALL_DIR)/lib -lmpich ../../lib/x...'
-      write(iout,*)'CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DP...'
+      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 \\'
@@ -31,7 +29,6 @@ C 0 0 703
       write(iout,*)'   molread_zs.o \\'
       write(iout,*)'   openunits.o \\'
       write(iout,*)'   readrtns.o \\'
-      write(iout,*)'   read_dist_constr.o \\'
       write(iout,*)'   arcos.o \\'
       write(iout,*)'   cartder.o \\'
       write(iout,*)'   cartprint.o \\'
@@ -53,11 +50,16 @@ C 0 0 703
       write(iout,*)'   slices.o \\'
       write(iout,*)'   store_parm.o \\'
       write(iout,*)'   timing.o \\'
+      write(iout,*)'   read_dist_constr.o \\'
+      write(iout,*)'   permut.o \\'
       write(iout,*)'   wham_calc1.o'
       write(iout,*)'objects_compar = \\'
       write(iout,*)'        readrtns_compar.o \\'
-      write(iout,*)'        readpdb.o permut.o fitsq.o contact.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,*)'4P: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE...'
+      write(iout,*)'E0LL2Y: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLI...'
       write(iout,*)'++++ End of compile info ++++'
       return
       end

diff --git a/source/wham/src-M/enecalc1.F b/source/wham/src-M/enecalc1.F
index 81668b5..8a52e49 100644 (file)
--- a/source/wham/src-M/enecalc1.F
+++ b/source/wham/src-M/enecalc1.F
@@ -160,12 +160,15 @@ c     &   " kfac",kfac,"quot",quot," fT",fT
 C        write (iout,*) "tuz przed energia"
         call etotal(energia(0),fT)
 C        write (iout,*) "tuz za energia"
-
+#define DEBUG
 #ifdef DEBUG
         write (iout,*) "Conformation",i
           write (iout,'(8f10.5)') ((c(l,k),l=1,3),k=1,nres)
           write (iout,'(8f10.5)') ((c(l,k+nres),l=1,3),k=nnt,nct)
         call enerprint(energia(0),fT)
+#endif
+#undef DEBUG
+#ifdef DEBUG
         write (iout,'(2i5,21f8.2)') i,iparm,(energia(k),k=1,21)
         write (iout,*) "ftors",ftors
         call briefout(i,energia(0))