From 9a54ab407f6d0d9d564d52763b3e2136450b9ffc Mon Sep 17 00:00:00 2001 From: Adam Liwo Date: Sat, 31 Oct 2015 18:56:12 +0100 Subject: [PATCH] Added directory analysis to compute teperature-averaged number of contacts, etc. Corrected electrostatic energy evaluation in cluster --- source/cluster/wham/src-M/energy_p_new.F | 2 +- source/wham/src-M/Makefile | 77 +----------------------------- source/wham/src-M/Makefile_MPICH_ifort | 2 +- source/wham/src-M/cinfo.f | 32 +++++++------ source/wham/src-M/enecalc1.F | 5 +- 5 files changed, 24 insertions(+), 94 deletions(-) mode change 100644 => 120000 source/wham/src-M/Makefile 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 --- 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 index 24b3056..0000000 --- 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 index 0000000..8453cdd --- /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 --- 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 --- 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 --- 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)) -- 1.7.9.5