--- /dev/null
+BIN=/home/adam/UNRES/bin
+INSTALL_DIR = /usr/local/mpich-1.2.7p1-intel
+FC= ifort
+OPT = -O3 -ip -w
+FFLAGS = ${OPT} -I.
+CPPFLAGS = -DLINUX
+
+# Next for debugging
+#FC = f77
+#OPT = -g -fbounds-check
+#CPPFLAGS = -DLINUX -DG77
+
+LIBS =
+
+.SUFFIXES: .F
+.F.o:
+ $(FC) -c $(CPPFLAGS) $(FFLAGS) $<
+.f.o:
+ $(FC) -c $(CPPFLAGS) $(FFLAGS) $<
+
+objects = main_clust.o arcos.o cartprint.o chainbuild.o convert.o initialize.o \
+ matmult.o readrtns.o pinorm.o rescode.o intcor.o timing.o misc.o \
+ geomout.o readpdb.o fitsq.o hc.o \
+ track.o wrtclust.o srtclust.o noyes.o contact.o
+
+unres_clust: $(objects)
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} -c cinfo.f
+ $(FC) ${OPT} ${objects} cinfo.o ${LIBS} -o ../../../../bin/cluster/unres_clust-ifort.exe
+
+clean:
+ /bin/rm *.o
+
+move:
+ mv *.o ${OBJ}
--- /dev/null
+BIN=/home/adam/UNRES/CLUSTER/bin
+FC= pgf90
+OPT = -O3
+#OPT = -C -g
+FFLAGS = ${OPT} -I.
+LIBS =
+CPPFLAGS = -DLINUX
+
+.SUFFIXES: .F
+.F.o:
+ $(FC) -c $(CPPFLAGS) $(FFLAGS) $<
+.f.o:
+ $(FC) -c $(CPPFLAGS) $(FFLAGS) $<
+
+objects = main_clust.o arcos.o cartprint.o chainbuild.o convert.o initialize.o \
+ matmult.o readrtns.o pinorm.o rescode.o intcor.o timing.o misc.o \
+ geomout.o readpdb.o fitsq.o hc.o \
+ track.o wrtclust.o srtclust.o noyes.o contact.o
+
+unres_clust: $(objects)
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} -c cinfo.f
+ $(FC) ${OPT} ${objects} cinfo.o ${LIBS} -o ${BIN}/unres_clust-pff90.exe
+
+clean:
+ /bin/rm *.o
+
+move:
+ mv *.o ${OBJ}
--- /dev/null
+#include <stdio.h>
+#include <sys/utsname.h>
+#include <sys/types.h>
+#include <time.h>
+#include <string.h>
+
+main()
+{
+FILE *in, *in1, *out;
+int i,j,k,iv1,iv2,iv3;
+char *p1,buf[500],buf1[500],buf2[100],buf3[100];
+struct utsname Name;
+time_t Tp;
+
+in=fopen("cinfo.f","r");
+out=fopen("cinfo.f.new","w");
+if (fgets(buf,498,in) != NULL)
+ fprintf(out,"C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C\n");
+if (fgets(buf,498,in) != NULL)
+ sscanf(&buf[1],"%d %d %d",&iv1,&iv2,&iv3);
+iv3++;
+fprintf(out,"C %d %d %d\n",iv1,iv2,iv3);
+fprintf(out," subroutine cinfo\n");
+fprintf(out," include 'COMMON.IOUNITS'\n");
+fprintf(out," write(iout,*)'++++ Compile info ++++'\n");
+fprintf(out," write(iout,*)'Version %d.%-d build %d'\n",iv1,iv2,iv3);
+uname(&Name);
+time(&Tp);
+system("whoami > tmptmp");
+in1=fopen("tmptmp","r");
+if (fscanf(in1,"%s",buf1) != EOF)
+{
+p1=ctime(&Tp);
+p1[strlen(p1)-1]='\0';
+fprintf(out," write(iout,*)'compiled %s'\n",p1);
+fprintf(out," write(iout,*)'compiled by %s@%s'\n",buf1,Name.nodename);
+fprintf(out," write(iout,*)'OS name: %s '\n",Name.sysname);
+fprintf(out," write(iout,*)'OS release: %s '\n",Name.release);
+fprintf(out," write(iout,*)'OS version:',\n");
+fprintf(out," & ' %s '\n",Name.version);
+fprintf(out," write(iout,*)'flags:'\n");
+}
+system("rm tmptmp");
+fclose(in1);
+in1=fopen("Makefile","r");
+while(fgets(buf,498,in1) != NULL)
+ {
+ if((p1=strchr(buf,'=')) != NULL && buf[0] != '#')
+ {
+ buf[strlen(buf)-1]='\0';
+ if(strlen(buf) > 49)
+ {
+ buf[47]='\0';
+ strcat(buf,"...");
+ }
+ else
+ {
+ while(buf[strlen(buf)-1]=='\\')
+ {
+ strcat(buf,"\\");
+ fprintf(out," write(iout,*)'%s'\n",buf);
+ if (fgets(buf,498,in1) != NULL)
+ buf[strlen(buf)-1]='\0';
+ if(strlen(buf) > 49)
+ {
+ buf[47]='\0';
+ strcat(buf,"...");
+ }
+ }
+ }
+
+ fprintf(out," write(iout,*)'%s'\n",buf);
+ }
+ }
+fprintf(out," write(iout,*)'++++ End of compile info ++++'\n");
+fprintf(out," return\n");
+fprintf(out," end\n");
+fclose(out);
+fclose(in1);
+fclose(in);
+system("mv cinfo.f.new cinfo.f");
+}
--- /dev/null
+##################################################################
+INSTALL_DIR = /users/software/mpich2-1.0.7
+
+FC= gfortran
+
+OPT = -O
+
+FFLAGS = ${OPT} -c -I. -Iinclude_unres -I$(INSTALL_DIR)/include
+
+LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpthread xdrf/libxdrf.a
+
+.c.o:
+ cc -c -DLINUX -DPGI $*.c
+
+.f.o:
+ ${FC} ${FFLAGS} $*.f
+
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} ${FFLAGS} $*.F
+
+object = main_clust.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \
+ matmult.o readrtns.o pinorm.o rescode.o intcor.o timing.o misc.o \
+ geomout.o readpdb.o read_coords.o parmread.o probabl.o fitsq.o hc.o \
+ track.o wrtclust.o srtclust.o noyes.o contact.o printmat.o \
+ int_from_cart1.o energy_p_new.o icant.o proc_proc.o work_partition.o \
+ setup_var.o read_ref_str.o gnmr1.o permut.o
+
+all: no_option
+ @echo "Specify force field: GAB, 4P or E0LL2Y"
+
+no_option:
+
+GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DCLUST -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+GAB: BIN = ../../../../bin/cluster/unres_clustMD-mult_ifort_MPICH_GAB.exe
+GAB: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${object} ${LIBS} -o ${BIN}
+
+4P: CPPFLAGS = -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DCLUST -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+4P: BIN = ../../../../bin/cluster/unres_clustMD-mult_ifort_MPICH_4P.exe
+4P: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${object} ${LIBS} -o ${BIN}
+
+E0LL2Y: CPPFLAGS = -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DCLUST -DSPLITELE -DLANG0
+E0LL2Y: BIN = ../../../../bin/cluster/unres_clustMD-mult_ifort_MPICH_E0LL2Y.exe
+E0LL2Y: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${object} ${LIBS} -o ${BIN}
+
+xdrf/libxdrf.a:
+ cd xdrf && make
+
+
+clean:
+ /bin/rm -f *.o && /bin/rm -f compinfo && cd xdrf && make clean
+
+
--- /dev/null
+#include <stdio.h>
+#include <sys/utsname.h>
+#include <sys/types.h>
+#include <time.h>
+#include <string.h>
+
+main()
+{
+FILE *in, *in1, *out;
+int i,j,k,iv1,iv2,iv3;
+char *p1,buf[500],buf1[500],buf2[100],buf3[100];
+struct utsname Name;
+time_t Tp;
+
+in=fopen("cinfo.f","r");
+out=fopen("cinfo.f.new","w");
+if (fgets(buf,498,in) != NULL)
+ fprintf(out,"C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C\n");
+if (fgets(buf,498,in) != NULL)
+ sscanf(&buf[1],"%d %d %d",&iv1,&iv2,&iv3);
+iv3++;
+fprintf(out,"C %d %d %d\n",iv1,iv2,iv3);
+fprintf(out," subroutine cinfo\n");
+fprintf(out," include 'COMMON.IOUNITS'\n");
+fprintf(out," write(iout,*)'++++ Compile info ++++'\n");
+fprintf(out," write(iout,*)'Version %d.%-d build %d'\n",iv1,iv2,iv3);
+uname(&Name);
+time(&Tp);
+system("whoami > tmptmp");
+in1=fopen("tmptmp","r");
+if (fscanf(in1,"%s",buf1) != EOF)
+{
+p1=ctime(&Tp);
+p1[strlen(p1)-1]='\0';
+fprintf(out," write(iout,*)'compiled %s'\n",p1);
+fprintf(out," write(iout,*)'compiled by %s@%s'\n",buf1,Name.nodename);
+fprintf(out," write(iout,*)'OS name: %s '\n",Name.sysname);
+fprintf(out," write(iout,*)'OS release: %s '\n",Name.release);
+fprintf(out," write(iout,*)'OS version:',\n");
+fprintf(out," & ' %s '\n",Name.version);
+fprintf(out," write(iout,*)'flags:'\n");
+}
+system("rm tmptmp");
+fclose(in1);
+in1=fopen("Makefile","r");
+while(fgets(buf,498,in1) != NULL)
+ {
+ if((p1=strchr(buf,'=')) != NULL && buf[0] != '#')
+ {
+ buf[strlen(buf)-1]='\0';
+ if(strlen(buf) > 49)
+ {
+ buf[47]='\0';
+ strcat(buf,"...");
+ }
+ else
+ {
+ while(buf[strlen(buf)-1]=='\\')
+ {
+ strcat(buf,"\\");
+ fprintf(out," write(iout,*)'%s'\n",buf);
+ if (fgets(buf,498,in1) != NULL)
+ buf[strlen(buf)-1]='\0';
+ if(strlen(buf) > 49)
+ {
+ buf[47]='\0';
+ strcat(buf,"...");
+ }
+ }
+ }
+
+ fprintf(out," write(iout,*)'%s'\n",buf);
+ }
+ }
+fprintf(out," write(iout,*)'++++ End of compile info ++++'\n");
+fprintf(out," return\n");
+fprintf(out," end\n");
+fclose(out);
+fclose(in1);
+fclose(in);
+system("mv cinfo.f.new cinfo.f");
+}
--- /dev/null
+##################################################################
+INSTALL_DIR = /users/software/mpich2-1.0.7
+
+FC= gfortran
+
+OPT = -O
+
+FFLAGS = ${OPT} -c -I. -Iinclude_unres -I$(INSTALL_DIR)/include
+
+LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpthread xdrf/libxdrf.a
+
+.c.o:
+ cc -c -DLINUX -DPGI $*.c
+
+.f.o:
+ ${FC} ${FFLAGS} $*.f
+
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} ${FFLAGS} $*.F
+
+object = main_clust.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \
+ matmult.o readrtns.o pinorm.o rescode.o intcor.o timing.o misc.o \
+ geomout.o readpdb.o read_coords.o parmread.o probabl.o fitsq.o hc.o \
+ track.o wrtclust.o srtclust.o noyes.o contact.o printmat.o \
+ int_from_cart1.o energy_p_new.o icant.o proc_proc.o work_partition.o \
+ setup_var.o read_ref_str.o gnmr1.o ssMD.o
+
+all: no_option
+ @echo "Specify force field: GAB, 4P or E0LL2Y"
+
+no_option:
+
+GAB: CPPFLAGS = -DPROCOR -DLINUX -DG77 -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DCLUST -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+GAB: BIN = ../../../../bin/cluster/unres_clustMD_gfort_MPICH_GAB.exe
+GAB: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${object} ${LIBS} -o ${BIN}
+
+4P: CPPFLAGS = -DLINUX -DG77 -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DCLUST -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+4P: BIN = ../../../../bin/cluster/unres_clustMD_gfort_MPICH_4P.exe
+4P: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${object} ${LIBS} -o ${BIN}
+
+E0LL2Y: CPPFLAGS = -DLINUX -DG77 -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DCLUST -DSPLITELE -DLANG0
+E0LL2Y: BIN = ../../../../bin/cluster/unres_clustMD_gfort_MPICH_E0LL2Y.exe
+E0LL2Y: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${object} ${LIBS} -o ${BIN}
+
+xdrf/libxdrf.a:
+ cd xdrf && make
+
+clean:
+ /bin/rm -f *.o && /bin/rm -f compinfo && cd xdrf && make clean
+
+
--- /dev/null
+#include <stdio.h>
+#include <sys/utsname.h>
+#include <sys/types.h>
+#include <time.h>
+#include <string.h>
+
+main()
+{
+FILE *in, *in1, *out;
+int i,j,k,iv1,iv2,iv3;
+char *p1,buf[500],buf1[500],buf2[100],buf3[100];
+struct utsname Name;
+time_t Tp;
+
+in=fopen("cinfo.f","r");
+out=fopen("cinfo.f.new","w");
+if (fgets(buf,498,in) != NULL)
+ fprintf(out,"C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C\n");
+if (fgets(buf,498,in) != NULL)
+ sscanf(&buf[1],"%d %d %d",&iv1,&iv2,&iv3);
+iv3++;
+fprintf(out,"C %d %d %d\n",iv1,iv2,iv3);
+fprintf(out," subroutine cinfo\n");
+fprintf(out," include 'COMMON.IOUNITS'\n");
+fprintf(out," write(iout,*)'++++ Compile info ++++'\n");
+fprintf(out," write(iout,*)'Version %d.%-d build %d'\n",iv1,iv2,iv3);
+uname(&Name);
+time(&Tp);
+system("whoami > tmptmp");
+in1=fopen("tmptmp","r");
+if (fscanf(in1,"%s",buf1) != EOF)
+{
+p1=ctime(&Tp);
+p1[strlen(p1)-1]='\0';
+fprintf(out," write(iout,*)'compiled %s'\n",p1);
+fprintf(out," write(iout,*)'compiled by %s@%s'\n",buf1,Name.nodename);
+fprintf(out," write(iout,*)'OS name: %s '\n",Name.sysname);
+fprintf(out," write(iout,*)'OS release: %s '\n",Name.release);
+fprintf(out," write(iout,*)'OS version:',\n");
+fprintf(out," & ' %s '\n",Name.version);
+fprintf(out," write(iout,*)'flags:'\n");
+}
+system("rm tmptmp");
+fclose(in1);
+in1=fopen("Makefile","r");
+while(fgets(buf,498,in1) != NULL)
+ {
+ if((p1=strchr(buf,'=')) != NULL && buf[0] != '#')
+ {
+ buf[strlen(buf)-1]='\0';
+ if(strlen(buf) > 49)
+ {
+ buf[47]='\0';
+ strcat(buf,"...");
+ }
+ else
+ {
+ while(buf[strlen(buf)-1]=='\\')
+ {
+ strcat(buf,"\\");
+ fprintf(out," write(iout,*)'%s'\n",buf);
+ if (fgets(buf,498,in1) != NULL)
+ buf[strlen(buf)-1]='\0';
+ if(strlen(buf) > 49)
+ {
+ buf[47]='\0';
+ strcat(buf,"...");
+ }
+ }
+ }
+
+ fprintf(out," write(iout,*)'%s'\n",buf);
+ }
+ }
+fprintf(out," write(iout,*)'++++ End of compile info ++++'\n");
+fprintf(out," return\n");
+fprintf(out," end\n");
+fclose(out);
+fclose(in1);
+fclose(in);
+system("mv cinfo.f.new cinfo.f");
+}
--- /dev/null
+ double precision gcart, gxcart, gradcag,gradxag
+ common /mdgrad/ gcart(3,0:MAXRES), gxcart(3,0:MAXRES),
+ & gradcag(3,MAXRES),gradxag(3,MAXRES)
+ integer dimen,dimen1, dimen3, ifrag(2,50,maxprocs/20),
+ & ipair(2,100,maxprocs/20),iset,
+ & mset(maxprocs/20),nset
+ double precision IP,ISC(ntyp+1),mp,
+ & msc(ntyp+1),d_t_work(MAXRES6),
+ & d_t_work_new(MAXRES6),d_t(3,0:MAXRES2),d_t_new(3,0:MAXRES2),
+ & d_af_work(MAXRES6),d_as_work(MAXRES6),
+ & d_t_old(3,0:MAXRES2),d_a_old(3,0:MAXRES2),d_a_short(3,0:MAXRES2),
+ & Gmat(MAXRES2,MAXRES2),Ginv(MAXRES2,MAXRES2),A(MAXRES2,MAXRES2),
+ & d_a(3,0:MAXRES2),d_a_work(6*MAXRES),kinetic_force(MAXRES6),
+ & Gsqrp(MAXRES2,MAXRES2),Gsqrm(MAXRES2,MAXRES2),
+ & vtot(MAXRES2),Gvec(maxres2,maxres2),Geigen(maxres2)
+ double precision v_ini,d_time,d_time0,t_bath,tau_bath,
+ & EK,potE,potEcomp(0:n_ene+4),totE,totT,amax,kinetic_T,dvmax,damax,
+ & edriftmax,
+ & eq_time,wfrag(50,maxprocs/20),wpair(100,maxprocs/20),
+ & qfrag(50),qpair(100),
+ & qinfrag(50,maxprocs/20),qinpair(100,maxprocs/20),
+ & Ucdfrag,Ucdpair,dUdconst(3,0:MAXRES),Uconst,
+ & dUdxconst(3,0:MAXRES),dqwol(3,0:MAXRES),dxqwol(3,0:MAXRES),
+ & utheta(maxfrag_back),ugamma(maxfrag_back),uscdiff(maxfrag_back),
+ & dutheta(maxres),dugamma(maxres),duscdiff(3,maxres),
+ & duscdiffx(3,maxres),wfrag_back(3,maxfrag_back,maxprocs/20),
+ & uconst_back
+ integer n_timestep,ntwx,ntwe,lang,count_reset_moment,
+ & count_reset_vel,reset_fricmat,nfrag,npair,nfrag_back,
+ & ifrag_back(3,maxfrag_back,maxprocs/20),ntime_split,ntime_split0,
+ & maxtime_split
+ integer nresn,nyosh,nnos
+ double precision glogs,qmass,vlogs,xlogs
+ logical large,print_compon,tbf,rest,reset_moment,reset_vel,
+ & surfarea,rattle,usampl,mdpdb,RESPA,tnp,tnp1,tnh,xiresp
+ integer igmult_start,igmult_end,my_ng_count,ng_start,ng_counts,
+ & nginv_start,nginv_counts,myginv_ng_count
+ common /back_constr/ uconst_back,utheta,ugamma,uscdiff,
+ & dutheta,dugamma,duscdiff,duscdiffx,
+ & wfrag_back,nfrag_back,ifrag_back
+ common /qmeas/ qfrag,qpair,qinfrag,qinpair,wfrag,wpair,eq_time,
+ & Ucdfrag,Ucdpair,dUdconst,dUdxconst,dqwol,dxqwol,Uconst,
+ & iset,mset,nset,usampl,ifrag,ipair,npair,nfrag
+ common /mdpar/ v_ini,d_time,d_time0,scal_fric,
+ & t_bath,tau_bath,dvmax,damax,n_timestep,mdpdb,
+ & ntime_split,ntime_split0,maxtime_split,
+ & ntwx,ntwe,large,print_compon,tbf,rest,tnp,tnp1,tnh
+ common /MDcalc/ totT,totE,potE,potEcomp,EK,amax,edriftmax,
+ & kinetic_T
+ common /lagrange/ d_t,d_t_old,d_t_new,d_t_work,
+ & d_t_work_new,d_a,d_a_old,d_a_work,d_af_work,d_as_work,d_a_short,
+ & kinetic_force,
+ & A,Ginv,Gmat,Gvec,Geigen,Gsqrp,Gsqrm,
+ & vtot,dimen,dimen1,dimen3,lang,
+ & reset_moment,reset_vel,count_reset_moment,count_reset_vel,
+ & rattle,RESPA
+ common /inertia/ IP,ISC,MP,MSC
+ double precision scal_fric,rwat,etawat,gamp,
+ & gamsc(ntyp),stdfp,stdfsc(ntyp),stdforcp(MAXRES),
+ & stdforcsc(MAXRES),pstok,restok(ntyp+1),cPoise,Rb
+ common /langevin/ pstok,restok,gamp,gamsc,
+ & stdfp,stdfsc,stdforcp,stdforcsc,rwat,etawat,cPoise,Rb,surfarea,
+ & reset_fricmat
+ common /mdpmpi/ igmult_start,igmult_end,my_ng_count,
+ & myginv_ng_count,
+ & ng_start(0:MaxProcs-1),ng_counts(0:MaxProcs-1),
+ & nginv_start(0:MaxProcs),nginv_counts(0:MaxProcs-1)
+ double precision pi_np,pistar,s_np,s12_np,Q_np,E_old,H0,E_long,
+ & sold_np,d_t_half,Csplit,hhh
+ common /nosepoincare/ pi_np,pistar,s_np,s12_np,Q_np,E_old,H0,
+ & E_long,sold_np,d_t_half(3,0:MAXRES2),Csplit,hhh
+ common /nosehoover/ glogs(maxmnh),qmass(maxmnh),
+ & vlogs(maxmnh),xlogs(maxmnh),
+ & nresn,nyosh,nnos,xiresp
+ integer hmc,hmc_acc
+ double precision dc_hmc,hmc_etot,totThmc
+ common /hmc_md/ dc_hmc(3,0:maxres2),hmc_etot,totThmc,hmc,hmc_acc
--- /dev/null
+ integer king,idint,idreal,idchar,is_done
+ parameter (king=0,idint=1105,idreal=1729,idchar=1597,is_done=1)
+ integer me,cg_rank,fg_rank,fg_rank1,nodes,Nprocs,nfgtasks,kolor,
+ & koniec(0:maxprocs-1),WhatsUp,ifinish(maxprocs-1),CG_COMM,FG_COMM,
+ & FG_COMM1,CONT_FROM_COMM,CONT_TO_COMM,lentyp(0:maxprocs-1),
+ & kolor1,key1,nfgtasks1,MyRank,
+ & max_gs_size
+ logical yourjob, finished, cgdone
+ common/setup/me,MyRank,cg_rank,fg_rank,fg_rank1,nodes,Nprocs,
+ & nfgtasks,nfgtasks1,
+ & max_gs_size,kolor,koniec,WhatsUp,ifinish,CG_COMM,FG_COMM,
+ & FG_COMM1,CONT_FROM_COMM,CONT_TO_COMM,lentyp
+ integer MPI_UYZ,MPI_UYZGRAD,MPI_MU,MPI_MAT1,MPI_MAT2,
+ & MPI_THET,MPI_GAM,
+ & MPI_ROTAT1(0:1),MPI_ROTAT2(0:1),MPI_ROTAT_OLD(0:1),
+ & MPI_PRECOMP11(0:1),MPI_PRECOMP12(0:1),MPI_PRECOMP22(0:1),
+ & MPI_PRECOMP23(0:1)
+ common /types/ MPI_UYZ,MPI_UYZGRAD,MPI_MU,MPI_MAT1,MPI_MAT2,
+ & MPI_THET,MPI_GAM,
+ & MPI_ROTAT1,MPI_ROTAT2,MPI_ROTAT_OLD,MPI_PRECOMP11,MPI_PRECOMP12,
+ & MPI_PRECOMP22,MPI_PRECOMP23
--- /dev/null
+#################################################################################
+FC = mpixlf77
+OPT = -O4 -qarch=qp -qtune=qp -qnocr
+#OPT = -O3 -qarch=qp -qtune=qp -qdebug=function_trace
+#OPT = -O -qarch=qp -qtune=qp
+#OPT = -O0 -C -g -qarch=qp -qtune=qp #-qdebug=function_trace
+#-Minline=name:scalar2,scalar,transpose2,matvec2,prodmat3 \
+#-Mprefetch=distance:8,nta
+
+#OPT1 = -O -g -qarch=qp -qtune=qp
+#OPT1 = -O -g -qarch=qp -qtune=qp -qdebug=function_trace
+OPT1 = ${OPT}
+#OPT2 = -O2 -qarch=qp -qtune=qp
+#OPT2 = -O2 -qarch=qp -qtune=qp -qdebug=function_trace
+OPT2 = ${OPT}
+#OPTE = -O4 -qarch=qp -qtune=qp
+#OPTE = -O4 -qarch=qp -qtune=qp
+OPTE=${OPT}
+
+CFLAGS = -c
+FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
+FFLAGS1 = -c ${OPT1} -I$(INSTALL_DIR)/include
+FFLAGS2 = -c ${OPT2} -I$(INSTALL_DIR)/include
+FFLAGSE = -c ${OPTE} -I$(INSTALL_DIR)/include
+
+LIBS = xdrf/libxdrf.a
+
+ARCH = LINUX
+PP = /lib/cpp -P
+
+all: no_option
+ @echo "Specify force field: GAB, E0LL2Y, 4P or CASP3"
+
+.SUFFIXES: .F
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+
+object = unres_csa.o arcos.o cartprint.o chainbuild.o initialize_p.o \
+ matmult.o readrtns_csa.o parmread.o \
+ pinorm.o randgens.o rescode.o intcor.o timing.o misc.o intlocal.o \
+ cartder.o checkder_p.o econstr_local.o energy_p_new_barrier.o \
+ gradient_p.o minimize_p.o sumsld.o \
+ cored.o rmdd.o geomout_min.o readpdb.o \
+ intcartderiv.o \
+ MP.o printmat.o convert.o int_to_cart.o \
+ dfa.o \
+ together.o csa.o minim_jlee.o shift.o diff12.o bank.o newconf.o ran.o \
+ indexx.o prng_32.o contact.o gen_rand_conf.o \
+ sc_move.o test.o local_move.o rmsd.o fitsq.o elecont.o djacob.o \
+ distfit.o banach.o TMscore_subroutine.o minim_mult.o refsys.o
+
+no_option:
+
+GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+GAB: BIN = ../../../bin/unres/CSA/unres_csa_xlf77_MPICH_GAB.exe
+LIBS = -lpthread -L$(INSTALL_DIR)/lib -lmpich
+GAB: ${object}
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0
+E0LL2Y: BIN = ../../../bin/unres/CSA/unres_csa_xlf77_MPICH_E0LL2Y.exe
+E0LL2Y: ${object}
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+CASP3: CPPFLAGS = -DLINUX -DPGI -DISNAN -DMP -DMPI -DUNRES \
+ -DSPLITELE -DAMD64 -DLANG0 -DMOMENT \
+ -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DCRYST_TOR
+CASP3: BIN = ../../../bin/unres/CSA/unres_csa_xlf77_MPICH_CASP3.exe
+CASP3: ${object}
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+4P: CPPFLAGS = -DLINUX -DPGI -DISNAN -DMP -DMPI -DUNRES \
+ -DSPLITELE -DAMD64 -DLANG0 \
+ -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+4P: BIN = ../../../bin/unres/CSA/unres_csa_xlf77_MPICH_4P.exe
+4P: ${object}
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+clean:
+ /bin/rm -f *.o && /bin/rm -f compinfo
+
+test.o: test.F
+ ${FC} ${FFLAGS} ${CPPFLAGS} test.F
+
+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
+
+energy_p_new-sep_barrier.o : energy_p_new-sep_barrier.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new-sep_barrier.F
+
+lagrangian_lesyng.o : lagrangian_lesyng.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} lagrangian_lesyng.F
+
+MD_A-MTS.o : MD_A-MTS.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} MD_A-MTS.F
+
+blas.o : blas.f
+ ${FC} ${FFLAGS1} blas.f
+
+add.o : add.f
+ ${FC} ${FFLAGS1} add.f
+
+eigen.o : eigen.f
+ ${FC} ${FFLAGS2} eigen.f
+
+proc_proc.o: proc_proc.c
+ ${CC} ${CFLAGS} proc_proc.c
--- /dev/null
+###################################################################
+INSTALL_DIR = /users/software/mpich2-1.0.7
+
+FC= gfortran
+
+OPT = -O
+
+FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
+FFLAGS1 = -c -I$(INSTALL_DIR)/include
+FFLAGS2 = -c -O0 -I$(INSTALL_DIR)/include
+FFLAGS3 = -c -O -I$(INSTALL_DIR)/include
+FFLAGSE = -c -O3 -I$(INSTALL_DIR)/include
+
+LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpthread
+
+ARCH = LINUX
+PP = /lib/cpp -P
+
+
+all: no_option
+ @echo "Specify force field: GAB, E0LL2Y, 4P or CASP3"
+
+.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 refsys.o
+
+no_option:
+
+GAB: CPPFLAGS = -DPROCOR -DLINUX -DG77 -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+GAB: BIN = ../../../bin/unres/CSA/unres_csa_gfort_MPICH_GAB.exe
+GAB: ${object}
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DG77 -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0
+E0LL2Y: BIN = ../../../bin/unres/CSA/unres_csa_gfort_MPICH_E0LL2Y.exe
+E0LL2Y: ${object}
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+CASP3: CPPFLAGS = -DLINUX -DG77 -DISNAN -DMP -DMPI -DUNRES \
+ -DSPLITELE -DAMD64 -DLANG0 -DMOMENT \
+ -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DCRYST_TOR
+CASP3: BIN = ../../../bin/unres/CSA/unres_csa_gfort_MPICH_CASP3.exe
+CASP3: ${object}
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+4P: CPPFLAGS = -DLINUX -DG77 -DISNAN -DMP -DMPI -DUNRES \
+ -DSPLITELE -DAMD64 -DLANG0 \
+ -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+4P: BIN = ../../../bin/unres/CSA/unres_csa_gfort_MPICH_4P.exe
+4P: ${object}
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+clean:
+ /bin/rm -f *.o && /bin/rm -f compinfo
+
+test.o: test.F
+ ${FC} ${FFLAGS} ${CPPFLAGS} test.F
+
+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
+
+energy_p_new-sep_barrier.o : energy_p_new-sep_barrier.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new-sep_barrier.F
+
+lagrangian_lesyng.o : lagrangian_lesyng.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} lagrangian_lesyng.F
+
+MD_A-MTS.o : MD_A-MTS.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} MD_A-MTS.F
+
+blas.o : blas.f
+ ${FC} ${FFLAGS1} blas.f
+
+add.o : add.f
+ ${FC} ${FFLAGS1} add.f
+
+eigen.o : eigen.f
+ ${FC} ${FFLAGS2} eigen.f
+
+proc_proc.o: proc_proc.c
+ ${CC} ${CFLAGS} proc_proc.c
--- /dev/null
+###################################################################
+INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh
+
+
+FC= ifort
+
+OPT = -O3 -ip
+
+FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
+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
+
+ARCH = LINUX
+PP = /lib/cpp -P
+
+
+all: no_option
+ @echo "Specify force field: GAB, E0LL2Y, 4P or CASP3"
+
+.SUFFIXES: .F
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+
+object = unres_csa.o arcos.o cartprint.o chainbuild.o initialize_p.o \
+ matmult.o readrtns_csa.o parmread.o \
+ pinorm.o randgens.o rescode.o intcor.o timing.o misc.o intlocal.o \
+ cartder.o checkder_p.o econstr_local.o energy_p_new_barrier.o \
+ gradient_p.o minimize_p.o sumsld.o \
+ cored.o rmdd.o geomout_min.o readpdb.o \
+ intcartderiv.o \
+ MP.o printmat.o convert.o int_to_cart.o \
+ dfa.o \
+ together.o csa.o minim_jlee.o shift.o diff12.o bank.o newconf.o ran.o \
+ indexx.o prng_32.o contact.o gen_rand_conf.o \
+ sc_move.o test.o local_move.o rmsd.o fitsq.o elecont.o djacob.o \
+ distfit.o banach.o TMscore_subroutine.o minim_mult.o refsys.o
+
+no_option:
+
+GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+GAB: BIN = ../../../bin/unres/CSA/unres_csa_ifort_MPICH_GAB.exe
+LIBS = -lpthread -L$(INSTALL_DIR)/lib -lmpich
+GAB: ${object}
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0
+E0LL2Y: BIN = ../../../bin/unres/CSA/unres_csa_ifort_MPICH_E0LL2Y.exe
+E0LL2Y: ${object}
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+CASP3: CPPFLAGS = -DLINUX -DPGI -DISNAN -DMP -DMPI -DUNRES \
+ -DSPLITELE -DAMD64 -DLANG0 -DMOMENT \
+ -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DCRYST_TOR
+CASP3: BIN = ../../../bin/unres/CSA/unres_csa_ifort_MPICH_CASP3.exe
+CASP3: ${object}
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+4P: CPPFLAGS = -DLINUX -DPGI -DISNAN -DMP -DMPI -DUNRES \
+ -DSPLITELE -DAMD64 -DLANG0 \
+ -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+4P: BIN = ../../../bin/unres/CSA/unres_csa_ifort_MPICH_4P.exe
+4P: ${object}
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+clean:
+ /bin/rm -f *.o && /bin/rm -f compinfo
+
+test.o: test.F
+ ${FC} ${FFLAGS} ${CPPFLAGS} test.F
+
+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
+
+energy_p_new-sep_barrier.o : energy_p_new-sep_barrier.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new-sep_barrier.F
+
+lagrangian_lesyng.o : lagrangian_lesyng.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} lagrangian_lesyng.F
+
+MD_A-MTS.o : MD_A-MTS.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} MD_A-MTS.F
+
+blas.o : blas.f
+ ${FC} ${FFLAGS1} blas.f
+
+add.o : add.f
+ ${FC} ${FFLAGS1} add.f
+
+eigen.o : eigen.f
+ ${FC} ${FFLAGS2} eigen.f
+
+proc_proc.o: proc_proc.c
+ ${CC} ${CFLAGS} proc_proc.c
--- /dev/null
+ subroutine make_array
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CSA'
+
+ccccccccccccccccccccccccc
+c Level-2: group
+ccccccccccccccccccccccccc
+
+ indg=0
+ do k=1,numch
+ccccccccccccccccccccccccccccccccccccccccc
+! Groups the THETAs and the GAMMAs
+ do j=2,nres-1
+ indg=indg+1
+ if (j.lt.nres-1) then
+ ngroup(indg)=2
+ else
+ ngroup(indg)=1
+ endif
+ do i=1,ngroup(indg)
+ igroup(1,i,indg)=i
+ igroup(2,i,indg)=j
+ igroup(3,i,indg)=k
+ enddo
+ enddo
+ccccccccccccccccccccccccccccccccccccccccc
+ enddo
+! Groups the ALPHAs and the BETAs
+ do k=1,numch
+ do j=2,nres-1
+ if(itype(j).ne.10) then
+ indg=indg+1
+ ngroup(indg)=2
+ do i=1,ngroup(indg)
+ igroup(1,i,indg)=i+2
+ igroup(2,i,indg)=j
+ igroup(3,i,indg)=k
+ enddo
+ endif
+ enddo
+ enddo
+
+ ntotgr=indg
+ write(iout,*)
+ write(iout,*) "# of groups: ",ntotgr
+ do i=1,ntotgr
+ write(iout,41) i,ngroup(i),((igroup(k,j,i),k=1,3),j=1,ngroup(i))
+ enddo
+! close(iout)
+
+ 40 format(i3,3x,3i3)
+ 41 format(2i3,3x,6(3i3,2x))
+
+ return
+ end
+ccccccccccccccccccccccccccccccccccccccccccccccccc
+ccccccccccccccccccccccccccccccccccccccccccccccccc
+ subroutine make_ranvar(n,m,idum)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.VAR'
+ include 'COMMON.BANK'
+c al m=0
+ print *,'HOHOHOHO Make_RanVar!!!!!',n,m
+ itrial=0
+ do while(m.lt.n .and. itrial.le.10000)
+ itrial=itrial+1
+ jeden=1
+ call gen_rand_conf(jeden,*10)
+ call intout
+ m=m+1
+ do j=2,nres-1
+ dihang_in(1,j,1,m)=theta(j+1)
+ dihang_in(2,j,1,m)=phi(j+2)
+ dihang_in(3,j,1,m)=alph(j)
+ dihang_in(4,j,1,m)=omeg(j)
+ enddo
+ dihang_in(2,nres-1,1,m)=0.0d0
+ goto 20
+ 10 write (iout,*) 'Failed to generate conformation #',m+1,
+ & ' itrial=',itrial
+ 20 continue
+ enddo
+ print *,'Make_RanVar!!!!! m=',m,' itrial=',itrial
+
+ return
+ end
+ccccccccccccccccccccccccccccccccccccccccccccccccc
+ccccccccccccccccccccccccccccccccccccccccccccccccc
+ subroutine make_ranvar_reg(n,idum)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.VAR'
+ include 'COMMON.BANK'
+ include 'COMMON.GEO'
+ m=0
+ print *,'HOHOHOHO Make_RanVar_reg!!!!!'
+ itrial=0
+ do while(m.lt.n .and. itrial.le.10000)
+ itrial=itrial+1
+ jeden=1
+ call gen_rand_conf(jeden,*10)
+! call intout
+ m=m+1
+ do j=2,nres-1
+ dihang_in(1,j,1,m)=theta(j+1)
+ dihang_in(2,j,1,m)=phi(j+2)
+ dihang_in(3,j,1,m)=alph(j)
+ dihang_in(4,j,1,m)=omeg(j)
+ if(m.le.n*0.1) then
+ dihang_in(1,j,1,m)=90.0*deg2rad
+ dihang_in(2,j,1,m)=50.0*deg2rad
+ endif
+ enddo
+ dihang_in(2,nres-1,1,m)=0.0d0
+ goto 20
+ 10 write (iout,*) 'Failed to generate conformation #',m+1,
+ & ' itrial=',itrial
+ 20 continue
+ enddo
+ print *,'Make_RanVar!!!!! m=',m,' itrial=',itrial
+
+ return
+ end
+ccccccccccccccccccccccccccccccccccccccccccccccccc
+ccccccccccccccccccccccccccccccccccccccccccccccccc
+ subroutine from_pdb(n,idum)
+c This subroutine stores the UNRES int variables generated from
+c subroutine readpdb into the 1st conformation of in dihang_in.
+c Subsequent n-1 conformations of dihang_in have identical values
+c of theta and phi as the 1st conformation but random values for
+c alph and omeg.
+c The array cref (also generated from subroutine readpdb) is stored
+c to crefjlee to be used for rmsd calculation in CSA, if necessary.
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.VAR'
+ include 'COMMON.BANK'
+ include 'COMMON.GEO'
+
+ m=1
+ do j=2,nres-1
+ dihang_in(1,j,1,m)=theta(j+1)
+ dihang_in(2,j,1,m)=phi(j+2)
+ dihang_in(3,j,1,m)=alph(j)
+ dihang_in(4,j,1,m)=omeg(j)
+ enddo
+ dihang_in(2,nres-1,1,k)=0.0d0
+
+ do m=2,n
+ do k=2,nres-1
+ dihang_in(1,k,1,m)=dihang_in(1,k,1,1)
+ dihang_in(2,k,1,m)=dihang_in(2,k,1,1)
+ if(dabs(dihang_in(3,k,1,1)).gt.1.d-6) then
+ dihang_in(3,k,1,m)=90.d0*ran1(idum)+90.d0
+ dihang_in(3,k,1,m)=dihang_in(3,k,1,m)*deg2rad
+ endif
+ if(dabs(dihang_in(4,k,1,1)).gt.1.d-6) then
+ dihang_in(4,k,1,m)=360.d0*ran1(idum)-180.d0
+ dihang_in(4,k,1,m)=dihang_in(4,k,1,m)*deg2rad
+ endif
+ enddo
+ enddo
+
+c Store cref to crefjlee (they are in COMMON.CHAIN).
+ do k=1,2*nres
+ do kk=1,3
+ crefjlee(kk,k)=cref(kk,k)
+ enddo
+ enddo
+
+ open(icsa_native_int,file=csa_native_int,status="old")
+ do m=1,n
+ write(icsa_native_int,*) m,e
+ write(icsa_native_int,200)
+ & (dihang_in(1,k,1,m)*rad2deg,k=2,nres-1)
+ write(icsa_native_int,200)
+ & (dihang_in(2,k,1,m)*rad2deg,k=2,nres-2)
+ write(icsa_native_int,200)
+ & (dihang_in(3,k,1,m)*rad2deg,k=2,nres-1)
+ write(icsa_native_int,200)
+ & (dihang_in(4,k,1,m)*rad2deg,k=2,nres-1)
+ enddo
+
+ do k=1,nres
+ write(icsa_native_int,200) (crefjlee(i,k),i=1,3)
+ enddo
+ close(icsa_native_int)
+
+ 200 format (8f10.4)
+
+ return
+ end
+ccccccccccccccccccccccccccccccccccccccccccccccccc
+ccccccccccccccccccccccccccccccccccccccccccccccccc
+ subroutine from_int(n,mm,idum)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.VAR'
+ include 'COMMON.INTERACT'
+ include 'COMMON.BANK'
+ include 'COMMON.GEO'
+ include 'COMMON.CONTACTS'
+#ifdef MOMENT
+ include 'COMMON.CONTACTS.MOMENT'
+#endif
+ integer ilen
+ external ilen
+ logical fail
+ double precision energia(0:n_ene)
+
+ open(icsa_native_int,file=csa_native_int,status="old")
+ read (icsa_native_int,*)
+ call read_angles(icsa_native_int,*10)
+ goto 11
+ 10 write (iout,'(2a)') "CHUJ NASTAPIL - error in ",
+ & csa_native_int(:ilen(csa_native_int))
+ 11 continue
+ call intout
+ do j=2,nres-1
+ dihang_in(1,j,1,1)=theta(j+1)
+ dihang_in(2,j,1,1)=phi(j+2)
+ dihang_in(3,j,1,1)=alph(j)
+ dihang_in(4,j,1,1)=omeg(j)
+ enddo
+ dihang_in(2,nres-1,1,1)=0.0d0
+
+c read(icsa_native_int,*) ind,e
+c read(icsa_native_int,200) (dihang_in(1,k,1,1),k=2,nres-1)
+c read(icsa_native_int,200) (dihang_in(2,k,1,1),k=2,nres-2)
+c read(icsa_native_int,200) (dihang_in(3,k,1,1),k=2,nres-1)
+c read(icsa_native_int,200) (dihang_in(4,k,1,1),k=2,nres-1)
+c dihang_in(2,nres-1,1,1)=0.d0
+
+ maxsi=100
+ maxcount_fail=100
+
+ do m=mm+2,n
+c do k=2,nres-1
+c dihang_in(1,k,1,m)=dihang_in(1,k,1,1)
+c dihang_in(2,k,1,m)=dihang_in(2,k,1,1)
+c if(abs(dihang_in(3,k,1,1)).gt.1.d-3) then
+c dihang_in(3,k,1,m)=90.d0*ran1(idum)+90.d0
+c endif
+c if(abs(dihang_in(4,k,1,1)).gt.1.d-3) then
+c dihang_in(4,k,1,m)=360.d0*ran1(idum)-180.d0
+c endif
+c enddo
+c call intout
+ fail=.true.
+
+ icount_fail=0
+
+ DO WHILE (FAIL .AND. ICOUNT_FAIL .LE. MAXCOUNT_FAIL)
+
+ do i=nnt,nct
+ if (itype(i).ne.10) then
+cd print *,'i=',i,' itype=',itype(i),' theta=',theta(i+1)
+ fail=.true.
+ ii=0
+ do while (fail .and. ii .le. maxsi)
+ call gen_side(itype(i),theta(i+1),alph(i),omeg(i),fail)
+ ii = ii+1
+ enddo
+ endif
+ enddo
+ call chainbuild
+ call etotal(energia(0))
+ fail = (energia(0).ge.1.0d20)
+ icount_fail=icount_fail+1
+
+ ENDDO
+
+ if (icount_fail.gt.maxcount_fail) then
+ write (iout,*)
+ & 'Failed to generate non-overlaping near-native conf.',
+ & m
+ endif
+
+ do j=2,nres-1
+ dihang_in(1,j,1,m)=theta(j+1)
+ dihang_in(2,j,1,m)=phi(j+2)
+ dihang_in(3,j,1,m)=alph(j)
+ dihang_in(4,j,1,m)=omeg(j)
+ enddo
+ dihang_in(2,nres-1,1,m)=0.0d0
+ enddo
+
+c do m=1,n
+c write(icsa_native_int,*) m,e
+c write(icsa_native_int,200) (dihang_in(1,k,1,m),k=2,nres-1)
+c write(icsa_native_int,200) (dihang_in(2,k,1,m),k=2,nres-2)
+c write(icsa_native_int,200) (dihang_in(3,k,1,m),k=2,nres-1)
+c write(icsa_native_int,200) (dihang_in(4,k,1,m),k=2,nres-1)
+c enddo
+c close(icsa_native_int)
+
+c do m=mm+2,n
+c do i=1,4
+c do j=2,nres-1
+c dihang_in(i,j,1,m)=dihang_in(i,j,1,m)*deg2rad
+c enddo
+c enddo
+c enddo
+
+ call dihang_to_c(dihang_in(1,1,1,1))
+
+c Store c to cref (they are in COMMON.CHAIN).
+ do k=1,2*nres
+ do kk=1,3
+ crefjlee(kk,k)=c(kk,k)
+ enddo
+ enddo
+
+ call contact(.true.,ncont_ref,icont_ref,co)
+
+c do k=1,nres
+c write(icsa_native_int,200) (crefjlee(i,k),i=1,3)
+c enddo
+ close(icsa_native_int)
+
+ 200 format (8f10.4)
+
+ return
+ end
+ccccccccccccccccccccccccccccccccccccccccccccccccc
+ccccccccccccccccccccccccccccccccccccccccccccccccc
+ subroutine dihang_to_c(aarray)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.CSA'
+ include 'COMMON.BANK'
+ include 'COMMON.CHAIN'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+
+ dimension aarray(mxang,maxres,mxch)
+
+c do i=4,nres
+c phi(i)=dihang_in(1,i-2,1,1)
+c enddo
+ do i=2,nres-1
+ theta(i+1)=aarray(1,i,1)
+ phi(i+2)=aarray(2,i,1)
+ alph(i)=aarray(3,i,1)
+ omeg(i)=aarray(4,i,1)
+ enddo
+
+ call chainbuild
+
+ return
+ end
+ccccccccccccccccccccccccccccccccccccccccccccccccc
+ccccccccccccccccccccccccccccccccccccccccccccccccc
--- /dev/null
+#################################################################################
+FC = mpixlf77
+OPT = -O4 -qarch=qp -qtune=qp -qnocr
+#OPT = -O3 -qarch=qp -qtune=qp -qdebug=function_trace
+#OPT = -O -qarch=qp -qtune=qp
+#OPT = -O0 -C -g -qarch=qp -qtune=qp #-qdebug=function_trace
+#-Minline=name:scalar2,scalar,transpose2,matvec2,prodmat3 \
+#-Mprefetch=distance:8,nta
+
+#OPT1 = -O -g -qarch=qp -qtune=qp
+#OPT1 = -O -g -qarch=qp -qtune=qp -qdebug=function_trace
+OPT1 = ${OPT}
+#OPT2 = -O2 -qarch=qp -qtune=qp
+#OPT2 = -O2 -qarch=qp -qtune=qp -qdebug=function_trace
+OPT2 = ${OPT}
+#OPTE = -O4 -qarch=qp -qtune=qp
+#OPTE = -O4 -qarch=qp -qtune=qp
+OPTE=${OPT}
+
+CFLAGS = -c
+FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
+FFLAGS1 = -c ${OPT1} -I$(INSTALL_DIR)/include
+FFLAGS2 = -c ${OPT2} -I$(INSTALL_DIR)/include
+FFLAGSE = -c ${OPTE} -I$(INSTALL_DIR)/include
+
+LIBS = xdrf/libxdrf.a
+
+ARCH = LINUX
+PP = /lib/cpp -P
+
+all: no_option
+ @echo "Specify force field: GAB, E0LL2Y, 4P or CASP3"
+
+.SUFFIXES: .F
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+
+object = unres_csa.o arcos.o cartprint.o chainbuild.o initialize_p.o \
+ matmult.o readrtns_csa.o parmread.o \
+ pinorm.o randgens.o rescode.o intcor.o timing.o misc.o intlocal.o \
+ cartder.o checkder_p.o econstr_local.o energy_p_new_barrier.o \
+ gradient_p.o minimize_p.o sumsld.o \
+ cored.o rmdd.o geomout_min.o readpdb.o \
+ intcartderiv.o \
+ MP.o printmat.o convert.o int_to_cart.o \
+ dfa.o \
+ together.o csa.o minim_jlee.o shift.o diff12.o bank.o newconf.o ran.o \
+ indexx.o prng_32.o contact.o gen_rand_conf.o \
+ sc_move.o test.o local_move.o rmsd.o fitsq.o elecont.o djacob.o \
+ distfit.o banach.o TMscore_subroutine.o minim_mult.o refsys.o
+
+no_option:
+
+GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+GAB: BIN = ../../../bin/unres/CSA/unres_csa-DL_xlf77_MPICH_GAB.exe
+LIBS = -lpthread -L$(INSTALL_DIR)/lib -lmpich
+GAB: ${object}
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0
+E0LL2Y: BIN = ../../../bin/unres/CSA/unres_csa-DL_xlf77_MPICH_E0LL2Y.exe
+E0LL2Y: ${object}
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+4P: CPPFLAGS = -DLINUX -DPGI -DISNAN -DMP -DMPI -DUNRES \
+ -DSPLITELE -DAMD64 -DLANG0 \
+ -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+4P: BIN = ../../../bin/unres/CSA/unres_csa-DL_xlf77_MPICH_4P.exe
+4P: ${object}
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+clean:
+ /bin/rm -f *.o && /bin/rm -f compinfo
+
+test.o: test.F
+ ${FC} ${FFLAGS} ${CPPFLAGS} test.F
+
+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
+
+energy_p_new-sep_barrier.o : energy_p_new-sep_barrier.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new-sep_barrier.F
+
+lagrangian_lesyng.o : lagrangian_lesyng.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} lagrangian_lesyng.F
+
+MD_A-MTS.o : MD_A-MTS.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} MD_A-MTS.F
+
+blas.o : blas.f
+ ${FC} ${FFLAGS1} blas.f
+
+add.o : add.f
+ ${FC} ${FFLAGS1} add.f
+
+eigen.o : eigen.f
+ ${FC} ${FFLAGS2} eigen.f
+
+proc_proc.o: proc_proc.c
+ ${CC} ${CFLAGS} proc_proc.c
--- /dev/null
+###################################################################
+INSTALL_DIR = /users/software/mpich2-1.0.7
+
+FC= gfortran
+
+OPT = -O
+
+FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
+FFLAGS1 = -c -I$(INSTALL_DIR)/include
+FFLAGS2 = -c -O0 -I$(INSTALL_DIR)/include
+FFLAGS3 = -c -O -I$(INSTALL_DIR)/include
+FFLAGSE = -c -O3 -I$(INSTALL_DIR)/include
+
+LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpthread
+
+ARCH = LINUX
+PP = /lib/cpp -P
+
+
+all: no_option
+ @echo "Specify force field: GAB, E0LL2Y, 4P or CASP3"
+
+.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 refsys.o
+
+no_option:
+
+GAB: CPPFLAGS = -DPROCOR -DLINUX -DG77 -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+GAB: BIN = ../../../bin/unres/CSA/unres_csa-DL_gfort_MPICH_GAB.exe
+GAB: ${object}
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DG77 -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0
+E0LL2Y: BIN = ../../../bin/unres/CSA/unres_csa-DL_gfort_MPICH_E0LL2Y.exe
+E0LL2Y: ${object}
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+4P: CPPFLAGS = -DLINUX -DG77 -DISNAN -DMP -DMPI -DUNRES \
+ -DSPLITELE -DAMD64 -DLANG0 \
+ -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+4P: BIN = ../../../bin/unres/CSA/unres_csa-DL_gfort_MPICH_4P.exe
+4P: ${object}
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+clean:
+ /bin/rm -f *.o && /bin/rm -f compinfo
+
+test.o: test.F
+ ${FC} ${FFLAGS} ${CPPFLAGS} test.F
+
+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
+
+energy_p_new-sep_barrier.o : energy_p_new-sep_barrier.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new-sep_barrier.F
+
+lagrangian_lesyng.o : lagrangian_lesyng.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} lagrangian_lesyng.F
+
+MD_A-MTS.o : MD_A-MTS.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} MD_A-MTS.F
+
+blas.o : blas.f
+ ${FC} ${FFLAGS1} blas.f
+
+add.o : add.f
+ ${FC} ${FFLAGS1} add.f
+
+eigen.o : eigen.f
+ ${FC} ${FFLAGS2} eigen.f
+
+proc_proc.o: proc_proc.c
+ ${CC} ${CFLAGS} proc_proc.c
--- /dev/null
+###################################################################
+INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh
+
+
+FC= ifort
+
+OPT = -O3 -ip
+
+FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
+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
+
+ARCH = LINUX
+PP = /lib/cpp -P
+
+
+all: no_option
+ @echo "Specify force field: GAB, E0LL2Y, 4P or CASP3"
+
+.SUFFIXES: .F
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+
+object = unres_csa.o arcos.o cartprint.o chainbuild.o initialize_p.o \
+ matmult.o readrtns_csa.o parmread.o \
+ pinorm.o randgens.o rescode.o intcor.o timing.o misc.o intlocal.o \
+ cartder.o checkder_p.o econstr_local.o energy_p_new_barrier.o \
+ gradient_p.o minimize_p.o sumsld.o \
+ cored.o rmdd.o geomout_min.o readpdb.o \
+ intcartderiv.o \
+ MP.o printmat.o convert.o int_to_cart.o \
+ dfa.o \
+ together.o csa.o minim_jlee.o shift.o diff12.o bank.o newconf.o ran.o \
+ indexx.o prng_32.o contact.o gen_rand_conf.o \
+ sc_move.o test.o local_move.o rmsd.o fitsq.o elecont.o djacob.o \
+ distfit.o banach.o TMscore_subroutine.o minim_mult.o refsys.o
+
+no_option:
+
+GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+GAB: BIN = ../../../bin/unres/CSA/unres_csa-DL_ifort_MPICH_GAB.exe
+LIBS = -lpthread -L$(INSTALL_DIR)/lib -lmpich
+GAB: ${object}
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0
+E0LL2Y: BIN = ../../../bin/unres/CSA/unres_csa-DL_ifort_MPICH_E0LL2Y.exe
+E0LL2Y: ${object}
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+4P: CPPFLAGS = -DLINUX -DPGI -DISNAN -DMP -DMPI -DUNRES \
+ -DSPLITELE -DAMD64 -DLANG0 \
+ -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+4P: BIN = ../../../bin/unres/CSA/unres_csa-DL_ifort_MPICH_4P.exe
+4P: ${object}
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+clean:
+ /bin/rm -f *.o && /bin/rm -f compinfo
+
+test.o: test.F
+ ${FC} ${FFLAGS} ${CPPFLAGS} test.F
+
+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
+
+energy_p_new-sep_barrier.o : energy_p_new-sep_barrier.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new-sep_barrier.F
+
+lagrangian_lesyng.o : lagrangian_lesyng.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} lagrangian_lesyng.F
+
+MD_A-MTS.o : MD_A-MTS.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} MD_A-MTS.F
+
+blas.o : blas.f
+ ${FC} ${FFLAGS1} blas.f
+
+add.o : add.f
+ ${FC} ${FFLAGS1} add.f
+
+eigen.o : eigen.f
+ ${FC} ${FFLAGS2} eigen.f
+
+proc_proc.o: proc_proc.c
+ ${CC} ${CFLAGS} proc_proc.c
--- /dev/null
+###################################################################
+INSTALL_DIR = /users/software/mpich2-1.0.7
+
+FC= gfortran
+
+OPT = -O
+
+FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
+FFLAGS1 = -c -I$(INSTALL_DIR)/include
+FFLAGS2 = -c -O0 -I$(INSTALL_DIR)/include
+FFLAGS3 = -c -O -I$(INSTALL_DIR)/include
+FFLAGSE = -c -O3 -I$(INSTALL_DIR)/include
+
+LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpthread
+
+ARCH = LINUX
+PP = /lib/cpp -P
+
+all: no_option
+ @echo "Specify force field: GAB, 4P or E0LL2Y"
+
+.SUFFIXES: .F
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+
+object = unres.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \
+ matmult.o readrtns_CSA.o parmread.o gen_rand_conf.o printmat.o map.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 \
+ energy_p_new-sep_barrier.o gradient_p.o minimize_p.o sumsld.o \
+ cored.o rmdd.o geomout.o readpdb.o permut.o regularize.o thread.o fitsq.o mcm.o \
+ mc.o bond_move.o refsys.o check_sc_distr.o check_bond.o contact.o djacob.o \
+ eigen.o blas.o add.o entmcm.o minim_mcmf.o \
+ together.o csa.o minim_jlee.o shift.o diff12.o bank.o newconf.o ran.o \
+ indexx.o MP.o compare_s1.o prng_32.o \
+ test.o banach.o distfit.o rmsd.o elecont.o dihed_cons.o \
+ sc_move.o local_move.o \
+ intcartderiv.o lagrangian_lesyng.o\
+ stochfric.o kinetic_lesyng.o MD_A-MTS.o moments.o int_to_cart.o \
+ surfatom.o sort.o muca_md.o MREMD.o rattle.o gauss.o energy_split-sep.o \
+ q_measure.o gnmr1.o ssMD.o
+
+no_option:
+
+GAB: CPPFLAGS = -DPROCOR -DLINUX -DG77 -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+GAB: BIN = ../../../bin/unres/MD/unres-D-symetr_gfort_MPICH_GAB.exe
+GAB: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+4P: CPPFLAGS = -DLINUX -DG77 -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+4P: BIN = ../../../bin/unres/MD/unres-mult-symetr_gfort_MPICH_4P.exe
+4P: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DG77 -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0
+E0LL2Y: BIN = ../../../bin/unres/MD/unres-mult-symetr_gfort_MPICH_E0LL2Y.exe
+E0LL2Y: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+xdrf/libxdrf.a:
+ cd xdrf && make
+
+
+clean:
+ /bin/rm -f *.o && /bin/rm -f compinfo && cd xdrf && make clean
+
+test.o: test.F
+ ${FC} ${FFLAGS} ${CPPFLAGS} test.F
+
+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
+
+energy_p_new-sep_barrier.o : energy_p_new-sep_barrier.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new-sep_barrier.F
+
+lagrangian_lesyng.o : lagrangian_lesyng.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} lagrangian_lesyng.F
+
+MD_A-MTS.o : MD_A-MTS.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} MD_A-MTS.F
+
+blas.o : blas.f
+ ${FC} ${FFLAGS1} blas.f
+
+add.o : add.f
+ ${FC} ${FFLAGS1} add.f
+
+eigen.o : eigen.f
+ ${FC} ${FFLAGS2} eigen.f
+
+proc_proc.o: proc_proc.c
+ ${CC} ${CFLAGS} proc_proc.c
--- /dev/null
+###################################################################
+INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh
+
+
+FC= ifort
+
+OPT = -O3 -ip
+
+FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
+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
+
+ARCH = LINUX
+PP = /lib/cpp -P
+
+
+all: no_option
+ @echo "Specify force field: GAB, 4P or E0LL2Y"
+
+.SUFFIXES: .F
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+
+object = unres.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \
+ matmult.o readrtns_CSA.o parmread.o gen_rand_conf.o printmat.o map.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 \
+ energy_p_new-sep_barrier.o gradient_p.o minimize_p.o sumsld.o \
+ cored.o rmdd.o geomout.o readpdb.o permut.o regularize.o thread.o fitsq.o mcm.o \
+ mc.o bond_move.o refsys.o check_sc_distr.o check_bond.o contact.o djacob.o \
+ eigen.o blas.o add.o entmcm.o minim_mcmf.o \
+ together.o csa.o minim_jlee.o shift.o diff12.o bank.o newconf.o ran.o \
+ indexx.o MP.o compare_s1.o prng_32.o \
+ test.o banach.o distfit.o rmsd.o elecont.o dihed_cons.o \
+ sc_move.o local_move.o \
+ intcartderiv.o lagrangian_lesyng.o\
+ stochfric.o kinetic_lesyng.o MD_A-MTS.o moments.o int_to_cart.o \
+ surfatom.o sort.o muca_md.o MREMD.o rattle.o gauss.o energy_split-sep.o \
+ q_measure.o gnmr1.o ssMD.o
+
+no_option:
+
+GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+GAB: BIN = ../../../bin/unres/MD/unres-mult-symetr_ifort_MPICH_GAB.exe
+GAB: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+4P: CPPFLAGS = -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+4P: BIN = ../../../bin/unres/MD/unres-mult-symetr_ifort_MPICH_4P.exe
+4P: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0
+E0LL2Y: BIN = ../../../bin/unres/MD/unres-mult-symetr_ifort_MPICH_E0LL2Y.exe
+E0LL2Y: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+xdrf/libxdrf.a:
+ cd xdrf && make
+
+
+clean:
+ /bin/rm -f *.o && /bin/rm -f compinfo && cd xdrf && make clean
+
+test.o: test.F
+ ${FC} ${FFLAGS} ${CPPFLAGS} test.F
+
+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
+
+energy_p_new-sep_barrier.o : energy_p_new-sep_barrier.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new-sep_barrier.F
+
+lagrangian_lesyng.o : lagrangian_lesyng.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} lagrangian_lesyng.F
+
+MD_A-MTS.o : MD_A-MTS.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} MD_A-MTS.F
+
+blas.o : blas.f
+ ${FC} ${FFLAGS1} blas.f
+
+add.o : add.f
+ ${FC} ${FFLAGS1} add.f
+
+eigen.o : eigen.f
+ ${FC} ${FFLAGS2} eigen.f
+
+proc_proc.o: proc_proc.c
+ ${CC} ${CFLAGS} proc_proc.c
--- /dev/null
+#
+FC = mpixlf77
+OPT = -O4 -qarch=qp -qtune=qp -qnocr
+#OPT = -O3 -qarch=qp -qtune=qp -qdebug=function_trace
+#OPT = -O -qarch=qp -qtune=qp
+#OPT = -O0 -C -g -qarch=qp -qtune=qp #-qdebug=function_trace
+#-Minline=name:scalar2,scalar,transpose2,matvec2,prodmat3 \
+#-Mprefetch=distance:8,nta
+
+#OPT1 = -O -g -qarch=qp -qtune=qp
+#OPT1 = -O -g -qarch=qp -qtune=qp -qdebug=function_trace
+OPT1 = ${OPT}
+#OPT2 = -O2 -qarch=qp -qtune=qp
+#OPT2 = -O2 -qarch=qp -qtune=qp -qdebug=function_trace
+OPT2 = ${OPT}
+#OPTE = -O4 -qarch=qp -qtune=qp
+#OPTE = -O4 -qarch=qp -qtune=qp
+OPTE=${OPT}
+
+CFLAGS = -c
+FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
+FFLAGS1 = -c ${OPT1} -I$(INSTALL_DIR)/include
+FFLAGS2 = -c ${OPT2} -I$(INSTALL_DIR)/include
+FFLAGSE = -c ${OPTE} -I$(INSTALL_DIR)/include
+
+LIBS = xdrf/libxdrf.a
+
+ARCH = LINUX
+PP = /lib/cpp -P
+
+
+all: unres
+
+.SUFFIXES: .F
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+object = unres.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \
+ matmult.o readrtns_CSA.o parmread.o gen_rand_conf.o printmat.o map.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 \
+ energy_p_new-sep_barrier.o gradient_p.o minimize_p.o sumsld.o \
+ cored.o rmdd.o geomout.o readpdb.o permut.o regularize.o thread.o fitsq.o mcm.o \
+ mc.o bond_move.o refsys.o check_sc_distr.o check_bond.o contact.o djacob.o \
+ eigen.o blas.o add.o entmcm.o minim_mcmf.o \
+ together.o csa.o minim_jlee.o shift.o diff12.o bank.o newconf.o ran.o \
+ indexx.o MP.o compare_s1.o prng_32.o \
+ test.o banach.o distfit.o rmsd.o elecont.o dihed_cons.o \
+ sc_move.o local_move.o \
+ intcartderiv.o lagrangian_lesyng.o\
+ stochfric.o kinetic_lesyng.o MD_A-MTS.o moments.o int_to_cart.o \
+ surfatom.o sort.o muca_md.o MREMD.o rattle.o gauss.o energy_split-sep.o \
+ q_measure.o gnmr1.o ssMD.o
+
+all: no_option
+ @echo "Specify force field: GAB, 4P or E0LL2Y"
+
+GAB: CPPFLAGS = -WF,-DAIX -WF,-DPROCOR -WF,-DLINUX -WF,-DPGI -WF,-DUNRES -WF,-DISNAN -WF,-DMP -WF,-DMPI \
+ -WF,-DSPLITELE -WF,-DLANG0 -WF,-DCRYST_BOND -WF,-DCRYST_THETA -WF,-DCRYST_SC
+GAB: BIN = ../bin/unres-mult-symetr_xlf77_MPI_GAB.exe
+GAB: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+4P: CPPFLAGS = -WF,-DAIX -WF,-DLINUX -WF,-DPGI -WF,-DUNRES -WF,-DISNAN -WF,-DMP -WF,-DMPI \
+ -WF,-DSPLITELE -WF,-DLANG0 -WF,-DCRYST_BOND -WF,-DCRYST_THETA -WF,-DCRYST_SC
+4P: BIN = ../bin/unres-mult-symetr_xlf77_MPI_4P.exe
+4P: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+E0LL2Y: CPPFLAGS = -WF,-DAIX -WF,-DPROCOR -WF,-DLINUX -WF,-DPGI -WF,-DUNRES -WF,-DISNAN -WF,-DMP -WF,-DMPI \
+ -WF,-DSPLITELE -WF,-DLANG0
+E0LL2Y: BIN = ../bin/unres-mult-symetr_xlf77_MPI_E0LL2Y.exe
+E0LL2Y: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+xdrf/libxdrf.a:
+ cd xdrf && make
+
+
+clean:
+ /bin/rm -f *.o && /bin/rm -f compinfo && cd xdrf && make clean
+
+test.o: test.F
+ ${FC} ${FFLAGS} ${CPPFLAGS} test.F
+
+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
+
+energy_p_new-sep_barrier.o : energy_p_new-sep_barrier.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new-sep_barrier.F
+
+lagrangian_lesyng.o : lagrangian_lesyng.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} lagrangian_lesyng.F
+
+MD_A-MTS.o : MD_A-MTS.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} MD_A-MTS.F
+
+blas.o : blas.f
+ ${FC} ${FFLAGS1} blas.f
+
+add.o : add.f
+ ${FC} ${FFLAGS1} add.f
+
+eigen.o : eigen.f
+ ${FC} ${FFLAGS2} eigen.f
+
+proc_proc.o: proc_proc.c
+ ${CC} ${CFLAGS} proc_proc.c
--- /dev/null
+FC= gfortran
+FFLAGS = -c ${OPT} -I.
+FFLAGS1 = -c ${OPT1} -I.
+
+CC = cc
+
+CFLAGS = -DLINUX -DPGI -c
+
+OPT = -O -fbounds-check -g
+OPT1 = -g
+
+#OPT = -fbounds-check -g
+#OPT1 = -g
+
+# -Mvect <---slows down
+# -Minline=name:matmat2 <---false convergence
+
+LIBS = -Lxdrf -lxdrf
+#-DMOMENT
+#-DCO_BIAS
+#-DCRYST_TOR
+#-DDEBUG
+
+ARCH = LINUX
+PP = /lib/cpp -P
+
+all:
+ @echo "Specify force field: GAB, 4P or E0LL2Y"
+
+.SUFFIXES: .F
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+object = unres.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \
+ matmult.o readrtns_CSA.o parmread.o gen_rand_conf.o printmat.o map.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 \
+ energy_p_new-sep_barrier.o gradient_p.o minimize_p.o sumsld.o \
+ cored.o rmdd.o geomout.o readpdb.o permut.o regularize.o thread.o fitsq.o mcm.o \
+ mc.o bond_move.o refsys.o check_sc_distr.o check_bond.o contact.o djacob.o \
+ eigen.o blas.o add.o entmcm.o minim_mcmf.o \
+ together.o csa.o minim_jlee.o shift.o diff12.o bank.o newconf.o ran.o \
+ indexx.o MP.o compare_s1.o prng_32.o \
+ test.o banach.o distfit.o rmsd.o elecont.o dihed_cons.o \
+ sc_move.o local_move.o \
+ intcartderiv.o lagrangian_lesyng.o\
+ stochfric.o kinetic_lesyng.o MD_A-MTS.o moments.o int_to_cart.o \
+ surfatom.o sort.o muca_md.o MREMD.o rattle.o gauss.o energy_split-sep.o \
+ q_measure.o gnmr1.o ssMD.o
+
+no_option:
+
+GAB: CPPFLAGS = -DPROCOR -DLINUX -DAMD64 -DUNRES -DISNAN \
+ -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+GAB: BIN = ../../../bin/unres/MD/unres-mult-symetr_gfortran_single_GAB.exe
+GAB: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+4P: CPPFLAGS = -DLINUX -DAMD64 -DUNRES -DISNAN \
+ -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+4P: BIN = ../../../bin/unres/MD/unres-mult-symetr_gfortran_single_4P.exe
+4P: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DAMD64 -DUNRES -DISNAN \
+ -DSPLITELE -DLANG0
+E0LL2Y: BIN = ../../../bin/unres/MD/unres-mult-symetr_gfortran_single_E0LL2Y.exe
+E0LL2Y: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+xdrf/libxdrf.a:
+ cd xdrf && make
+
+clean:
+ /bin/rm -f *.o && /bin/rm -f compinfo && cd xdrf && make clean
+
+newconf.o: newconf.F
+ ${FC} ${FFLAGS} ${CPPFLAGS} newconf.F
+
+bank.o: bank.F
+ ${FC} ${FFLAGS} ${CPPFLAGS} bank.F
+
+diff12.o: diff12.f
+ ${FC} ${FFLAGS} ${CPPFLAGS} diff12.f
+
+csa.o: csa.f
+ ${FC} ${FFLAGS1} ${CPPFLAGS} csa.f
+
+shift.o: shift.F
+ ${FC} ${FFLAGS1} ${CPPFLAGS} shift.F
+
+ran.o: ran.f
+ ${FC} ${FFLAGS1} ${CPPFLAGS} ran.f
+
+together.o: together.F
+ ${FC} ${FFLAGS} ${CPPFLAGS} together.F
+
+fitsq.o: fitsq.f
+ ${FC} ${FFLAGS1} ${CPPFLAGS} fitsq.f
+
+rmsd.o: rmsd.F
+ ${FC} ${FFLAGS1} ${CPPFLAGS} rmsd.F
+
+contact.o: contact.f
+ ${FC} ${FFLAGS1} ${CPPFLAGS} contact.f
+
+minim_jlee.o: minim_jlee.F
+ ${FC} ${FFLAGS1} ${CPPFLAGS} minim_jlee.F
+
+minimize_p.o: minimize_p.F
+ ${FC} ${FFLAGS1} ${CPPFLAGS} minimize_p.F
+
+gen_rand_conf.o: gen_rand_conf.F
+ ${FC} ${FFLAGS} ${CPPFLAGS} gen_rand_conf.F
+
+
+test.o: test.F
+ ${FC} ${FFLAGS1} ${CPPFLAGS} test.F
+
+elecont.o: elecont.f
+ ${FC} ${FFLAGS} ${CPPFLAGS} elecont.f
+
+eigen.o: eigen.f
+ ${FC} ${FFLAGS1} eigen.f
+
+blas.o: blas.f
+ ${FC} ${FFLAGS1} blas.f
+
+add.o: add.f
+ ${FC} ${FFLAGS1} add.f
+
+proc_proc.o: proc_proc.c
+ ${CC} ${CFLAGS} proc_proc.c
--- /dev/null
+FC = ifort
+FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
+FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)/include
+FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include
+FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report -I$(INSTALL_DIR)/include
+
+CC = cc
+
+CFLAGS = -DLINUX -DPGI -c
+
+OPT = -O3 -ip -w
+
+# -Mvect <---slows down
+# -Minline=name:matmat2 <---false convergence
+
+LIBS = -Lxdrf -lxdrf
+#-DMOMENT
+#-DCO_BIAS
+#-DCRYST_TOR
+#-DDEBUG
+
+ARCH = LINUX
+PP = /lib/cpp -P
+
+all:
+ @echo "Specify force field: GAB, 4P or E0LL2Y"
+
+.SUFFIXES: .F
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+object = unres.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \
+ matmult.o readrtns.o parmread.o gen_rand_conf.o printmat.o map.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 \
+ energy_p_new-sep_barrier.o gradient_p.o minimize_p.o sumsld.o \
+ cored.o rmdd.o geomout.o readpdb.o regularize.o thread.o fitsq.o mcm.o \
+ mc.o bond_move.o refsys.o check_sc_distr.o check_bond.o contact.o djacob.o \
+ eigen.o blas.o add.o entmcm.o minim_mcmf.o \
+ MP.o compare_s1.o prng.o \
+ banach.o rmsd.o elecont.o dihed_cons.o \
+ sc_move.o local_move.o \
+ intcartderiv.o lagrangian_lesyng.o\
+ stochfric.o kinetic_lesyng.o MD_A-MTS.o moments.o int_to_cart.o \
+ surfatom.o sort.o muca_md.o MREMD.o rattle.o gauss.o energy_split-sep.o \
+ q_measure.o gnmr1.o test.o ssMD.o
+
+no_option:
+
+GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN \
+ -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+GAB: BIN = ../../../bin/unres/MD/unres-mult_ifort_single_GAB.exe
+GAB: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+4P: CPPFLAGS = -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN \
+ -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+4P: BIN = ../../../bin/unres/MD/unres-mult_ifort_single_4P.exe
+4P: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN \
+ -DSPLITELE -DLANG0
+E0LL2Y: BIN = ../../../bin/unres/MD/unres-mult_ifort_single_E0LL2Y.exe
+E0LL2Y: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+xdrf/libxdrf.a:
+ cd xdrf && make
+
+clean:
+ /bin/rm -f *.o && /bin/rm -f compinfo && cd xdrf && make clean
+
+test.o: test.F
+ ${FC} ${FFLAGS} ${CPPFLAGS} test.F
+
+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
+
+energy_p_new-sep_barrier.o : energy_p_new-sep_barrier.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new-sep_barrier.F
+
+lagrangian_lesyng.o : lagrangian_lesyng.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} lagrangian_lesyng.F
+
+MD_A-MTS.o : MD_A-MTS.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} MD_A-MTS.F
+
+blas.o : blas.f
+ ${FC} ${FFLAGS1} blas.f
+
+add.o : add.f
+ ${FC} ${FFLAGS1} add.f
+
+eigen.o : eigen.f
+ ${FC} ${FFLAGS2} eigen.f
+
+proc_proc.o: proc_proc.c
+ ${CC} ${CFLAGS} proc_proc.c
--- /dev/null
+###################################################################
+INSTALL_DIR = /users/software/mpich2-1.0.7
+
+FC= gfortran
+
+OPT = -O
+
+FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
+FFLAGS1 = -c -I$(INSTALL_DIR)/include
+FFLAGS2 = -c -O0 -I$(INSTALL_DIR)/include
+FFLAGS3 = -c -O -I$(INSTALL_DIR)/include
+FFLAGSE = -c -O3 -I$(INSTALL_DIR)/include
+
+LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpthread xdrf/libxdrf.a
+
+ARCH = LINUX
+PP = /lib/cpp -P
+
+all: no_option
+ @echo "Specify force field: GAB, 4P or E0LL2Y"
+
+.SUFFIXES: .F
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+
+object = unres.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \
+ matmult.o readrtns.o parmread.o gen_rand_conf.o printmat.o map.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 \
+ energy_p_new-sep_barrier.o gradient_p.o minimize_p.o sumsld.o \
+ cored.o rmdd.o geomout.o readpdb.o regularize.o thread.o fitsq.o mcm.o \
+ mc.o bond_move.o refsys.o check_sc_distr.o check_bond.o contact.o djacob.o \
+ eigen.o blas.o add.o entmcm.o minim_mcmf.o \
+ MP.o compare_s1.o prng_32.o \
+ banach.o rmsd.o elecont.o dihed_cons.o \
+ sc_move.o local_move.o \
+ intcartderiv.o lagrangian_lesyng.o\
+ stochfric.o kinetic_lesyng.o MD_A-MTS.o moments.o int_to_cart.o \
+ surfatom.o sort.o muca_md.o MREMD.o rattle.o gauss.o energy_split-sep.o \
+ q_measure.o gnmr1.o test.o ssMD.o
+
+no_option:
+
+GAB: CPPFLAGS = -DPROCOR -DLINUX -DG77 -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+GAB: BIN = ../../../bin/unres/MD/unres_gfort_MPICH_GAB.exe
+GAB: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+4P: CPPFLAGS = -DLINUX -DG77 -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+4P: BIN = ../../../bin/unres/MD/unres_gfort_MPICH_4P.exe
+4P: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DG77 -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0
+E0LL2Y: BIN = ../../../bin/unres/MD/unres_gfort_MPICH_E0LL2Y.exe
+E0LL2Y: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+xdrf/libxdrf.a:
+ cd xdrf && make
+
+
+clean:
+ /bin/rm -f *.o && /bin/rm -f compinfo && cd xdrf && make clean
+
+test.o: test.F
+ ${FC} ${FFLAGS} ${CPPFLAGS} test.F
+
+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
+
+energy_p_new-sep_barrier.o : energy_p_new-sep_barrier.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new-sep_barrier.F
+
+lagrangian_lesyng.o : lagrangian_lesyng.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} lagrangian_lesyng.F
+
+MD_A-MTS.o : MD_A-MTS.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} MD_A-MTS.F
+
+blas.o : blas.f
+ ${FC} ${FFLAGS1} blas.f
+
+add.o : add.f
+ ${FC} ${FFLAGS1} add.f
+
+eigen.o : eigen.f
+ ${FC} ${FFLAGS2} eigen.f
+
+proc_proc.o: proc_proc.c
+ ${CC} ${CFLAGS} proc_proc.c
--- /dev/null
+#
+FC = mpixlf77
+OPT = -O4 -qarch=qp -qtune=qp -qnocr
+#OPT = -O3 -qarch=qp -qtune=qp -qdebug=function_trace
+#OPT = -O -qarch=qp -qtune=qp
+#OPT = -O0 -C -g -qarch=qp -qtune=qp #-qdebug=function_trace
+#-Minline=name:scalar2,scalar,transpose2,matvec2,prodmat3 \
+#-Mprefetch=distance:8,nta
+
+#OPT1 = -O -g -qarch=qp -qtune=qp
+#OPT1 = -O -g -qarch=qp -qtune=qp -qdebug=function_trace
+OPT1 = ${OPT}
+#OPT2 = -O2 -qarch=qp -qtune=qp
+#OPT2 = -O2 -qarch=qp -qtune=qp -qdebug=function_trace
+OPT2 = ${OPT}
+#OPTE = -O4 -qarch=qp -qtune=qp
+#OPTE = -O4 -qarch=qp -qtune=qp
+OPTE=${OPT}
+
+CFLAGS = -c
+FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
+FFLAGS1 = -c ${OPT1} -I$(INSTALL_DIR)/include
+FFLAGS2 = -c ${OPT2} -I$(INSTALL_DIR)/include
+FFLAGSE = -c ${OPTE} -I$(INSTALL_DIR)/include
+
+LIBS = xdrf/libxdrf.a
+
+ARCH = LINUX
+PP = /lib/cpp -P
+
+
+all: unres
+
+.SUFFIXES: .F
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+
+object = unres.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \
+ matmult.o readrtns.o parmread.o gen_rand_conf.o printmat.o map.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 \
+ energy_p_new-sep_barrier.o gradient_p.o minimize_p.o sumsld.o \
+ cored.o rmdd.o geomout.o readpdb.o regularize.o thread.o fitsq.o mcm.o \
+ mc.o bond_move.o refsys.o check_sc_distr.o check_bond.o contact.o djacob.o \
+ eigen.o blas.o add.o entmcm.o minim_mcmf.o \
+ MP.o compare_s1.o prng_32.o \
+ banach.o rmsd.o elecont.o dihed_cons.o \
+ sc_move.o local_move.o \
+ intcartderiv.o lagrangian_lesyng.o\
+ stochfric.o kinetic_lesyng.o MD_A-MTS.o moments.o int_to_cart.o \
+ surfatom.o sort.o muca_md.o MREMD.o rattle.o gauss.o energy_split-sep.o \
+ q_measure.o gnmr1.o test.o ssMD.o
+
+all: no_option
+ @echo "Specify force field: GAB, 4P or E0LL2Y"
+
+GAB: CPPFLAGS = -WF,-DAIX -WF,-DPROCOR -WF,-DLINUX -WF,-DPGI -WF,-DUNRES -WF,-DISNAN -WF,-DMP -WF,-DMPI \
+ -WF,-DSPLITELE -WF,-DLANG0 -WF,-DCRYST_BOND -WF,-DCRYST_THETA -WF,-DCRYST_SC
+GAB: BIN = ../bin/unres_xlf77_MPI_GAB.exe
+GAB: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+4P: CPPFLAGS = -WF,-DAIX -WF,-DLINUX -WF,-DPGI -WF,-DUNRES -WF,-DISNAN -WF,-DMP -WF,-DMPI \
+ -WF,-DSPLITELE -WF,-DLANG0 -WF,-DCRYST_BOND -WF,-DCRYST_THETA -WF,-DCRYST_SC
+4P: BIN = ../bin/unres_xlf77_MPI_4P.exe
+4P: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+E0LL2Y: CPPFLAGS = -WF,-DAIX -WF,-DPROCOR -WF,-DLINUX -WF,-DPGI -WF,-DUNRES -WF,-DISNAN -WF,-DMP -WF,-DMPI \
+ -WF,-DSPLITELE -WF,-DLANG0
+E0LL2Y: BIN = ../bin/unres_xlf77_MPI_E0LL2Y.exe
+E0LL2Y: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+xdrf/libxdrf.a:
+ cd xdrf && make
+
+
+clean:
+ /bin/rm -f *.o && /bin/rm -f compinfo && cd xdrf && make clean
+
+test.o: test.F
+ ${FC} ${FFLAGS} ${CPPFLAGS} test.F
+
+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
+
+energy_p_new-sep_barrier.o : energy_p_new-sep_barrier.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new-sep_barrier.F
+
+lagrangian_lesyng.o : lagrangian_lesyng.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} lagrangian_lesyng.F
+
+MD_A-MTS.o : MD_A-MTS.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} MD_A-MTS.F
+
+blas.o : blas.f
+ ${FC} ${FFLAGS1} blas.f
+
+add.o : add.f
+ ${FC} ${FFLAGS1} add.f
+
+eigen.o : eigen.f
+ ${FC} ${FFLAGS2} eigen.f
+
+proc_proc.o: proc_proc.c
+ ${CC} ${CFLAGS} proc_proc.c
--- /dev/null
+INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh
+BIN = ../../../bin/wham
+FC= ifort
+OPT = -mcmodel=medium -O3 -ip -w
+#OPT = -mcmodel=medium -g -CB
+FFLAGS = ${OPT} -c -I. -I./include_unres -I$(INSTALL_DIR)/include
+LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpmpich xdrf/libxdrf.a
+
+.f.o:
+ ${FC} ${FFLAGS} $*.f
+
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+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 \
+ 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 \
+ read_dist_constr.o \
+ permut.o \
+ wham_calc1.o
+
+objects_compar = \
+ readrtns_compar.o \
+ readpdb.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
+
+all: no_option
+ @echo "Specify force field: GAB, 4P or E0LL2Y"
+
+no_option:
+
+GAB: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI -DISNAN -DAMD64 \
+ -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DWHAM
+GAB: ${objects} ${objects_compar} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo
+ ${FC} -c ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \
+ ${LIBS} -static-intel -o ${BIN}/wham-mult_ifort_MPICH-GAB.exe
+
+4P: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPGI -DISNAN -DAMD64 \
+ -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DWHAM
+4P: ${objects} ${objects_compar} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo
+ ${FC} -c ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \
+ ${LIBS} -static-intel -o ${BIN}/wham-mult_ifort_MPICH_D-4P.exe
+
+E0LL2Y: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI -DISNAN -DAMD64 -DWHAM
+E0LL2Y: ${objects} ${objects_compar} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo
+ ${FC} -c ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \
+ ${LIBS} -static-intel -o ${BIN}/wham-mult_ifort_MPICH_D-E0LL2Y.exe
+
+xdrf/libxdrf.a:
+ cd xdrf && make
+
+
+clean:
+ /bin/rm -f *.o && /bin/rm -f compinfo && cd xdrf && make clean
+
--- /dev/null
+INSTALL_DIR = /users/software/mpich-1.2.7p1_pgi_9.0_64bit_ssh
+CC = cc
+FC = pgf90
+#OPT = -mcmodel=medium -Mlarge_arrays -fast -pc 64 -tp amd64 -C -g
+OPT = -mcmodel=medium -Mlarge_arrays -tp amd64
+#FFLAGS = ${OPT} -g -c -I. -I./include_unres -I$(INSTALL_DIR)/include
+FFLAGS = ${OPT} -c -C -g -I. -I./include_unres -I$(INSTALL_DIR)/include
+#FFLAGS = ${OPT} -c -I. -I./include_unres -I$(INSTALL_DIR)/include
+LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpmpich xdrf/libxdrf.a
+
+.f.o:
+ ${FC} ${FFLAGS} $*.f
+
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+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 \
+ 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 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
+
+all: no_option
+ @echo "Specify force field: GAB, 4P or E0LL2Y"
+
+no_option:
+
+GAB: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI -DISNAN -DAMD64 \
+ -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DWHAM
+GAB: ${objects} ${objects_compar} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo
+ ${FC} -c ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \
+ ${LIBS} -static-intel -o ${BIN}/wham-mult_pgf90_MPICH_GAB.exe
+
+4P: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPGI -DISNAN -DAMD64 \
+ -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DWHAM
+4P: ${objects} ${objects_compar} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo
+ ${FC} -c ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \
+ ${LIBS} -static-intel -o ${BIN}/wham-mult_pgf90_MPICH_4P.exe
+
+E0LL2Y: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI -DISNAN -DAMD64 -DWHAM
+E0LL2Y: ${objects} ${objects_compar} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo
+ ${FC} -c ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \
+ ${LIBS} -static-intel -o ${BIN}/wham-mult_pgf90_MPICH_E0LL2Y.exe
+
+xdrf/libxdrf.a:
+ cd xdrf && make
+
+
+clean:
+ /bin/rm -f *.o && /bin/rm -f compinfo && cd xdrf && make clean
+
--- /dev/null
+../../lib/xdrf
\ No newline at end of file
--- /dev/null
+INSTALL_DIR = /users/software/mpich-1.2.7p1_pgi_9.0_64bit_ssh
+CC = cc
+FC = pgf90
+#OPT = -mcmodel=medium -Mlarge_arrays -fast -pc 64 -tp amd64 -C -g
+OPT = -mcmodel=medium -Mlarge_arrays -tp amd64
+#FFLAGS = ${OPT} -g -c -I. -I./include_unres -I$(INSTALL_DIR)/include
+FFLAGS = ${OPT} -c -C -g -I. -I./include_unres -I$(INSTALL_DIR)/include
+#FFLAGS = ${OPT} -c -I. -I./include_unres -I$(INSTALL_DIR)/include
+LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpmpich xdrf/libxdrf.a
+
+.f.o:
+ ${FC} ${FFLAGS} $*.f
+
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+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 \
+ 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 \
+ ssMD.o
+
+objects_compar = \
+ readrtns_compar.o \
+ readpdb.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
+
+all: no_option
+ @echo "Specify force field: GAB, 4P or E0LL2Y"
+
+no_option:
+
+GAB: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI -DISNAN -DAMD64 \
+ -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DWHAM
+GAB: ${objects} ${objects_compar} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo
+ ${FC} -c ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \
+ ${LIBS} -static-intel -o ${BIN}/wham_pgf90_MPICH_GAB.exe
+
+4P: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPGI -DISNAN -DAMD64 \
+ -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DWHAM
+4P: ${objects} ${objects_compar} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo
+ ${FC} -c ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \
+ ${LIBS} -static-intel -o ${BIN}/wham_pgf90_MPICH_4P.exe
+
+E0LL2Y: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI -DISNAN -DAMD64 -DWHAM
+E0LL2Y: ${objects} ${objects_compar} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo
+ ${FC} -c ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \
+ ${LIBS} -static-intel -o ${BIN}/wham_pgf90_MPICH_E0LL2Y.exe
+
+xdrf/libxdrf.a:
+ cd xdrf && make
+
+
+clean:
+ /bin/rm -f *.o && /bin/rm -f compinfo && cd xdrf && make clean
+
--- /dev/null
+# Set of programs to convert UNRES xdrf format (compressed Cartesian coordinates) to PDF
+# or raw-Cartesian format (*.x) or to extract backbone angular coordinates (*.ang)
+# The pdb files can be constructed from canonical or MREMD trajectories.
+#
+# The xdrf library is required
+#
+# Programs
+#
+# xdrf2pdb : converts a single cx trajectory file to PDB format
+# xdrf2x : converts a single cx trajectory file to raw-coordinate (x) format
+# xdrf2ang : extracts backbone angles from a cx trajectory file
+# xdrf2pdb-m : converts a selected trajectory of a MREMD run dumpend into a cx file to PDB format
+#
+# xdrf2pdb1 : converts conformation(s) selected from a wham post-processing run into PDB format
+# xdrf2x1 : converts conformation(s) selected from a wham post-processing run into raw (x) format.
+#
+# 9/23/2010 A. Liwo
+
+FC=gfortran
+
+BINDIR = ../../../bin/xdrfpdb
+
+#OPT = -fast
+OPT =
+
+FFLAGS = -c ${OPT}
+
+CPPFLAGS = -DLINUX -DUNRES -DMP -DMPI -DSPLITELE -DPROCOR -DNEWUNRES
+
+M4 = m4
+M4FILE = underscore.m4
+
+.SUFFIXES: .F
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+.f.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.f
+.c.o:
+ ${CC} -c ${CPPFLAGS} $*.c
+
+xdrf2pdb: xdrf2pdb.o geomout.o misc.o rescode.o nazwy.o xdrf/libxdrf.a
+ ${FC} -Bstatic -o ${BINDIR}/xdrf2pdb-mult xdrf2pdb.o geomout.o rescode.o misc.o nazwy.o xdrf/libxdrf.a
+
+xdrf2pdb1: xdrf2pdb1.o geomout.o misc.o rescode.o nazwy.o xdrf/libxdrf.a
+ ${FC} -Bstatic -o ${BINDIR}/xdrf2pdb1-mult xdrf2pdb1.o geomout.o rescode.o misc.o nazwy.o xdrf/libxdrf.a
+
+xdrf2pdb-m: xdrf2pdb-m.o geomout.o misc.o rescode.o nazwy.o xdrf/libxdrf.a
+ ${FC} -Bstatic -o ${BINDIR}/xdrf2pdb-m-mult xdrf2pdb-m.o geomout.o rescode.o misc.o nazwy.o xdrf/libxdrf.a
+
+xdrf2x: xdrf2x.o xdrf/libxdrf.a
+ ${FC} -o xdrf2x xdrf2x-mult.o xdrf/libxdrf.a
+
+xdrf2x1: xdrf2x1.o xdrf/libxdrf.a
+ ${FC} -o xdrf2x1-mult xdrf2x1.o xdrf/libxdrf.a
+
+clean:
+ rm -f *.o
--- /dev/null
+# Set of programs to convert UNRES xdrf format (compressed Cartesian coordinates) to PDF
+# or raw-Cartesian format (*.x) or to extract backbone angular coordinates (*.ang)
+# The pdb files can be constructed from canonical or MREMD trajectories.
+#
+# The xdrf library is required
+#
+# Programs
+#
+# xdrf2pdb : converts a single cx trajectory file to PDB format
+# xdrf2x : converts a single cx trajectory file to raw-coordinate (x) format
+# xdrf2ang : extracts backbone angles from a cx trajectory file
+# xdrf2pdb-m : converts a selected trajectory of a MREMD run dumpend into a cx file to PDB format
+#
+# xdrf2pdb1 : converts conformation(s) selected from a wham post-processing run into PDB format
+# xdrf2x1 : converts conformation(s) selected from a wham post-processing run into raw (x) format.
+#
+# 9/23/2010 A. Liwo
+
+FC=ifort
+
+BINDIR = ../../../bin/xdrfpdb
+
+#OPT = -fast
+OPT =
+
+FFLAGS = -c ${OPT}
+
+CPPFLAGS = -DLINUX -DUNRES -DMP -DMPI -DSPLITELE -DPROCOR -DNEWUNRES
+
+M4 = m4
+M4FILE = underscore.m4
+
+.SUFFIXES: .F
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+.f.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.f
+.c.o:
+ ${CC} -c ${CPPFLAGS} $*.c
+
+xdrf2pdb: xdrf2pdb.o geomout.o misc.o rescode.o nazwy.o xdrf/libxdrf.a
+ ${FC} -Bstatic -o ${BINDIR}/xdrf2pdb-mult xdrf2pdb.o geomout.o rescode.o misc.o nazwy.o xdrf/libxdrf.a
+
+xdrf2pdb1: xdrf2pdb1.o geomout.o misc.o rescode.o nazwy.o xdrf/libxdrf.a
+ ${FC} -Bstatic -o ${BINDIR}/xdrf2pdb1-mult xdrf2pdb1.o geomout.o rescode.o misc.o nazwy.o xdrf/libxdrf.a
+
+xdrf2pdb-m: xdrf2pdb-m.o geomout.o misc.o rescode.o nazwy.o xdrf/libxdrf.a
+ ${FC} -Bstatic -o ${BINDIR}/xdrf2pdb-m-mult xdrf2pdb-m.o geomout.o rescode.o misc.o nazwy.o xdrf/libxdrf.a
+
+xdrf2x: xdrf2x.o xdrf/libxdrf.a
+ ${FC} -o xdrf2x xdrf2x-mult.o xdrf/libxdrf.a
+
+xdrf2x1: xdrf2x1.o xdrf/libxdrf.a
+ ${FC} -o xdrf2x1-mult xdrf2x1.o xdrf/libxdrf.a
+
+xdrf/libxdrf.a:
+ cd xdrf && make
+
+clean:
+ rm -f *.o
--- /dev/null
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.SBRIDGE'
+ real*4 coord(3,1000)
+ real*4 prec,potE,efree,rmsdev
+ real*8 etot
+ character*80 arg,seqfile,pdbfile
+ character*3 sequenc(maxres)
+ character*50 tytul
+ character*8 onethree,cfreq
+ character*8 ucase
+ external ucase
+ logical oneletter
+ integer rescode
+ external rescode
+ logical ilen,iblnk
+
+ ifreq=1
+ if (iargc().lt.4) then
+ print '(a)',
+ & "Usage: xdrf2pdb one/three seqfile cxfile conf [pdbfile]"
+ stop
+ endif
+ call getarg(1,onethree)
+ onethree = ucase(onethree)
+ if (onethree.eq.'ONE') then
+ oneletter = .true.
+ else if (onethree.eq.'THREE') then
+ oneletter = .false.
+ else
+ print *,"ONE or THREE must be specified"
+ endif
+ call getarg(2,seqfile)
+ open (1,file=seqfile,status='old')
+ if (oneletter) then
+ read(1,'(80a1)',end=10,err=10) (sequenc(i)(1:1),i=1,maxres)
+ 10 continue
+ nres=i
+ i=0
+ do while (.not.iblnk(sequenc(i+1)(1:1)))
+ i=i+1
+ enddo
+ nres=i
+ do i=1,nres
+ itype(i)=rescode(i,sequenc(i),1)
+ enddo
+ else
+ read(1,'(20(a3,1x))',end=11,err=11) (sequenc(i),i=1,maxres)
+ 11 continue
+ nres=i
+ print *,"nres",nres
+ do i=1,nres
+ print *,i," ",sequenc(i)
+ enddo
+ print *
+ i=0
+ do while (.not.iblnk(sequenc(i+1)(1:1)))
+ print *,i+1," ",sequenc(i+1)," ",sequenc(i+1)(1:1)
+ i=i+1
+ enddo
+ nres=i
+ print *,"nres",nres
+ do i=1,nres
+ itype(i)=rescode(i,sequenc(i),0)
+ enddo
+ print *,(itype(i),i=1,nres)
+ endif
+ call getarg(3,arg)
+ iext = index(arg,'.cx') - 1
+ if (iext.lt.0) then
+ print *,"Error - not a cx file"
+ stop
+ endif
+ print *,"arg ",arg
+ call getarg(4,cfreq)
+ read (cfreq,*) iconf
+ print *,"iconf",iconf
+ if (iargc().gt.4) then
+ call getarg(5,pdbfile)
+ else
+ pdbfile=arg(:iext)//'.pdb'
+ endif
+ open(9,file=pdbfile)
+ nnt = 1
+ if (itype(1).eq.21) nnt = 2
+ nct=nres
+ if (itype(nres).eq.21) nct = nres-1
+c if (nct.eq.nres-1) nres=nres-1
+c if (nnt.eq.2) nres=nres-1
+
+ print *,"nres",nres," nnt",nnt," nct",nct
+
+ call xdrfopen(ixdrf,arg, "r", iret)
+ print *,"iret",iret
+ kk = 0
+ do while(.true.)
+ prec=10000.0
+ isize=0
+ call xdrf3dfcoord(ixdrf, coord, isize, prec, iret)
+ call xdrfint(ixdrf, nss, iret)
+ do j=1,nss
+ call xdrfint(ixdrf, ihpb(j), iret)
+ call xdrfint(ixdrf, jhpb(j), iret)
+ enddo
+ call xdrffloat(ixdrf, potE, iret)
+ if(iret.eq.0) exit
+ kk = kk + 1
+ call xdrffloat(ixdrf, efree, iret)
+ call xdrffloat(ixdrf, rmsdev, iret)
+ call xdrfint(ixdrf, iscor, iret)
+ if (kk.eq.iconf) then
+ print *,"pote",pote," efree",efree," rmsdev",rmsdev
+
+ print *,"isize",isize
+
+ if (isize .ne. nres+nct-nnt+1) then
+ print *,"Error: inconsistent sizes",isize,nres+nct-nnt+1
+ endif
+ do i=1,nres
+ do j=1,3
+ c(j,i)=coord(j,i)
+ enddo
+ enddo
+ ii = 0
+ do i=nnt,nct
+ ii = ii + 1
+ do j=1,3
+ c(j,i+nres)=coord(j,ii+nres)
+ enddo
+ enddo
+ etot=potE
+ write (tytul,'(a,i6)') "Structure",kk
+ call pdbout(etot,tytul,9)
+ stop
+ endif
+ enddo
+
+ end
--- /dev/null
+ implicit real*8 (a-h,o-z)
+ integer ihpb(100),jhpb(100)
+ real*4 coord(3,1000)
+ real*4 prec,potE,efree,rmsdev,qfrag(100)
+ real*8 etot
+ character*80 arg,xfile
+ character*8 ucase,cfreq
+ external ucase
+ logical oneletter
+ integer rescode
+ external rescode
+
+ ifreq=1
+ if (iargc().lt.2) then
+ print '(a)',
+ & "Usage: xdrf2x1 cxfile conf [pdbfile]"
+ stop
+ endif
+ call getarg(1,arg)
+ iext = index(arg,'.cx') - 1
+ if (iext.lt.0) then
+ print *,"Error - not a cx file"
+ stop
+ endif
+ print *,"arg ",arg
+ call getarg(2,cfreq)
+ read (cfreq,*) iconf
+ print *,"iconf",iconf
+ if (iargc().gt.2) then
+ call getarg(3,pdbfile)
+ else
+ xfile=arg(:iext)//'.x'
+ endif
+ open(9,file=xfile)
+
+ call xdrfopen(ixdrf,arg, "r", iret)
+ print *,"iret",iret
+ kk = 0
+ do while(.true.)
+ prec=10000.0
+ isize=0
+ call xdrf3dfcoord(ixdrf, coord, isize, prec, iret)
+ call xdrfint(ixdrf, nss, iret)
+ do j=1,nss
+ call xdrfint(ixdrf, ihpb(j), iret)
+ call xdrfint(ixdrf, jhpb(j), iret)
+ enddo
+ call xdrffloat(ixdrf, potE, iret)
+ if(iret.eq.0) exit
+ kk = kk + 1
+ call xdrffloat(ixdrf, efree, iret)
+ call xdrffloat(ixdrf, rmsdev, iret)
+ call xdrfint(ixdrf, iscor, iret)
+ if (kk.eq.iconf) then
+ print *,"pote",pote," efree",efree," rmsdev",rmsdev
+
+ print *,"isize",isize
+
+ write (9,'(e15.8,2e15.5,f12.5,$)') time,potE,uconst,t_bath
+ write (9,'(i4,$)') nss,(ihpb(j),jhpb(j),j=1,nss)
+ write (9,'(i4,20f7.4)') nfrag,(qfrag(i),i=1,nfrag)
+ write (9,'(8f10.5)') ((coord(k,j),k=1,3),j=1,isize)
+ stop
+ endif
+ enddo
+
+ end
--- /dev/null
+# Set of programs to convert UNRES xdrf format (compressed Cartesian coordinates) to PDF
+# or raw-Cartesian format (*.x) or to extract backbone angular coordinates (*.ang)
+# The pdb files can be constructed from canonical or MREMD trajectories.
+#
+# The xdrf library is required
+#
+# Programs
+#
+# xdrf2pdb : converts a single cx trajectory file to PDB format
+# xdrf2x : converts a single cx trajectory file to raw-coordinate (x) format
+# xdrf2ang : extracts backbone angles from a cx trajectory file
+# xdrf2pdb-m : converts a selected trajectory of a MREMD run dumpend into a cx file to PDB format
+#
+# xdrf2pdb1 : converts conformation(s) selected from a wham post-processing run into PDB format
+# xdrf2x1 : converts conformation(s) selected from a wham post-processing run into raw (x) format.
+#
+# 9/23/2010 A. Liwo
+
+FC=gfortran
+
+BINDIR = ../../../bin/xdrfpdb
+
+#OPT = -fast
+OPT =
+
+FFLAGS = -c ${OPT}
+
+CPPFLAGS = -DNEWUNRES
+
+M4 = m4
+M4FILE = underscore.m4
+
+.SUFFIXES: .F
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+.c.o:
+ ${CC} -c ${CPPFLAGS} $*.c
+
+all:xdrf2pdb xdrf2pdb-m
+
+xdrf2pdb: xdrf2pdb.o geomout.o misc.o rescode.o nazwy.o xdrf/libxdrf.a
+ ${FC} -Bstatic -o ${BINDIR}/xdrf2pdb xdrf2pdb.o geomout.o rescode.o misc.o nazwy.o xdrf/libxdrf.a
+
+xdrf2pdb-m: xdrf2pdb-m.o geomout.o misc.o rescode.o nazwy.o xdrf/libxdrf.a
+ ${FC} -Bstatic -o ${BINDIR}/xdrf2pdb-m xdrf2pdb-m.o geomout.o rescode.o misc.o nazwy.o xdrf/libxdrf.a
+
+xdrf2pdb1: xdrf2pdb1.o geomout.o misc.o rescode.o nazwy.o xdrf/libxdrf.a
+ ${FC} -Bstatic -o ${BINDIR}/xdrf2pdb1 xdrf2pdb1.o geomout.o rescode.o misc.o nazwy.o xdrf/libxdrf.a
+
+xdrf2x: xdrf2x.o xdrf/libxdrf.a
+ ${FC} -o xdrf2x xdrf2x.o xdrf/libxdrf.a
+
+xdrf2x1: xdrf2x1.o xdrf/libxdrf.a
+ ${FC} -o xdrf2x1 xdrf2x1.o xdrf/libxdrf.a
+
+xdrf2ang: xdrf2ang.o misc.o rescode.o nazwy.o intcor.o arcos.o xdrf/libxdrf.a
+ ${FC} -Bstatic -o ${BINDIR}/xdrf2ang xdrf2ang.o rescode.o \
+ misc.o nazwy.o intcor.o arcos.o xdrf/libxdrf.a
+
+xdrf/libxdrf.a:
+ cd xdrf && make
+
+clean:
+ rm -f *.o && /bin/rm -f compinfo && cd xdrf && make clean
--- /dev/null
+# Set of programs to convert UNRES xdrf format (compressed Cartesian coordinates) to PDF
+# or raw-Cartesian format (*.x) or to extract backbone angular coordinates (*.ang)
+# The pdb files can be constructed from canonical or MREMD trajectories.
+#
+# The xdrf library is required
+#
+# Programs
+#
+# xdrf2pdb : converts a single cx trajectory file to PDB format
+# xdrf2x : converts a single cx trajectory file to raw-coordinate (x) format
+# xdrf2ang : extracts backbone angles from a cx trajectory file
+# xdrf2pdb-m : converts a selected trajectory of a MREMD run dumpend into a cx file to PDB format
+#
+# xdrf2pdb1 : converts conformation(s) selected from a wham post-processing run into PDB format
+# xdrf2x1 : converts conformation(s) selected from a wham post-processing run into raw (x) format.
+#
+# 9/23/2010 A. Liwo
+
+FC=ifort
+
+BINDIR = ../../../bin/xdrfpdb
+
+#OPT = -fast
+OPT =
+
+FFLAGS = -c ${OPT}
+
+CPPFLAGS = -DNEWUNRES
+
+M4 = m4
+M4FILE = underscore.m4
+
+.SUFFIXES: .F
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+.c.o:
+ ${CC} -c ${CPPFLAGS} $*.c
+
+all:xdrf2pdb xdrf2pdb-m
+
+xdrf2pdb: xdrf2pdb.o geomout.o misc.o rescode.o nazwy.o xdrf/libxdrf.a
+ ${FC} -Bstatic -o ${BINDIR}/xdrf2pdb xdrf2pdb.o geomout.o rescode.o misc.o nazwy.o xdrf/libxdrf.a
+
+xdrf2pdb-m: xdrf2pdb-m.o geomout.o misc.o rescode.o nazwy.o xdrf/libxdrf.a
+ ${FC} -Bstatic -o ${BINDIR}/xdrf2pdb-m xdrf2pdb-m.o geomout.o rescode.o misc.o nazwy.o xdrf/libxdrf.a
+
+xdrf2pdb1: xdrf2pdb1.o geomout.o misc.o rescode.o nazwy.o xdrf/libxdrf.a
+ ${FC} -Bstatic -o ${BINDIR}/xdrf2pdb1 xdrf2pdb1.o geomout.o rescode.o misc.o nazwy.o xdrf/libxdrf.a
+
+xdrf2x: xdrf2x.o xdrf/libxdrf.a
+ ${FC} -o xdrf2x xdrf2x.o xdrf/libxdrf.a
+
+xdrf2x1: xdrf2x1.o xdrf/libxdrf.a
+ ${FC} -o xdrf2x1 xdrf2x1.o xdrf/libxdrf.a
+
+xdrf2ang: xdrf2ang.o misc.o rescode.o nazwy.o intcor.o arcos.o xdrf/libxdrf.a
+ ${FC} -Bstatic -o ${BINDIR}/xdrf2ang xdrf2ang.o rescode.o \
+ misc.o nazwy.o intcor.o arcos.o xdrf/libxdrf.a
+
+xdrf/libxdrf.a:
+ cd xdrf && make
+
+clean:
+ rm -f *.o && /bin/rm -f compinfo && cd xdrf && make clean
--- /dev/null
+../../lib/xdrf
\ No newline at end of file
--- /dev/null
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.SBRIDGE'
+ real*4 coord(3,1000)
+ real*4 prec,potE,efree,rmsdev
+ real*8 etot
+ character*80 arg,seqfile,pdbfile
+ character*3 sequenc(maxres)
+ character*50 tytul
+ character*8 onethree,cfreq
+ character*8 ucase
+ external ucase
+ logical oneletter
+ integer rescode
+ external rescode
+
+ ifreq=1
+ if (iargc().lt.4) then
+ print '(a)',
+ & "Usage: xdrf2pdb one/three seqfile cxfile conf [pdbfile]"
+ stop
+ endif
+ call getarg(1,onethree)
+ onethree = ucase(onethree)
+ if (onethree.eq.'ONE') then
+ oneletter = .true.
+ else if (onethree.eq.'THREE') then
+ oneletter = .false.
+ else
+ print *,"ONE or THREE must be specified"
+ endif
+ call getarg(2,seqfile)
+ open (1,file=seqfile,status='old')
+ if (oneletter) then
+ read(1,'(80a1)',end=10,err=10) (sequenc(i)(1:1),i=1,maxres)
+ 10 continue
+ nres=i
+ i=0
+ do while (.not.iblnk(sequenc(i+1)(1:1)))
+ i=i+1
+ enddo
+ nres=i
+ do i=1,nres
+ itype(i)=rescode(i,sequenc(i),1)
+ enddo
+ else
+ read(1,'(20(a3,1x))',end=11,err=11) (sequenc(i),i=1,maxres)
+ 11 continue
+ nres=i
+ print *,"nres",nres
+ do i=1,nres
+ print *,i," ",sequenc(i)
+ enddo
+ print *
+ i=0
+ do while (.not.iblnk(sequenc(i+1)(1:1)))
+ print *,i+1," ",sequenc(i+1)," ",sequenc(i+1)(1:1)
+ i=i+1
+ enddo
+ nres=i
+ print *,"nres",nres
+ do i=1,nres
+ itype(i)=rescode(i,sequenc(i),0)
+ enddo
+ print *,(itype(i),i=1,nres)
+ endif
+ call getarg(3,arg)
+ iext = index(arg,'.cx') - 1
+ if (iext.lt.0) then
+ print *,"Error - not a cx file"
+ stop
+ endif
+ print *,"arg ",arg
+ call getarg(4,cfreq)
+ read (cfreq,*) iconf
+ print *,"iconf",iconf
+ if (iargc().gt.4) then
+ call getarg(5,pdbfile)
+ else
+ pdbfile=arg(:iext)//'.pdb'
+ endif
+ open(9,file=pdbfile)
+ nnt = 1
+ if (itype(1).eq.21) nnt = 2
+ nct=nres
+ if (itype(nres).eq.21) nct = nres-1
+c if (nct.eq.nres-1) nres=nres-1
+c if (nnt.eq.2) nres=nres-1
+
+ print *,"nres",nres," nnt",nnt," nct",nct
+
+ call xdrfopen(ixdrf,arg, "r", iret)
+ print *,"iret",iret
+ kk = 0
+ do while(.true.)
+ prec=10000.0
+ isize=0
+ call xdrf3dfcoord(ixdrf, coord, isize, prec, iret)
+ call xdrfint(ixdrf, nss, iret)
+ do j=1,nss
+ call xdrfint(ixdrf, ihpb(j), iret)
+ call xdrfint(ixdrf, jhpb(j), iret)
+ enddo
+ call xdrffloat(ixdrf, potE, iret)
+ if(iret.eq.0) exit
+ kk = kk + 1
+ call xdrffloat(ixdrf, efree, iret)
+ call xdrffloat(ixdrf, rmsdev, iret)
+ call xdrfint(ixdrf, iscor, iret)
+ if (kk.eq.iconf) then
+ print *,"pote",pote," efree",efree," rmsdev",rmsdev
+
+ print *,"isize",isize
+
+ if (isize .ne. nres+nct-nnt+1) then
+ print *,"Error: inconsistent sizes",isize,nres+nct-nnt+1
+ endif
+ do i=1,nres
+ do j=1,3
+ c(j,i)=coord(j,i)
+ enddo
+ enddo
+ ii = 0
+ do i=nnt,nct
+ ii = ii + 1
+ do j=1,3
+ c(j,i+nres)=coord(j,ii+nres)
+ enddo
+ enddo
+ etot=potE
+ write (tytul,'(a,i6)') "Structure",kk
+ call pdbout(etot,tytul,9)
+ stop
+ endif
+ enddo
+
+ end
--- /dev/null
+ implicit real*8 (a-h,o-z)
+ integer ihpb(100),jhpb(100)
+ real*4 coord(3,1000)
+ real*4 prec,potE,efree,rmsdev,qfrag(100)
+ real*8 etot
+ character*80 arg,xfile
+ character*8 ucase,cfreq
+ external ucase
+ logical oneletter
+ integer rescode
+ external rescode
+
+ ifreq=1
+ if (iargc().lt.2) then
+ print '(a)',
+ & "Usage: xdrf2x1 cxfile conf [pdbfile]"
+ stop
+ endif
+ call getarg(1,arg)
+ iext = index(arg,'.cx') - 1
+ if (iext.lt.0) then
+ print *,"Error - not a cx file"
+ stop
+ endif
+ print *,"arg ",arg
+ call getarg(2,cfreq)
+ read (cfreq,*) iconf
+ print *,"iconf",iconf
+ if (iargc().gt.2) then
+ call getarg(3,pdbfile)
+ else
+ xfile=arg(:iext)//'.x'
+ endif
+ open(9,file=xfile)
+
+ call xdrfopen(ixdrf,arg, "r", iret)
+ print *,"iret",iret
+ kk = 0
+ do while(.true.)
+ prec=10000.0
+ isize=0
+ call xdrf3dfcoord(ixdrf, coord, isize, prec, iret)
+ call xdrfint(ixdrf, nss, iret)
+ do j=1,nss
+ call xdrfint(ixdrf, ihpb(j), iret)
+ call xdrfint(ixdrf, jhpb(j), iret)
+ enddo
+ call xdrffloat(ixdrf, potE, iret)
+ if(iret.eq.0) exit
+ kk = kk + 1
+ call xdrffloat(ixdrf, efree, iret)
+ call xdrffloat(ixdrf, rmsdev, iret)
+ call xdrfint(ixdrf, iscor, iret)
+ if (kk.eq.iconf) then
+ print *,"pote",pote," efree",efree," rmsdev",rmsdev
+
+ print *,"isize",isize
+
+ write (9,'(e15.8,2e15.5,f12.5,$)') time,potE,uconst,t_bath
+ write (9,'(i4,$)') nss,(ihpb(j),jhpb(j),j=1,nss)
+ write (9,'(i4,20f7.4)') nfrag,(qfrag(i),i=1,nfrag)
+ write (9,'(8f10.5)') ((coord(k,j),k=1,3),j=1,isize)
+ stop
+ endif
+ enddo
+
+ end
projects / unres.git / commitdiff