From: Adam Liwo Date: Fri, 28 Nov 2014 10:45:13 +0000 (+0100) Subject: Trying to bring files - continued X-Git-Tag: v.3.2.1~15 X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=commitdiff_plain;h=a67fb1c3d80e370d951bfa338356af720229eb6c Trying to bring files - continued By Adam --- diff --git a/bin/xdrfpdb/xdrf2pdb b/bin/xdrfpdb/xdrf2pdb new file mode 100755 index 0000000..8b2f50a Binary files /dev/null and b/bin/xdrfpdb/xdrf2pdb differ diff --git a/bin/xdrfpdb/xdrf2pdb-m b/bin/xdrfpdb/xdrf2pdb-m new file mode 100755 index 0000000..cc1b0db Binary files /dev/null and b/bin/xdrfpdb/xdrf2pdb-m differ diff --git a/bin/xdrfpdb/xdrf2pdb-m-mult b/bin/xdrfpdb/xdrf2pdb-m-mult new file mode 100755 index 0000000..e437918 Binary files /dev/null and b/bin/xdrfpdb/xdrf2pdb-m-mult differ diff --git a/bin/xdrfpdb/xdrf2pdb-mult b/bin/xdrfpdb/xdrf2pdb-mult new file mode 100755 index 0000000..3f1f130 Binary files /dev/null and b/bin/xdrfpdb/xdrf2pdb-mult differ diff --git a/bin/xdrfpdb/xdrf2pdb1 b/bin/xdrfpdb/xdrf2pdb1 new file mode 100755 index 0000000..e67b02d Binary files /dev/null and b/bin/xdrfpdb/xdrf2pdb1 differ diff --git a/bin/xdrfpdb/xdrf2pdb1-mult b/bin/xdrfpdb/xdrf2pdb1-mult new file mode 100755 index 0000000..b2f6da6 Binary files /dev/null and b/bin/xdrfpdb/xdrf2pdb1-mult differ diff --git a/source/cluster/unres/src/Makefile_ifort b/source/cluster/unres/src/Makefile_ifort new file mode 100644 index 0000000..19e93e8 --- /dev/null +++ b/source/cluster/unres/src/Makefile_ifort @@ -0,0 +1,36 @@ +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} diff --git a/source/cluster/unres/src/Makefile_pgi b/source/cluster/unres/src/Makefile_pgi new file mode 100644 index 0000000..a44eb2a --- /dev/null +++ b/source/cluster/unres/src/Makefile_pgi @@ -0,0 +1,30 @@ +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} diff --git a/source/cluster/unres/src/compinfo.c b/source/cluster/unres/src/compinfo.c new file mode 100644 index 0000000..e28f686 --- /dev/null +++ b/source/cluster/unres/src/compinfo.c @@ -0,0 +1,82 @@ +#include +#include +#include +#include +#include + +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"); +} diff --git a/source/cluster/wham/src-M/Makefile-MPICH-gfortran b/source/cluster/wham/src-M/Makefile-MPICH-gfortran new file mode 100644 index 0000000..a2fd689 --- /dev/null +++ b/source/cluster/wham/src-M/Makefile-MPICH-gfortran @@ -0,0 +1,67 @@ +################################################################## +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 + + diff --git a/source/cluster/wham/src-M/compinfo.c b/source/cluster/wham/src-M/compinfo.c new file mode 100644 index 0000000..e28f686 --- /dev/null +++ b/source/cluster/wham/src-M/compinfo.c @@ -0,0 +1,82 @@ +#include +#include +#include +#include +#include + +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"); +} diff --git a/source/cluster/wham/src/Makefile-MPICH-gfortran b/source/cluster/wham/src/Makefile-MPICH-gfortran new file mode 100644 index 0000000..65249b6 --- /dev/null +++ b/source/cluster/wham/src/Makefile-MPICH-gfortran @@ -0,0 +1,66 @@ +################################################################## +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 + + diff --git a/source/cluster/wham/src/compinfo.c b/source/cluster/wham/src/compinfo.c new file mode 100644 index 0000000..e28f686 --- /dev/null +++ b/source/cluster/wham/src/compinfo.c @@ -0,0 +1,82 @@ +#include +#include +#include +#include +#include + +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"); +} diff --git a/source/cluster/wham/src/include_unres/COMMON.MD b/source/cluster/wham/src/include_unres/COMMON.MD new file mode 100644 index 0000000..40131bd --- /dev/null +++ b/source/cluster/wham/src/include_unres/COMMON.MD @@ -0,0 +1,77 @@ + 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 diff --git a/source/cluster/wham/src/include_unres/COMMON.SETUP b/source/cluster/wham/src/include_unres/COMMON.SETUP new file mode 100644 index 0000000..5039116 --- /dev/null +++ b/source/cluster/wham/src/include_unres/COMMON.SETUP @@ -0,0 +1,21 @@ + 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 diff --git a/source/unres/src_CSA/Makefile_MPICH_bluegene b/source/unres/src_CSA/Makefile_MPICH_bluegene new file mode 100644 index 0000000..bcfd204 --- /dev/null +++ b/source/unres/src_CSA/Makefile_MPICH_bluegene @@ -0,0 +1,152 @@ +################################################################################# +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 diff --git a/source/unres/src_CSA/Makefile_MPICH_gfortran b/source/unres/src_CSA/Makefile_MPICH_gfortran new file mode 100644 index 0000000..7f56636 --- /dev/null +++ b/source/unres/src_CSA/Makefile_MPICH_gfortran @@ -0,0 +1,140 @@ +################################################################### +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 diff --git a/source/unres/src_CSA/Makefile_MPICH_ifort b/source/unres/src_CSA/Makefile_MPICH_ifort new file mode 100644 index 0000000..1720452 --- /dev/null +++ b/source/unres/src_CSA/Makefile_MPICH_ifort @@ -0,0 +1,142 @@ +################################################################### +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 diff --git a/source/unres/src_CSA/csa.F b/source/unres/src_CSA/csa.F new file mode 100644 index 0000000..a5149f2 --- /dev/null +++ b/source/unres/src_CSA/csa.F @@ -0,0 +1,366 @@ + 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 diff --git a/source/unres/src_CSA_DiL/Makefile_MPICH_bluegene b/source/unres/src_CSA_DiL/Makefile_MPICH_bluegene new file mode 100644 index 0000000..1575096 --- /dev/null +++ b/source/unres/src_CSA_DiL/Makefile_MPICH_bluegene @@ -0,0 +1,142 @@ +################################################################################# +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 diff --git a/source/unres/src_CSA_DiL/Makefile_MPICH_gfortran b/source/unres/src_CSA_DiL/Makefile_MPICH_gfortran new file mode 100644 index 0000000..c6cca6c --- /dev/null +++ b/source/unres/src_CSA_DiL/Makefile_MPICH_gfortran @@ -0,0 +1,130 @@ +################################################################### +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 diff --git a/source/unres/src_CSA_DiL/Makefile_MPICH_ifort b/source/unres/src_CSA_DiL/Makefile_MPICH_ifort new file mode 100644 index 0000000..7e2c69c --- /dev/null +++ b/source/unres/src_CSA_DiL/Makefile_MPICH_ifort @@ -0,0 +1,132 @@ +################################################################### +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 diff --git a/source/unres/src_MD-M/Makefile_MPICH_gfortran b/source/unres/src_MD-M/Makefile_MPICH_gfortran new file mode 100644 index 0000000..a945ea9 --- /dev/null +++ b/source/unres/src_MD-M/Makefile_MPICH_gfortran @@ -0,0 +1,135 @@ +################################################################### +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 diff --git a/source/unres/src_MD-M/Makefile_MPICH_ifort b/source/unres/src_MD-M/Makefile_MPICH_ifort new file mode 100644 index 0000000..0d2a6d4 --- /dev/null +++ b/source/unres/src_MD-M/Makefile_MPICH_ifort @@ -0,0 +1,137 @@ +################################################################### +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 diff --git a/source/unres/src_MD-M/Makefile_bluegene b/source/unres/src_MD-M/Makefile_bluegene new file mode 100644 index 0000000..52bb470 --- /dev/null +++ b/source/unres/src_MD-M/Makefile_bluegene @@ -0,0 +1,147 @@ +# +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 diff --git a/source/unres/src_MD-M/Makefile_single_gfortran b/source/unres/src_MD-M/Makefile_single_gfortran new file mode 100644 index 0000000..845a5af --- /dev/null +++ b/source/unres/src_MD-M/Makefile_single_gfortran @@ -0,0 +1,142 @@ +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 diff --git a/source/unres/src_MD-M/Makefile_single_ifort b/source/unres/src_MD-M/Makefile_single_ifort new file mode 100644 index 0000000..90cb357 --- /dev/null +++ b/source/unres/src_MD-M/Makefile_single_ifort @@ -0,0 +1,138 @@ +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 diff --git a/source/unres/src_MD/Makefile_MPICH_gfortran b/source/unres/src_MD/Makefile_MPICH_gfortran new file mode 100644 index 0000000..dd0ca5a --- /dev/null +++ b/source/unres/src_MD/Makefile_MPICH_gfortran @@ -0,0 +1,134 @@ +################################################################### +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 diff --git a/source/unres/src_MD/Makefile_bluegene b/source/unres/src_MD/Makefile_bluegene new file mode 100644 index 0000000..2a1f293 --- /dev/null +++ b/source/unres/src_MD/Makefile_bluegene @@ -0,0 +1,147 @@ +# +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 diff --git a/source/wham/src-M/Makefile_MPICH_ifort b/source/wham/src-M/Makefile_MPICH_ifort new file mode 100644 index 0000000..07ffac6 --- /dev/null +++ b/source/wham/src-M/Makefile_MPICH_ifort @@ -0,0 +1,96 @@ +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 + diff --git a/source/wham/src-M/Makefile_MPICH_pgi b/source/wham/src-M/Makefile_MPICH_pgi new file mode 100644 index 0000000..6dbee82 --- /dev/null +++ b/source/wham/src-M/Makefile_MPICH_pgi @@ -0,0 +1,96 @@ +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 + diff --git a/source/wham/src-M/xdrf b/source/wham/src-M/xdrf new file mode 120000 index 0000000..26825c5 --- /dev/null +++ b/source/wham/src-M/xdrf @@ -0,0 +1 @@ +../../lib/xdrf \ No newline at end of file diff --git a/source/wham/src/Makefile_MPICH_pgi b/source/wham/src/Makefile_MPICH_pgi new file mode 100644 index 0000000..02396d0 --- /dev/null +++ b/source/wham/src/Makefile_MPICH_pgi @@ -0,0 +1,97 @@ +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 + diff --git a/source/xdrfpdb/src-M/Makefile_gfortran b/source/xdrfpdb/src-M/Makefile_gfortran new file mode 100644 index 0000000..f950535 --- /dev/null +++ b/source/xdrfpdb/src-M/Makefile_gfortran @@ -0,0 +1,57 @@ +# 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 diff --git a/source/xdrfpdb/src-M/Makefile_ifort b/source/xdrfpdb/src-M/Makefile_ifort new file mode 100644 index 0000000..efdc4d9 --- /dev/null +++ b/source/xdrfpdb/src-M/Makefile_ifort @@ -0,0 +1,60 @@ +# 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 diff --git a/source/xdrfpdb/src-M/xdrf2pdb1.f b/source/xdrfpdb/src-M/xdrf2pdb1.f new file mode 100644 index 0000000..7409d7d --- /dev/null +++ b/source/xdrfpdb/src-M/xdrf2pdb1.f @@ -0,0 +1,140 @@ + 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 diff --git a/source/xdrfpdb/src-M/xdrf2x1.f b/source/xdrfpdb/src-M/xdrf2x1.f new file mode 100644 index 0000000..53f8fb0 --- /dev/null +++ b/source/xdrfpdb/src-M/xdrf2x1.f @@ -0,0 +1,67 @@ + 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 diff --git a/source/xdrfpdb/src/Makefile_gfortran b/source/xdrfpdb/src/Makefile_gfortran new file mode 100644 index 0000000..fc18f46 --- /dev/null +++ b/source/xdrfpdb/src/Makefile_gfortran @@ -0,0 +1,64 @@ +# 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 diff --git a/source/xdrfpdb/src/Makefile_ifort b/source/xdrfpdb/src/Makefile_ifort new file mode 100644 index 0000000..a828e35 --- /dev/null +++ b/source/xdrfpdb/src/Makefile_ifort @@ -0,0 +1,64 @@ +# 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 diff --git a/source/xdrfpdb/src/xdrf b/source/xdrfpdb/src/xdrf new file mode 120000 index 0000000..26825c5 --- /dev/null +++ b/source/xdrfpdb/src/xdrf @@ -0,0 +1 @@ +../../lib/xdrf \ No newline at end of file diff --git a/source/xdrfpdb/src/xdrf2pdb1.f b/source/xdrfpdb/src/xdrf2pdb1.f new file mode 100644 index 0000000..f41d0a0 --- /dev/null +++ b/source/xdrfpdb/src/xdrf2pdb1.f @@ -0,0 +1,139 @@ + 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 diff --git a/source/xdrfpdb/src/xdrf2x1.f b/source/xdrfpdb/src/xdrf2x1.f new file mode 100644 index 0000000..53f8fb0 --- /dev/null +++ b/source/xdrfpdb/src/xdrf2x1.f @@ -0,0 +1,67 @@ + 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