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some corrections in xdrf2pdb-m for dyn_ss
author
Cezary Czaplewski
<czarek@chem.univ.gda.pl>
Tue, 7 May 2013 13:39:45 +0000
(15:39 +0200)
committer
Cezary Czaplewski
<czarek@chem.univ.gda.pl>
Tue, 7 May 2013 13:39:45 +0000
(15:39 +0200)
bin/unres/MD/unres_ifort_MPICH_GAB.exe
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bin/xdrf2pdb-m
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source/unres/src_MD/MREMD.F
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source/unres/src_MD/cinfo.f
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source/xdrfpdb/src/Makefile
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source/xdrfpdb/src/xdrf2pdb-m.F
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diff --git
a/bin/unres/MD/unres_ifort_MPICH_GAB.exe
b/bin/unres/MD/unres_ifort_MPICH_GAB.exe
index
acadf0e
..
bce0500
100755
(executable)
Binary files a/bin/unres/MD/unres_ifort_MPICH_GAB.exe and b/bin/unres/MD/unres_ifort_MPICH_GAB.exe differ
diff --git
a/bin/xdrf2pdb-m
b/bin/xdrf2pdb-m
index
201ccb1
..
f4d6531
100755
(executable)
Binary files a/bin/xdrf2pdb-m and b/bin/xdrf2pdb-m differ
diff --git
a/source/unres/src_MD/MREMD.F
b/source/unres/src_MD/MREMD.F
index
b4f14d5
..
34a5343
100644
(file)
--- a/
source/unres/src_MD/MREMD.F
+++ b/
source/unres/src_MD/MREMD.F
@@
-1704,7
+1704,6
@@
ctime call flush(iout)
call xdrffloat_(ixdrf, real(t_restart1(4,il)), iret)
call xdrfint_(ixdrf, nss, iret)
do j=1,nss
call xdrffloat_(ixdrf, real(t_restart1(4,il)), iret)
call xdrfint_(ixdrf, nss, iret)
do j=1,nss
- do j=1,nss
if (dyn_ss) then
call xdrfint(ixdrf, idssb(j)+nres, iret)
call xdrfint(ixdrf, jdssb(j)+nres, iret)
if (dyn_ss) then
call xdrfint(ixdrf, idssb(j)+nres, iret)
call xdrfint(ixdrf, jdssb(j)+nres, iret)
diff --git
a/source/unres/src_MD/cinfo.f
b/source/unres/src_MD/cinfo.f
index
c24db4a
..
be05bcd
100644
(file)
--- a/
source/unres/src_MD/cinfo.f
+++ b/
source/unres/src_MD/cinfo.f
@@
-1,15
+1,15
@@
C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
-C 3 2 109
+C 3 2 110
subroutine cinfo
include 'COMMON.IOUNITS'
write(iout,*)'++++ Compile info ++++'
subroutine cinfo
include 'COMMON.IOUNITS'
write(iout,*)'++++ Compile info ++++'
- write(iout,*)'Version 3.2 build 109'
- write(iout,*)'compiled Mon Apr 8 08:58:39 2013'
- write(iout,*)'compiled by cc178@matrix.chem.cornell.edu'
+ write(iout,*)'Version 3.2 build 110'
+ write(iout,*)'compiled Tue Apr 30 09:32:51 2013'
+ write(iout,*)'compiled by czarek@piasek3'
write(iout,*)'OS name: Linux '
write(iout,*)'OS name: Linux '
- write(iout,*)'OS release: 2.6.34.9-69.fc13.x86_64 '
+ write(iout,*)'OS release: 2.6.32-45-generic '
write(iout,*)'OS version:',
write(iout,*)'OS version:',
- & ' #1 SMP Tue May 3 09:23:03 UTC 2011 '
+ & ' #104-Ubuntu SMP Tue Feb 19 21:20:09 UTC 2013 '
write(iout,*)'flags:'
write(iout,*)'INSTALL_DIR = /users/software/mpich-1.2.7p1_int...'
write(iout,*)'FC= ifort'
write(iout,*)'flags:'
write(iout,*)'INSTALL_DIR = /users/software/mpich-1.2.7p1_int...'
write(iout,*)'FC= ifort'
diff --git
a/source/xdrfpdb/src/Makefile
b/source/xdrfpdb/src/Makefile
index
747d0c0
..
0e310ce
100644
(file)
--- a/
source/xdrfpdb/src/Makefile
+++ b/
source/xdrfpdb/src/Makefile
@@
-36,6
+36,8
@@
M4FILE = underscore.m4
.c.o:
${CC} -c ${CPPFLAGS} $*.c
.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: 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
diff --git
a/source/xdrfpdb/src/xdrf2pdb-m.F
b/source/xdrfpdb/src/xdrf2pdb-m.F
index
61893ef
..
199d23a
100644
(file)
--- a/
source/xdrfpdb/src/xdrf2pdb-m.F
+++ b/
source/xdrfpdb/src/xdrf2pdb-m.F
@@
-3,7
+3,7
@@
include 'COMMON.CHAIN'
include 'COMMON.INTERACT'
include 'COMMON.SBRIDGE'
include 'COMMON.CHAIN'
include 'COMMON.INTERACT'
include 'COMMON.SBRIDGE'
- real*4 coord(3,5000)
+ real*4 coord(3,2*maxres)
real*4 prec,time,potE,uconst,t_bath,qfrag(100)
real*8 etot
character*80 arg,seqfile,pdbfile
real*4 prec,time,potE,uconst,t_bath,qfrag(100)
real*8 etot
character*80 arg,seqfile,pdbfile
@@
-95,31
+95,38
@@
c print *,"ifreq",ifreq," ntraj",ntraj," itraj",itraj
kk = 0
do while(.true.)
call xdrffloat(ixdrf, time, iret)
kk = 0
do while(.true.)
call xdrffloat(ixdrf, time, iret)
+ print *,"time",time," iret",iret
if(iret.eq.0) exit
kk = kk + 1
call xdrffloat(ixdrf, potE, iret)
call xdrffloat(ixdrf, uconst, iret)
call xdrffloat(ixdrf, t_bath, iret)
print *,"potE",potE," uconst",uconst," t_bath",t_bath
if(iret.eq.0) exit
kk = kk + 1
call xdrffloat(ixdrf, potE, iret)
call xdrffloat(ixdrf, uconst, iret)
call xdrffloat(ixdrf, t_bath, iret)
print *,"potE",potE," uconst",uconst," t_bath",t_bath
-#ifdef NEWUNRES
- call xdrffloat(ixdrf, uconst_back, iret)
-#endif
- print *,"uconst_back",uconst_back
+c
+c uconst_back not written in MREMD.F code
+c#ifdef NEWUNRES
+c call xdrffloat(ixdrf, uconst_back, iret)
+c print *,"uconst_back",uconst_back
+c#endif
call xdrfint(ixdrf, nss, iret)
do j=1,nss
call xdrfint(ixdrf, ihpb(j), iret)
call xdrfint(ixdrf, jhpb(j), iret)
enddo
call xdrfint(ixdrf, nss, iret)
do j=1,nss
call xdrfint(ixdrf, ihpb(j), iret)
call xdrfint(ixdrf, jhpb(j), iret)
enddo
+ print *,"nss",nss
+ print *," ",(ihpb(j),"-",jhpb(j),j=1,nss)
call xdrfint(ixdrf, nfrag, iret)
call xdrfint(ixdrf, nfrag, iret)
+ call xdrfint(ixdrf, iset, iret)
do i=1,nfrag
call xdrffloat(ixdrf, qfrag(i), iret)
enddo
do i=1,nfrag
call xdrffloat(ixdrf, qfrag(i), iret)
enddo
+ print *,"nfrag",nfrag,"iset",iset
prec=10000.0
isize=0
print *," call xdrf3coord"
call xdrf3dfcoord(ixdrf, coord, isize, prec, iret)
prec=10000.0
isize=0
print *," call xdrf3coord"
call xdrf3dfcoord(ixdrf, coord, isize, prec, iret)
-
+ print *,"isize",isize
c write (*,'(e15.8,2e15.5,f12.5,$)') time,potE,uconst,t_bath
c write (*,'(i4,$)') nss,(ihpb(j),jhpb(j),j=1,nss)
c write (*,'(e15.8,2e15.5,f12.5,$)') time,potE,uconst,t_bath
c write (*,'(i4,$)') nss,(ihpb(j),jhpb(j),j=1,nss)