[Debichem-commits] r3007 - in /unstable/gromacs/debian: changelog man/g_dos.1 rules

nbreen-guest at users.alioth.debian.org nbreen-guest at users.alioth.debian.org
Wed Sep 21 22:51:47 UTC 2011


Author: nbreen-guest
Date: Wed Sep 21 22:51:46 2011
New Revision: 3007

URL: http://svn.debian.org/wsvn/debichem/?sc=1&rev=3007
Log:
man/g_dos.1: Create man page for new binary.

Added:
    unstable/gromacs/debian/man/g_dos.1
Modified:
    unstable/gromacs/debian/changelog
    unstable/gromacs/debian/rules

Modified: unstable/gromacs/debian/changelog
URL: http://svn.debian.org/wsvn/debichem/unstable/gromacs/debian/changelog?rev=3007&op=diff
==============================================================================
--- unstable/gromacs/debian/changelog (original)
+++ unstable/gromacs/debian/changelog Wed Sep 21 22:51:46 2011
@@ -1,11 +1,12 @@
-gromacs (4.5.5-1) UNRELEASED; urgency=low
+gromacs (4.5.5-1) unstable; urgency=low
 
   * New upstream release.
     - Remove patches/30_git_release-4.5-patches.dpatch.
+    - man/g_dos.1: Create man page for new binary.
   * rules: Add build-arch/build-indep targets.  Add preliminary support for
     building GPU-accelerated binaries: set DEB_BUILD_OPTIONS=gpu to try it.
 
- -- Nicholas Breen <nbreen at ofb.net>  Mon, 19 Sep 2011 14:49:41 -0700
+ -- Nicholas Breen <nbreen at ofb.net>  Wed, 21 Sep 2011 15:26:14 -0700
 
 gromacs (4.5.4-2) unstable; urgency=low
 

Added: unstable/gromacs/debian/man/g_dos.1
URL: http://svn.debian.org/wsvn/debichem/unstable/gromacs/debian/man/g_dos.1?rev=3007&op=file
==============================================================================
--- unstable/gromacs/debian/man/g_dos.1 (added)
+++ unstable/gromacs/debian/man/g_dos.1 Wed Sep 21 22:51:46 2011
@@ -1,0 +1,137 @@
+.TH g_dos 1 "Wed 21 Sep 2011" "" "GROMACS suite, VERSION 4.5.5"
+.SH NAME
+g_dos \- compute density of states from a simulation trajectory
+.B VERSION 4.5.5
+.SH SYNOPSIS
+\f3g_dos\fP
+.BI "\-f" " traj.trr "
+.BI "\-s" " topol.tpr "
+.BI "\-n" " index.ndx "
+.BI "\-vacf" " vacf.xvg "
+.BI "\-mvacf" " mvacf.xvg "
+.BI "\-dos" " dos.xvg "
+.BI "\-g" " dos.log "
+.BI "\-[no]h" ""
+.BI "\-[no]version" ""
+.BI "\-nice" " int "
+.BI "\-b" " time "
+.BI "\-e" " time "
+.BI "\-dt" " time "
+.BI "\-[no]w" ""
+.BI "\-xvg" " enum "
+.BI "\-[no]v" ""
+.BI "\-[no]recip" ""
+.BI "\-[no]abs" ""
+.BI "\-[no]normdos" ""
+.BI "\-T" " real "
+.BI "\-acflen" " int "
+.BI "\-[no]normalize" ""
+.BI "\-P" " enum "
+.BI "\-fitfn" " enum "
+.BI "\-ncskip" " int "
+.BI "\-beginfit" " real "
+.BI "\-endfit" " real "
+.SH DESCRIPTION
+\&\fB g_dos\fR computes the Density of States from a simulation.
+\&In order for this to be meaningful the velocities must be saved
+\&in the trajectory with sufficiently high frequency such as to cover
+\&all vibrations. For flexible systems that would be around a few fs
+\&between saving. Properties based on the DoS are printed on the
+\&standard output.
+.SH FILES
+.BI "\-f" " traj.trr" 
+.B Input
+ Full precision trajectory: trr trj cpt 
+
+.BI "\-s" " topol.tpr" 
+.B Input
+ Run input file: tpr tpb tpa 
+
+.BI "\-n" " index.ndx" 
+.B Input, Opt.
+ Index file 
+
+.BI "\-vacf" " vacf.xvg" 
+.B Output
+ xvgr/xmgr file 
+
+.BI "\-mvacf" " mvacf.xvg" 
+.B Output
+ xvgr/xmgr file 
+
+.BI "\-dos" " dos.xvg" 
+.B Output
+ xvgr/xmgr file 
+
+.BI "\-g" " dos.log" 
+.B Output
+ Log file 
+
+.SH OTHER OPTIONS
+.BI "\-[no]h"  "no    "
+ Print help info and quit
+
+.BI "\-[no]version"  "no    "
+ Print version info and quit
+
+.BI "\-nice"  " int" " 19" 
+ Set the nicelevel
+
+.BI "\-b"  " time" " 0     " 
+ First frame (ps) to read from trajectory
+
+.BI "\-e"  " time" " 0     " 
+ Last frame (ps) to read from trajectory
+
+.BI "\-dt"  " time" " 0     " 
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "\-[no]w"  "no    "
+ View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
+
+.BI "\-xvg"  " enum" " xmgrace" 
+ xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
+
+.BI "\-[no]v"  "yes   "
+ Be loud and noisy.
+
+.BI "\-[no]recip"  "no    "
+ Use cm\-1 on X\-axis instead of 1/ps for DoS plots.
+
+.BI "\-[no]abs"  "no    "
+ Use the absolute value of the Fourier transform of the VACF as the Density of States. Default is to use the real component only
+
+.BI "\-[no]normdos"  "no    "
+ Normalize the DoS such that it adds up to 3N. This is a hack that should not be necessary.
+
+.BI "\-T"  " real" " 298.15" 
+ Temperature in the simulation
+
+.BI "\-acflen"  " int" " \-1" 
+ Length of the ACF, default is half the number of frames
+
+.BI "\-[no]normalize"  "yes   "
+ Normalize ACF
+
+.BI "\-P"  " enum" " 0" 
+ Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR
+
+.BI "\-fitfn"  " enum" " none" 
+ Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR
+
+.BI "\-ncskip"  " int" " 0" 
+ Skip N points in the output file of correlation functions
+
+.BI "\-beginfit"  " real" " 0     " 
+ Time where to begin the exponential fit of the correlation function
+
+.BI "\-endfit"  " real" " \-1    " 
+ Time where to end the exponential fit of the correlation function, \-1 is until the end
+
+.SH KNOWN PROBLEMS
+\- This program needs a lot of memory: total usage equals the number of atoms times 3 times number of frames times 4 (or 8 when run in double precision).
+
+.SH SEE ALSO
+.BR gromacs(7)
+
+More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.

Modified: unstable/gromacs/debian/rules
URL: http://svn.debian.org/wsvn/debichem/unstable/gromacs/debian/rules?rev=3007&op=diff
==============================================================================
--- unstable/gromacs/debian/rules (original)
+++ unstable/gromacs/debian/rules Wed Sep 21 22:51:46 2011
@@ -180,7 +180,7 @@
 	$(MAKE) -C build/basic install DESTDIR=$(CURDIR)/debian/gromacs
 	$(MAKE) -C build/basic-dp install DESTDIR=$(CURDIR)/debian/gromacs
 	rm -f $(CURDIR)/debian/gromacs/usr/share/man/man1/*_d.1
-	dh_installman -pgromacs debian/man/g_luck.1 debian/man/g_kinetics.1 debian/man/g_options.1
+	dh_installman -pgromacs debian/man/g_*.1
 	for manpage in $(CURDIR)/debian/gromacs/usr/share/man/man1/*.1; do \
 		dh_link -pgromacs usr/share/man/man1/`basename $${manpage}` usr/share/man/man1/`basename $${manpage} .1`_d.1 ; \
 	done




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