head	1.74;
access;
symbols
	release-2-12:1.74
	release-2-12-beta-1:1.72
	release-2-11:1.68
	release-2-11-beta-2:1.67
	release-2-11-beta-1:1.66
	release-2-10:1.64
	release-2-10-beta-2:1.63
	release-2-10-beta-1:1.61
	release-2-9:1.59
	release-2-9-beta-3:1.58
	release-2-9-beta-2:1.57
	release-2-9-beta-1:1.56
	release-2-8:1.55
	release-2-8-beta-3:1.54
	release-2-8-beta-2:1.53
	release-2-8-beta-1:1.52
	release-2-7:1.50
	release-2-7-beta-4:1.49
	release-2-7-beta-3:1.48
	release-2-7-beta-2:1.47
	release-2-7-beta-1:1.45
	release-2-6:1.39
	release-2-6-beta-2:1.38
	release-2-6-beta-1:1.37
	release-2-5:1.34
	release-2-5-beta-3:1.33
	release-2-5-beta-2:1.32
	release-2-5-beta-1:1.27
	release-2-4:1.26
	release-2-4-beta-2:1.24
	release-2-4-beta-1:1.21
	release-2-3:1.20
	release-2-3-beta-2:1.19
	release-2-3-beta-1:1.18
	release-2-2:1.16
	release-2-2-beta-3:1.15
	release-2-2-beta-2:1.14
	release-2-2-beta-1:1.12
	release-2-1:1.10
	release-2-1-beta-4:1.10
	release-2-1-beta-3:1.10
	release-2-1-beta-2:1.10
	release-2-1-beta-1:1.7
	release-2-0-pre-charm-syntax:1.7
	release-2-0:1.7
	release-2-0-beta-3:1.5
	release-2-0-beta-2:1.4;
locks; strict;
comment	@# @;


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desc
@@


1.74
log
@Update to 2.12.
@
text
@#####
# define version
#####
NAMD_VERSION = 2.12

#####
# specific names of programs used in make commands
#####
CCPP		= CC
CC		= cc
CD		= cd
COPY		= cp
MOVE		= mv -f
DELETE		= rm -f
ECHO		= echo
TAR		= tar
COMPRESS	= compress
AR		= ar rsc
RANLIB		= /bin/true
COCMD		= co
SHELL 		= /bin/sh


DOCDIR		= .
MAIN_UG_FILE	= $(DOCDIR)/ug

SRCFILES = ug.bib namd_begindoc.tex namd_copyright.tex namd_macros.tex \
namd_title.tex namd_version.tex ug.tex ug_accel.tex ug_avail.tex \
ug_dynamics.tex ug_forcefield.tex ug_performance.tex ug_userdef.tex \
ug_intro.tex ug_io.tex ug_macros.tex ug_runit.tex ug_sample.tex ug_start.tex \
ug_xplor.tex ug_fenergy.tex ug_psfgen.tex psfgen_macros.tex ug_alchemy.tex \
ug_colvars-cv.tex colvars-cv.tex ug_colvars.bib ug_colvars_macros.tex \
ug_colvars.tex ug_analysis.tex ug_gbis.tex

PDFFIGS = figures/fmaOn.pdf figures/pairlistdist.pdf \
figures/shifting.pdf figures/switching.pdf figures/dual_top.pdf

### run pdflatex
pdf:	$(DOCDIR)/ug.pdf

### run latex2html
html:	$(DOCDIR)/ug.tar.gz

$(DOCDIR)/ug.tar.gz: $(DOCDIR)/ug.pdf
	latex2html -local_icons -split 5 -toc_depth 4 -toc_stars \
	-t "NAMD $(NAMD_VERSION) User's Guide" -address "http://www.ks.uiuc.edu/Research/namd/" \
	-up_url "../../" -up_title "Main NAMD Page" ug
	chmod -R a+rX ug
	tar czvf ug.tar.gz ug

$(DOCDIR)/ug.pdf: $(SRCFILES) $(PDFFIGS)
	$(ECHO) "Creating NAMD $(NAMD_VERSION) User's Guide ..." ; \
	$(CD) $(DOCDIR); \
	pdflatex $(MAIN_UG_FILE); \
	bibtex $(MAIN_UG_FILE); \
	bibtex ug_alchemy; \
	makeindex $(MAIN_UG_FILE).idx; \
	pdflatex $(MAIN_UG_FILE); \
	makeindex $(MAIN_UG_FILE).idx; \
	pdflatex $(MAIN_UG_FILE); \

DISTILL = distill -compatlevel 2.1

# need to specify page size because distill can't figure it out (yet?)

#figures/fmaOn.pdf: figures/fmaOn.eps
#	$(DISTILL) -pagesize 301 174 pts < $^ > $@@

#figures/pairlistdist.pdf: figures/pairlistdist.eps
#	$(DISTILL) -pagesize 240 240 pts < $^ > $@@

#figures/shifting.pdf: figures/shifting.eps
#	$(DISTILL) -pagesize 301 165 pts < $^ > $@@

#figures/switching.pdf: figures/switching.eps
#	$(DISTILL) -pagesize 310 165 pts < $^ > $@@

#figures/dual_top.pdf: figures/dual_top.eps
#	$(DISTILL) -pagesize 584 220 pts < $^ > $@@

$(DOCDIR)/ug.dvi: $(SRCFILES)
	$(ECHO) "Creating NAMD $(NAMD_VERSION) User's Guide ..." ; \
	$(CD) $(DOCDIR); \
	latex $(MAIN_UG_FILE); \
	bibtex $(MAIN_UG_FILE); \
	makeindex $(MAIN_UG_FILE).idx; \
	latex $(MAIN_UG_FILE); \
	makeindex $(MAIN_UG_FILE).idx; \
	latex $(MAIN_UG_FILE); \
	# dvips -t letter -o ug.ps ug.dvi

namd_version.tex: Makefile
	$(DELETE) namd_version.tex ; \
	env echo '\newcommand{\NAMDVER}{$(NAMD_VERSION)}' > namd_version.tex

psfgen_macros.tex: ../psfgen/doc/ug_macros.tex
	$(DELETE) psfgen_macros.tex ; \
	grep PSFGEN ../psfgen/doc/ug_macros.tex > psfgen_macros.tex

ug_psfgen.tex: ../psfgen/doc/ug_psfgen.tex
	$(DELETE) ug_psfgen.tex ; \
	sed -e '20,$$ s/\\subsection{/\\subsubsection{/' \
	    -e '20,$$ s/\\section{/\\subsection{/' \
	    -e '20,$$ s/\\subsection\*{/\\subsubsection\*{/' \
	../psfgen/doc/ug_psfgen.tex > ug_psfgen.tex

clean:
	$(DELETE) namd_version.tex ; \
	$(DELETE) psfgen_macros.tex ; \
	$(DELETE) ug_psfgen.tex ; \
	$(DELETE) $(DOCDIR)/ug.ps ; \
	$(DELETE) $(DOCDIR)/ug.aux ; \
	$(DELETE) $(DOCDIR)/ug.bbl ; \
	$(DELETE) $(DOCDIR)/ug.blg ; \
	$(DELETE) $(DOCDIR)/ug.dvi ; \
	$(DELETE) $(DOCDIR)/ug.lof ; \
	$(DELETE) $(DOCDIR)/ug.log ; \
	$(DELETE) $(DOCDIR)/ug.idx ; \
	$(DELETE) $(DOCDIR)/ug.ilg ; \
	$(DELETE) $(DOCDIR)/ug.ind ; \
	$(DELETE) $(DOCDIR)/ug.toc ; \
	$(DELETE) $(DOCDIR)/ug.pdf ; \
	$(DELETE) $(DOCDIR)/ug.tar.gz; \
#	$(DELETE) $(PDFFIGS)
@


1.73
log
@Remove unused ug_eabf.tex file to avoid confusion.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.12b1
@


1.72
log
@Update to 2.12b1.
@
text
@d33 1
a33 1
ug_colvars.tex ug_analysis.tex ug_gbis.tex ug_eabf.tex
@


1.71
log
@Add dependency.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.11
@


1.70
log
@Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot.
@
text
@d32 1
a32 1
colvars-cv.tex ug_colvars.bib ug_colvars_macros.tex \
@


1.69
log
@Work around unusual sh echo behavior on Ubuntu when creating namd_version.tex.
@
text
@d33 1
a33 1
ug_colvars.tex ug_analysis.tex ug_gbis.tex
@


1.68
log
@Update to 2.11.
@
text
@d94 1
a94 1
	echo "\\newcommand{\\NAMDVER}{$(NAMD_VERSION)}" > namd_version.tex
@


1.67
log
@Update to 2.11b2.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.11b2
@


1.66
log
@Update to 2.11b1.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.11b1
@


1.65
log
@Major update to collective variables module from Giacomo Fiorin and Jerome Henin: Tcl scripts to expand existing functionality, improvements to histogram bias, colvarsConfig is now optional ("cv" command), and bug fixes.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.10
@


1.64
log
@Increase version to 2.10.
@
text
@d32 1
@


1.63
log
@Increase version to 2.10b2.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.10b2
@


1.62
log
@Removed call to csh for regenerating namd_version.tex .
Seems that newer version of csh is processing escape backslashes differently.
Instead we'll let Bourne shell do its thing.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.10b1
@


1.61
log
@updates for 2.10b1 release
@
text
@d93 1
a93 1
	csh -c "echo \\\\newcommand\{\\\\NAMDVER\} \{$(NAMD_VERSION)\} > namd_version.tex"
@


1.60
log
@Switch gtar to tar.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.9
@


1.59
log
@Update to version 2.9.
@
text
@d48 1
a48 1
	gtar czvf ug.tar.gz ug
@


1.58
log
@Update to version 2.9b3.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.9b3
@


1.57
log
@Version 2.9b2.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.9b2
@


1.56
log
@Update docs/notes/announcement and bump version to 2.9b1.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.9b1
@


1.55
log
@Update version to 2.8.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.8
d45 1
a45 1
	-t "NAMD $(NAMD_VERSION) User's Guide" -address "namd@@ks.uiuc.edu" \
@


1.54
log
@Update version to 2.8b3.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.8b3
@


1.53
log
@Update version to 2.8b2.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.8b2
@


1.52
log
@Update versions to 2.8b1.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.8b1
@


1.51
log
@adding users guide chapter for implicit solvent as well as shortening superfluous gbis communication by sending messages of size zero instead of messages of size nAtoms
@
text
@d4 1
a4 1
NAMD_VERSION = 2.7
@


1.50
log
@Update version to 2.7.
@
text
@d32 1
a32 1
ug_colvars.tex ug_analysis.tex
@


1.49
log
@Update version to 2.7b4.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.7b4
@


1.48
log
@updating NAMD and Charm++ versions.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.7b3
@


1.47
log
@update versions to 2.7b1 and charm-6.1.3
@
text
@d4 1
a4 1
NAMD_VERSION = 2.7b2
@


1.46
log
@build tarfile automatically
@
text
@d4 1
a4 1
NAMD_VERSION = 2.7b1
@


1.45
log
@only build pdf before html since dvi build fails
@
text
@d41 3
a43 1
html:	$(DOCDIR)/ug.pdf
d47 2
d122 1
@


1.44
log
@Build pdf by default (used to be ps).
@
text
@d41 1
a41 1
html:	$(DOCDIR)/ug.dvi
@


1.43
log
@Update versions to NAMD 2.7b1 and Charm++ 6.1.
@
text
@d37 2
a38 2
### latex the documentation
doc:	$(DOCDIR)/ug.ps 
d41 1
a41 1
html:	$(DOCDIR)/ug.ps
a45 3
### run pdflatex
pdf:	$(DOCDIR)/ug.pdf

d76 1
a76 1
$(DOCDIR)/ug.ps: $(SRCFILES)
d85 1
a85 1
	dvips -t letter -o ug.ps ug.dvi
@


1.42
log
@modified list of source files, clean shouldn't remove PDF figures
@
text
@d4 1
a4 1
NAMD_VERSION = 2.6
@


1.41
log
@Initial add of colvar module  (Following files added: src/GlobalMasterColvars.h src/colvar.C src/colvar.h src/colvaratoms.C src/colvaratoms.h src/colvarbias.C src/colvarbias.h src/colvarbias_abf.C src/colvarbias_abf.h src/colvarbias_meta.C src/colvarbias_meta.h src/colvarcomp.C src/colvarcomp.h src/colvarcomp_angles.C src/colvarcomp_coordnums.C src/colvarcomp_distances.C src/colvarcomp_protein.C src/colvarcomp_rotations.C src/colvarmodule.C src/colvarmodule.h src/colvarparse.C src/colvarparse.h src/colvarproxy.h src/colvarproxy_namd.C src/colvarproxy_namd.h src/colvartypes.h src/colvarvalue.C src/colvarvalue.h ug/ug_colvars.tex) --cbh
@
text
@d28 2
a29 1
namd_title.tex namd_version.tex ug.tex ug_add.tex ug_avail.tex ug_basic.tex \
d32 1
a32 1
ug_colvars.tex
d121 1
a121 1
	$(DELETE) $(PDFFIGS)
@


1.40
log
@Add in Chipot's changes to the fep documentation
@
text
@d31 1
a31 1
ug_abf.tex
@


1.39
log
@Update to version 2.6.
@
text
@d53 1
@


1.38
log
@Updates for 2.6b2 release.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.6b2
d88 1
a88 1
namd_version.tex:
@


1.37
log
@Update version numbers to 2.6b1.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.6b1
@


1.36
log
@Include pdf files in CVS.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.5
d90 1
a90 1
	echo '\\newcommand{\\NAMDVER}' "{$(NAMD_VERSION)}" > namd_version.tex
@


1.35
log
@Add adaptive biasing force method from Chipot.
@
text
@d62 2
a63 2
figures/fmaOn.pdf: figures/fmaOn.eps
	$(DISTILL) -pagesize 301 174 pts < $^ > $@@
d65 2
a66 2
figures/pairlistdist.pdf: figures/pairlistdist.eps
	$(DISTILL) -pagesize 240 240 pts < $^ > $@@
d68 2
a69 2
figures/shifting.pdf: figures/shifting.eps
	$(DISTILL) -pagesize 301 165 pts < $^ > $@@
d71 2
a72 2
figures/switching.pdf: figures/switching.eps
	$(DISTILL) -pagesize 310 165 pts < $^ > $@@
d74 2
a75 2
figures/dual_top.pdf: figures/dual_top.eps
	$(DISTILL) -pagesize 584 220 pts < $^ > $@@
@


1.34
log
@Bump version to 2.5.
@
text
@d30 2
a31 1
ug_xplor.tex ug_fenergy.tex ug_psfgen.tex psfgen_macros.tex ug_alchemy.tex
@


1.33
log
@Bump version to 2.5b3.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.5b3
@


1.32
log
@Fixed index again.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.5b2
@


1.31
log
@Cleaned up index.
@
text
@d52 1
a52 1
	makeindex $(MAIN_UG_FILE); \
d54 1
a54 1
	makeindex $(MAIN_UG_FILE); \
d81 1
a81 1
	makeindex $(MAIN_UG_FILE); \
d83 1
a83 1
	makeindex $(MAIN_UG_FILE); \
@


1.30
log
@Copied in release notes, added index, various cleanups.
@
text
@a49 1
	touch $(MAIN_UG_FILE).ind; \
a78 1
	touch $(MAIN_UG_FILE).ind; \
@


1.29
log
@Fixed section -> subsection code.
@
text
@d50 1
d53 1
d55 1
d80 1
d83 1
d85 1
d115 3
@


1.28
log
@Version updates - now 2.5b2
@
text
@d93 3
a95 2
	sed -e "20,$$ s/\\subsection{/\\subsubsection{/" \
	    -e "20,$$ s/\\section{/\\subsection{/" \
@


1.27
log
@Updated version to 2.5b1.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.5b1
@


1.26
log
@Added ug.bib to dependencies.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.4
@


1.25
log
@Updated version to 2.4.
@
text
@d27 1
a27 1
SRCFILES = namd_begindoc.tex namd_copyright.tex namd_macros.tex \
@


1.24
log
@Added alchemical free energy docs "as is", fixed only to build.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.4b2
@


1.23
log
@Updated version to 2.4b2.
@
text
@d30 1
a30 1
ug_xplor.tex ug_fenergy.tex ug_psfgen.tex psfgen_macros.tex
d33 1
a33 1
figures/shifting.pdf figures/switching.pdf
d55 2
d60 1
a60 1
	distill -pagesize 301 174 pts figures/fmaOn.eps
d63 1
a63 1
	distill -pagesize 240 240 pts figures/pairlistdist.eps
d66 1
a66 1
	distill -pagesize 301 165 pts figures/shifting.eps
d69 4
a72 1
	distill -pagesize 310 165 pts figures/switching.eps
@


1.22
log
@Moved psfgen to separate directory tree based on Justin's version.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.4b1
@


1.21
log
@Changes for version 2.4b1.  Only need to change version in one place now.
@
text
@d30 1
a30 1
ug_xplor.tex ug_fenergy.tex ug_psfgen.tex
d82 10
d94 2
@


1.20
log
@Updated version to 2.3.
@
text
@d2 5
d41 1
a41 1
	-t "NAMD 2.3 User's Guide" -address "namd@@ks.uiuc.edu" \
d48 1
a48 1
	$(ECHO) "Creating User's Guide ..." ; \
d70 1
a70 1
	$(ECHO) "Creating User's Guide ..." ; \
d78 3
d83 1
@


1.19
log
@version 2.3b2
@
text
@d36 1
a36 1
	-t "NAMD 2.3b2 User's Guide" -address "namd@@ks.uiuc.edu" \
@


1.18
log
@Added documentation on psfgen.
@
text
@d36 1
a36 1
	-t "NAMD 2.3b1 User's Guide" -address "namd@@ks.uiuc.edu" \
@


1.17
log
@Many updates and cleanups for 2.3.
@
text
@d25 1
a25 1
ug_xplor.tex ug_fenergy.tex
@


1.16
log
@Updated to 2.2.
@
text
@d36 1
a36 1
	-t "NAMD 2.2 User's Guide" -address "namd@@ks.uiuc.edu" \
@


1.15
log
@Updated version to 2.2b3.
@
text
@d36 1
a36 1
	-t "NAMD 2.2b3 User's Guide" -address "namd@@ks.uiuc.edu" \
@


1.14
log
@updated
@
text
@d36 1
a36 1
	-t "NAMD 2.2b2 User's Guide" -address "namd@@ks.uiuc.edu" \
@


1.13
log
@Fixed 2.1 -> 2.2b1.  Whoops.
@
text
@d36 1
a36 1
	-t "NAMD 2.2b1 User's Guide" -address "namd@@ks.uiuc.edu" \
@


1.12
log
@Now using -toc_stars workaround until latex2html is fixed.
@
text
@d36 1
a36 1
	-t "NAMD 2.1 User's Guide" -address "namd@@ks.uiuc.edu" \
@


1.11
log
@Using CSS to change background color as workaround to LaTeX2HTML bug.
@
text
@d35 1
a35 1
	latex2html -local_icons -split 5 -toc_depth 4 \
d37 1
a37 2
	-up_url "../../" -up_title "Main NAMD Page" ug; \
	echo 'body { background-color : white }' >> ug/ug.css
@


1.10
log
@Updated version number.
@
text
@d37 2
a38 1
	-up_url "../../" -up_title "Main NAMD Page" ug 
@


1.9
log
@Now works with LaTeX 2e and can produce PDF files.
@
text
@d36 1
a36 1
	-t "NAMD 2.0 User's Guide" -address "namd@@ks.uiuc.edu" \
@


1.8
log
@Various doc updates for 2.1.
@
text
@d22 8
d39 26
a64 4
$(DOCDIR)/ug.ps: namd_begindoc.tex namd_copyright.tex namd_macros.tex \
namd_title.tex namd_version.tex ug.tex ug_add.tex ug_avail.tex ug_basic.tex \
ug_intro.tex ug_io.tex ug_macros.tex ug_runit.tex ug_sample.tex ug_start.tex \
ug_xplor.tex ug_fenergy.tex
d82 3
a84 1
	$(DELETE) $(DOCDIR)/ug.toc
@


1.7
log
@Many changes, now mostly ready for 2.0 release.
@
text
@d41 1
a41 1
	dvips -o ug.ps ug.dvi
@


1.6
log
@Added html target to preserve latex2html arguments.
@
text
@d27 3
a29 1
	latex2html -local_icons -split 5 -toc_depth 4 ug 
@


1.5
log
@Added free energy documentation from David Hurwitz.
@
text
@d25 4
@


1.4
log
@Documented new features in 2.0.  Added authors.  Still needs converse docs.
@
text
@d28 1
a28 1
ug_xplor.tex
@


1.3
log
@*** empty log message ***
@
text
@d25 4
a28 1
$(DOCDIR)/ug.ps: 
@


1.2
log
@*** empty log message ***
@
text
@d40 1
a43 1

@


1.1
log
@user guide, first draft
@
text
@d36 7
a42 1
	$(DELETE) $(DOCDIR)/ug.ps
@
