Initial public commit. Code version = 0.90.

AUTHORS

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+Aten is the work of Tristan Youngs ([email protected]), made possible with the occasional
+helping hands of (in no particular order):
+
+M. Montgomery
+S. Cromie
+A. Croft
+A. Elena
+

COPYING

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+/usr/share/automake-1.9/COPYING

INSTALL

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+/usr/share/automake-1.9/INSTALL

ISSUES_TODO

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+Issues with the current version:
+	- Closing main window with [x] does not ask to save modified models.
+	- Save image provokes GLXBadExtension error (on some cards), affects canvas on others.
+	- Spherical regions in disordered builder have poor randomness.
+	- Interpolation of surface triangles is 'simple' (0.5 along edges)
+	- OpenGL transparency issues (polygon artefacts - need ordering?)
+
+General To-Do list:
+	- Ewald sum (fourier calculation, reciprocal cell?) for non-orthogonal cells
+	- Molecular dynamics
+	- Trajectory playback / use of camera/rotation from parent model
+	- Calculate average molecule geometry (analyse)
+	- Complete spacegroups list
+	- UFF - oxidation state, energy conversion, torsions, angle periodicity
+	- Improve SD minimiser
+	- Add NR / simplex minimisers
+	- View along cell axes (or Miller planes)
+	- Reset view (whole model on screen)
+	- Cambridge database import filter (need to be able to evaluate numerical expressions)
+	- Accelrys MSI import filter
+	- EPSR Ato import / export? filters
+	- Ability to evaluate numerical expressions in filters (and scripts)
+
+General Qt To-Do list:
+	- Forcefield Qt stack page and manager/edit window
+	- Prefs window (partial)
+	- Minimiser Qt stack page (partial)
+	- Disorder Qt stack page (partial)
+	- Trajectory playback
+	- Progress dialogs are not application modal
+
+Manual To-Do list:
+	- Section on forcefields
+	- Section on Qt GUI
+	- Filters Handbook is incomplete 
+
+Optimisation To-Do list:
+	- Hemispherical Ewald summmation
+	- Filters / variable_list - can enum and store common variable pointers (e.g. "e", "r.x") to save lookup time
+	- For large systems (10000+ atoms) autocreate_patterns() is a bottleneck, as is model::copy(model*)

Makefile.am

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+SUBDIRS = src
+
+EXTRA_DIST = scripts/*.txt doc/manual.pdf src/gui-qt/icons/*.svg src/gui-gtk/icons/*/*.xpm
+
+#filterdir = $(datadir)/aten/filters
+#filter_DATA = data/filters/*
+
+atendir = $(datadir)/aten
+
+aten_DATA = data/spgrp.dat
+
+filterdir = $(atendir)/filters
+filter_DATA = data/filters/*
+

README

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+                                *** Introduction ***
+
+Aten is a code to do 'stuff' with coordinates / starting configurations for
+computational chemistry and physics codes. It was written primarily as a 
+means for brushing up on C++ and OpenGL but has ballooned into something 
+that I find useful most days at work as a researcher.
+
+It is not guaranteed to work, and is not a full-time project (paid work always
+gets preference!). However it will be fixed and extended where possible, and 
+contributions (especially forcefields and filters) are welcome.
+
+Find a bug? Report it.
+
+Suggestions / comments? Send them on, but be original (writing "Your code sucks."
+is fair enough, but be brave and give a little detail).
+
+Want to add something in? Great! E-mail me about it. This software is provided
+under the GPL, so you can take / change / redistribute at will, but it would be
+nice to be putting everything into the same pot.
+
+
+                                *** Installation ***
+
+Full instructions can be found in the manual. Briefly:
+
+1) Run './autogen.sh' (if you got Aten via svn)
+
+2) Run './configure' without options use standard locations and build in the Qt GUI.
+	Use --prefix to specify the install location
+	Use --with-gui to specify a different gui (currently 'qt', 'gtk', or 'none')
+	Use --with-qt=frameworks to use native Qt installation on Macs (otherwise
+		the Fink / MacPorts version will be used and detected with pkg-config).
+
+3) Run 'make'.
+
+4) Run 'make install' as root or, if you wish, put the code where you want it.
+	Note for custom installs: the contents of the 'data' directory must be
+	in a location accessible to all users.
+
+5) Set the environment variable ATENDATA to point to the installed data files.
+	For my default configuration (SuSE Linux 10.2) it's /usr/local/share/aten.
+	For example, using 'bash': export ATENDATA='/usr/local/share/aten'.
+	It's a good idea to put this in your .login, .bashrc or whatever is relevant.
+
+
+Tris Youngs
+[email protected]
+October 2007

aten.kdevelop

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+<?xml version = '1.0'?>
+<kdevelop>
+  <general>
+    <author>Tris Youngs</author>
+    <email>[email protected]</email>
+    <version>ATEN_VERSION</version>
+    <projectmanagement>KDevAutoProject</projectmanagement>
+    <primarylanguage>C</primarylanguage>
+    <ignoreparts/>
+    <projectname>aten</projectname>
+    <projectdirectory>.</projectdirectory>
+    <absoluteprojectpath>false</absoluteprojectpath>
+    <description/>
+    <defaultencoding/>
+    <versioncontrol>kdevsubversion</versioncontrol>
+  </general>
+  <kdevautoproject>
+    <general>
+      <useconfiguration>default</useconfiguration>
+    </general>
+    <run>
+      <mainprogram/>
+      <programargs/>
+      <globaldebugarguments/>
+      <globalcwd/>
+      <useglobalprogram>false</useglobalprogram>
+      <terminal>false</terminal>
+      <autocompile>false</autocompile>
+      <autoinstall>false</autoinstall>
+      <autokdesu>false</autokdesu>
+      <envvars/>
+    </run>
+    <configurations>
+      <optimized>
+        <builddir>optimized</builddir>
+        <ccompiler>GccOptions</ccompiler>
+        <cxxcompiler>GppOptions</cxxcompiler>
+        <f77compiler>G77Options</f77compiler>
+        <cflags>-O2 -g0</cflags>
+      </optimized>
+      <debug>
+        <configargs>--enable-debug=full</configargs>
+        <builddir>debug</builddir>
+        <ccompiler>GccOptions</ccompiler>
+        <cxxcompiler>GppOptions</cxxcompiler>
+        <f77compiler>G77Options</f77compiler>
+        <cflags>-O0 -g3</cflags>
+      </debug>
+      <default>
+        <envvars/>
+      </default>
+    </configurations>
+    <make>
+      <envvars>
+        <envvar value="1" name="WANT_AUTOCONF_2_5" />
+        <envvar value="1" name="WANT_AUTOMAKE_1_6" />
+      </envvars>
+      <abortonerror>true</abortonerror>
+      <runmultiplejobs>false</runmultiplejobs>
+      <numberofjobs>1</numberofjobs>
+      <dontact>false</dontact>
+      <makebin/>
+      <prio>0</prio>
+    </make>
+  </kdevautoproject>
+  <kdevdebugger>
+    <general>
+      <dbgshell>libtool</dbgshell>
+      <gdbpath/>
+      <configGdbScript/>
+      <runShellScript/>
+      <runGdbScript/>
+      <breakonloadinglibs>true</breakonloadinglibs>
+      <separatetty>false</separatetty>
+      <floatingtoolbar>false</floatingtoolbar>
+    </general>
+    <display>
+      <staticmembers>false</staticmembers>
+      <demanglenames>true</demanglenames>
+      <outputradix>10</outputradix>
+    </display>
+  </kdevdebugger>
+  <kdevdoctreeview>
+    <ignoretocs>
+      <toc>ada</toc>
+      <toc>ada_bugs_gcc</toc>
+      <toc>bash</toc>
+      <toc>bash_bugs</toc>
+      <toc>clanlib</toc>
+      <toc>fortran_bugs_gcc</toc>
+      <toc>gnome1</toc>
+      <toc>gnustep</toc>
+      <toc>gtk</toc>
+      <toc>gtk_bugs</toc>
+      <toc>haskell</toc>
+      <toc>haskell_bugs_ghc</toc>
+      <toc>java_bugs_gcc</toc>
+      <toc>java_bugs_sun</toc>
+      <toc>kde2book</toc>
+      <toc>libstdc++</toc>
+      <toc>opengl</toc>
+      <toc>pascal_bugs_fp</toc>
+      <toc>php</toc>
+      <toc>php_bugs</toc>
+      <toc>perl</toc>
+      <toc>perl_bugs</toc>
+      <toc>python</toc>
+      <toc>python_bugs</toc>
+      <toc>qt-kdev3</toc>
+      <toc>ruby</toc>
+      <toc>ruby_bugs</toc>
+      <toc>sdl</toc>
+      <toc>stl</toc>
+      <toc>sw</toc>
+      <toc>w3c-dom-level2-html</toc>
+      <toc>w3c-svg</toc>
+      <toc>w3c-uaag10</toc>
+      <toc>wxwidgets_bugs</toc>
+    </ignoretocs>
+    <ignoreqt_xml>
+      <toc>Guide to the Qt Translation Tools</toc>
+      <toc>Qt Assistant Manual</toc>
+      <toc>Qt Designer Manual</toc>
+      <toc>Qt Reference Documentation</toc>
+      <toc>qmake User Guide</toc>
+    </ignoreqt_xml>
+    <ignoredoxygen>
+      <toc>KDE Libraries (Doxygen)</toc>
+    </ignoredoxygen>
+  </kdevdoctreeview>
+  <kdevfilecreate>
+    <filetypes/>
+    <useglobaltypes>
+      <type ext="c" />
+      <type ext="h" />
+    </useglobaltypes>
+  </kdevfilecreate>
+  <kdevcppsupport>
+    <qt>
+      <used>true</used>
+      <version>4</version>
+      <includestyle>4</includestyle>
+      <root>/usr/lib/qt3</root>
+      <designerintegration>ExternalDesigner</designerintegration>
+      <qmake>/usr/lib/qt3/bin/qmake</qmake>
+      <designer>/usr/bin/designer</designer>
+      <designerpluginpaths>
+        <path>/usr/lib/qt4/plugins</path>
+      </designerpluginpaths>
+    </qt>
+    <references/>
+    <codecompletion>
+      <automaticCodeCompletion>false</automaticCodeCompletion>
+      <automaticArgumentsHint>true</automaticArgumentsHint>
+      <automaticHeaderCompletion>true</automaticHeaderCompletion>
+      <codeCompletionDelay>250</codeCompletionDelay>
+      <argumentsHintDelay>400</argumentsHintDelay>
+      <headerCompletionDelay>250</headerCompletionDelay>
+      <showOnlyAccessibleItems>false</showOnlyAccessibleItems>
+      <completionBoxItemOrder>0</completionBoxItemOrder>
+      <howEvaluationContextMenu>true</howEvaluationContextMenu>
+      <showCommentWithArgumentHint>true</showCommentWithArgumentHint>
+      <statusBarTypeEvaluation>false</statusBarTypeEvaluation>
+      <namespaceAliases>std=_GLIBCXX_STD;__gnu_cxx=std</namespaceAliases>
+      <processPrimaryTypes>true</processPrimaryTypes>
+      <processFunctionArguments>false</processFunctionArguments>
+      <preProcessAllHeaders>false</preProcessAllHeaders>
+      <parseMissingHeadersExperimental>false</parseMissingHeadersExperimental>
+      <resolveIncludePathsUsingMakeExperimental>false</resolveIncludePathsUsingMakeExperimental>
+      <alwaysParseInBackground>true</alwaysParseInBackground>
+      <usePermanentCaching>true</usePermanentCaching>
+      <alwaysIncludeNamespaces>false</alwaysIncludeNamespaces>
+      <includePaths>.;</includePaths>
+    </codecompletion>
+    <creategettersetter>
+      <prefixGet/>
+      <prefixSet>set</prefixSet>
+      <prefixVariable>m_,_</prefixVariable>
+      <parameterName>theValue</parameterName>
+      <inlineGet>true</inlineGet>
+      <inlineSet>true</inlineSet>
+    </creategettersetter>
+    <splitheadersource>
+      <enabled>false</enabled>
+      <synchronize>true</synchronize>
+      <orientation>Vertical</orientation>
+    </splitheadersource>
+  </kdevcppsupport>
+  <kdevfileview>
+    <groups>
+      <hidenonprojectfiles>false</hidenonprojectfiles>
+      <hidenonlocation>false</hidenonlocation>
+    </groups>
+    <tree>
+      <hidepatterns>*.o,*.lo,CVS</hidepatterns>
+      <hidenonprojectfiles>false</hidenonprojectfiles>
+      <showvcsfields>false</showvcsfields>
+    </tree>
+  </kdevfileview>
+  <cppsupportpart>
+    <filetemplates>
+      <interfacesuffix>.h</interfacesuffix>
+      <implementationsuffix>.cpp</implementationsuffix>
+    </filetemplates>
+  </cppsupportpart>
+  <kdevdocumentation>
+    <projectdoc>
+      <docsystem/>
+      <docurl/>
+      <usermanualurl/>
+    </projectdoc>
+  </kdevdocumentation>
+</kdevelop>

autogen.sh

@@ -0,0 +1,51 @@
+#! /bin/sh
+
+# $Id: autogen.sh,v 1.4 2002/12/02 01:39:49 murrayc Exp $
+#
+# Copyright (c) 2002  Daniel Elstner  <[email protected]>
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License VERSION 2 as
+# published by the Free Software Foundation.  You are not allowed to
+# use any other version of the license; unless you got the explicit
+# permission from the author to do so.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+
+
+dir=`echo "$0" | sed 's,[^/]*$,,'`
+test "x${dir}" = "x" && dir='.'
+
+if test "x`cd "${dir}" 2>/dev/null && pwd`" != "x`pwd`"
+then
+    echo "This script must be executed directly from the source directory."
+    exit 1
+fi
+
+rm -f config.cache acconfig.h
+
+echo "- libtoolize."		&& \
+libtoolize --force		&& \
+echo "- aclocal."		&& \
+aclocal				&& \
+echo "- autoconf."		&& \
+autoconf			&& \
+echo "- autoheader."		&& \
+autoheader			&& \
+echo "- automake."		&& \
+automake --add-missing --gnu	&& \
+echo "Success. Run './configure' to set up the build." && \
+exit 0
+#echo				&& \
+#./configure "$@"		&& exit 0
+# Modified (./configure call removed) T. Youngs 1/10/2007.
+
+exit 1
+