debian/0000755000000000000000000000000012166000032007154 5ustar debian/compat0000644000000000000000000000000211757246226010400 0ustar 7 debian/patches/0000755000000000000000000000000011761774715010635 5ustar debian/patches/debian-changes-3.6.0.2515-10000644000000000000000000002473111761774715014612 0ustar Description: Upstream changes introduced in version 3.6.0.2515-1 This patch has been created by dpkg-source during the package build. Here's the last changelog entry, hopefully it gives details on why those changes were made: . python-ase (3.6.0.2515-1) unstable; urgency=low . * Initial upload (Closes: #602126). . The person named in the Author field signed this changelog entry. Author: Ask Hjorth Larsen Bug-Debian: http://bugs.debian.org/602126 --- The information above should follow the Patch Tagging Guidelines, please checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here are templates for supplementary fields that you might want to add: Origin: , Bug: Bug-Debian: http://bugs.debian.org/ Forwarded: Reviewed-By: Last-Update: --- python-ase-3.6.0.2515.orig/setup.py +++ python-ase-3.6.0.2515/setup.py @@ -3,7 +3,8 @@ # Copyright (C) 2007 CAMP # Please see the accompanying LICENSE file for further information. -from distutils.core import setup +from distutils.core import setup, Command +from distutils.command.build_py import build_py as _build_py from glob import glob from os.path import join @@ -15,8 +16,8 @@ ASE is a python package providing an ope Environment in the python scripting language.""" -if sys.version_info < (2, 3, 0, 'final', 0): - raise SystemExit, 'Python 2.3 or later is required!' +if sys.version_info < (2, 4, 0, 'final', 0): + raise SystemExit, 'Python 2.4 or later is required!' packages = ['ase', 'ase.cluster', @@ -52,31 +53,79 @@ packages = ['ase', package_dir={'ase': 'ase'} -package_data={'ase': ['lattice/spacegroup/spacegroup.dat', - 'gui/po/ag.pot', - 'gui/po/makefile', - 'gui/po/??_??/LC_MESSAGES/ag.po']} - -# Compile makes sense only when building -if 'build' in sys.argv or 'build_ext' in sys.argv or 'install' in sys.argv: - msgfmt = 'msgfmt' - # Compile translation files (requires gettext) - status = os.system(msgfmt + ' -V') - if status == 0: - for pofile in glob('ase/gui/po/??_??/LC_MESSAGES/ag.po'): - mofile = os.path.join(os.path.split(pofile)[0], 'ag.mo') - os.system(msgfmt + ' -cv %s --output-file=%s' % (pofile, mofile)) - package_data['ase'].append('gui/po/??_??/LC_MESSAGES/ag.mo') +package_data={'ase': ['lattice/spacegroup/spacegroup.dat']} + +class test(Command): + description = 'build and run test suite; exit code is number of failures' + user_options = [] + + def __init__(self, dist): + Command.__init__(self, dist) + self.sub_commands = ['build'] + + def initialize_options(self): + pass + + def finalize_options(self): + pass + + def run(self): + self.run_command('build') + buildcmd = self.get_finalized_command('build') + sys.path.insert(0, buildcmd.build_lib) + + from ase.test import test as _test + testdir = '%s/testase-tempfiles' % buildcmd.build_base + origcwd = os.getcwd() + if not os.path.exists(testdir): + os.mkdir(testdir) + os.chdir(testdir) + try: + results = _test(2, display=False) + if results.failures or results.errors: + print >> sys.stderr, 'Test suite failed' + raise SystemExit(len(results.failures) + len(results.errors)) + finally: + os.chdir(origcwd) + +class build_py(_build_py): + """Custom distutils command to build translations.""" + def __init__(self, *args, **kwargs): + _build_py.__init__(self, *args, **kwargs) + # Keep list of files to appease bdist_rpm. We have to keep track of + # all the installed files for no particular reason. + self.mofiles = [] + + def run(self): + """Compile translation files (requires gettext).""" + _build_py.run(self) + msgfmt = 'msgfmt' + status = os.system(msgfmt + ' -V') + if status == 0: + for pofile in glob('ase/gui/po/??_??/LC_MESSAGES/ag.po'): + dirname = join(self.build_lib, os.path.dirname(pofile)) + if not os.path.isdir(dirname): + os.makedirs(dirname) + mofile = join(dirname, 'ag.mo') + status = os.system('%s -cv %s --output-file=%s 2>&1' % + (msgfmt, pofile, mofile)) + assert status == 0, 'msgfmt failed!' + self.mofiles.append(mofile) + + def get_outputs(self, *args, **kwargs): + return _build_py.get_outputs(self, *args, **kwargs) + self.mofiles # Get the current version number: execfile('ase/svnversion_io.py') # write ase/svnversion.py and get svnversion execfile('ase/version.py') # get version_base -if svnversion: +if svnversion and os.name not in ['ce', 'nt']: # MSI accepts only version X.X.X version = version_base + '.' + svnversion else: version = version_base -setup(name = 'python-ase', +scripts = ['tools/ag', 'tools/ase', 'tools/ASE2ase', 'tools/testase'] + +setup(name='python-ase', version=version, description='Atomic Simulation Environment', url='https://wiki.fysik.dtu.dk/ase', @@ -87,5 +136,7 @@ setup(name = 'python-ase', packages=packages, package_dir=package_dir, package_data=package_data, - scripts=['tools/ag', 'tools/ase', 'tools/ASE2ase.py', 'tools/testase.py'], - long_description=long_description) + scripts=scripts, + long_description=long_description, + cmdclass={'build_py': build_py, + 'test': test}) --- /dev/null +++ python-ase-3.6.0.2515/tools/testase @@ -0,0 +1,18 @@ +#!/usr/bin/env python + +from optparse import OptionParser + +description = """Run ASE test suite. ***WARNING***: This will leave a +large number of files in current working directory, so be sure to do +it in a new directory!""" + +p = OptionParser(usage='%prog [OPTION]', description=description) +p.add_option('--no-display', action='store_true', + help='do not open graphical windows') + +opts, args = p.parse_args() +if len(args) != 0: + raise p.error('Unexpected arguments: %s' % args) + +from ase.test import test +test(2, display=not opts.no_display) --- python-ase-3.6.0.2515.orig/tools/trajectoryinfo +++ python-ase-3.6.0.2515/tools/trajectoryinfo @@ -1,15 +1,22 @@ #!/usr/bin/env python +import os +from optparse import OptionParser from ase.io.trajectory import print_trajectory_info from ase.io.bundletrajectory import print_bundletrajectory_info -import sys -import os -if len(sys.argv) <= 1: - print >>sys.stderr, "Usage: trajectoryinfo file.traj [file2.traj ...]" - sys.exit(1) +description = 'Print summary of information from trajectory files.' + +p = OptionParser(usage='%prog file.traj [file2.traj ...]', + description=description) + +opts, args = p.parse_args() + +if len(args) == 0: + p.print_help() + raise SystemExit(1) -for f in sys.argv[1:]: +for f in args: if os.path.isfile(f): print_trajectory_info(f) elif os.path.isdir(f): --- /dev/null +++ python-ase-3.6.0.2515/tools/ASE2ase @@ -0,0 +1,91 @@ +#!/usr/bin/env python + +from optparse import OptionParser + +description = """Convert ASE2 script FILEs to ase3. FILEs will be +modified in-place to be compatible with ase3. Original files are +backed up.""" + +p = OptionParser(usage='%prog FILE...', description=description) + +opts, args = p.parse_args() + +def convert(filename): + lines = open(filename).readlines() + t1 = ''.join(lines) + + first = True + for i in range(len(lines)): + line = lines[i] + if line.startswith('from ASE'): + if first: + lines[i] = 'from ase.all import *\n' + first = False + else: + lines[i] = '' + + t = ''.join(lines) + + for old, new in [('GetCartesianPositions', 'get_positions'), + ('SetCartesianPositions', 'set_positions'), + ('GetPotentialEnergy', 'get_potential_energy'), + ('SetCalculator', 'set_calculator'), + ('GetScaledPositions', 'get_scaled_positions'), + ('SetScaledPositions', 'set_scaled_positions'), + ('SetUnitCell', 'set_cell'), + ('GetUnitCell', 'get_cell'), + ('GetBoundaryConditions', 'get_pbc'), + ('GetCartesianForces', 'get_forces'), + ('GetCartesianVelocities', 'get_velocities'), + ('SetCartesianVelocities', 'set_velocities'), + ('GetCartesianMomenta', 'get_momenta'), + ('SetCartesianMomenta', 'set_momenta'), + ('ListOfAtoms', 'Atoms'), + ('periodic', 'pbc'), + ('pbcity', 'periodicity'), + ('.Converge(', '.run('), + ('Repeat', 'repeat'), + ('Numeric', 'numpy'), + ('numpyal', 'Numerical'), + ('GetAtomicNumber()', 'number'), + ('GetChemicalSymbol()', 'symbol'), + ('GetCartesianPosition()', 'position'), + ('GetTag()', 'tag'), + ('GetCharge()', 'charge'), + ('GetMass()', 'mass'), + ('GetCartesianMomentum()', 'momentum'), + ('GetMagneticMoment()', 'magmom'), + ]: + t = t.replace(old, new) + + t2 = '' + while 1: + i = t.find('.') + i2 = t.find('def ') + if 0 <= i < i2: + n = 1 + elif i2 != -1: + n = 4 + i = i2 + else: + break + t2 += t[:i + n] + t = t[i + n:] + if t[0].isupper() and t[1].islower(): + j = t.find('(') + if j != -1 and t[2: j].isalpha(): + for k in range(j): + if t[k].isupper() and k > 0: + t2 += '_' + t2 += t[k].lower() + t = t[j:] + + t2 += t + + if t2 != t1: + print filename, len(t1) - len(t2) + open(filename + '.bak', 'w').write(t1) + open(filename, 'w').write(t2) + +for filename in args: + convert(filename) --- /dev/null +++ python-ase-3.6.0.2515/ase/svnversion.py @@ -0,0 +1 @@ +svnversion = "exportado" debian/patches/series0000644000000000000000000000003411761774216012043 0ustar debian-changes-3.6.0.2515-1 debian/rules0000755000000000000000000000024312165777407010265 0ustar #!/usr/bin/make -f %: dh $@ --with python2 override_dh_auto_test: python setup.py test override_dh_auto_clean: rm -rf build/testase-tempfiles dh_auto_clean debian/docs0000644000000000000000000000001311757246226010047 0ustar README.txt debian/control0000644000000000000000000000164412165777407010616 0ustar Source: python-ase Section: python Priority: optional Maintainer: Ask Hjorth Larsen Build-Depends: cdbs (>= 0.4.90~), debhelper (>= 7.0.50), python (>=2.6.6-3~), gettext (>=0.14.6), python-numpy Standards-Version: 3.9.1 X-Python-Version: >= 2.6 Homepage: https://wiki.fysik.dtu.dk/ase/ Package: python-ase Architecture: all Depends: python-numpy, ${python:Depends}, ${misc:Depends} Recommends: python-gtk2 Suggests: python-scipy, python-matplotlib Description: Atomic Simulation Environment for atomistic simulations ASE is an Atomistic Simulation Environment written in the Python programming language with the aim of setting up, stearing, and analyzing atomistic simulations. ASE is part of CAMPOS, the CAMP Open Source project. . ASE contains Python interfaces to several different electronic structure codes including Abinit, Asap, Dacapo, Elk, GPAW and SIESTA. . https://wiki.fysik.dtu.dk/ase/ debian/changelog0000644000000000000000000000055512165777407011065 0ustar python-ase (3.6.0.2515-1.1) unstable; urgency=low * Non-maintainer upload. * Convert to dh_python2. (Closes: #708890) -- Andrea Colangelo Wed, 03 Jul 2013 00:06:23 +0200 python-ase (3.6.0.2515-1) unstable; urgency=low * Initial upload (Closes: #602126). -- Ask Hjorth Larsen Sun, 27 May 2012 02:32:46 +0200 debian/README.Debian0000644000000000000000000000115711757246226011247 0ustar ASE for Debian -------------- A number of changes have been made to the ASE source to make it comply with Debian policy: * Rudimentary help2man-pages have been added for each executable script * All executables now have --help pages * The `.py' extension has been removed from all installed scripts * The installer has been changed so as not to compile mo-files in the source directory, but only put them in the installation The three latter changes are backported from ASE trunk and will automatically be part of future stable releases. Ask Hjorth Larsen , Fri May 11 16:45:38 CEST 2012 debian/copyright0000644000000000000000000001734711761716742011151 0ustar This package was debianized by Ask Hjorth Larsen on Wed, 14 Oct 2009 17:01:14 +0200. It was downloaded from https://wiki.fysik.dtu.dk/ase/download.html Upstream Authors: Alex Eftimiades Andrew Peterson Anthony Goodrow Ask Hjorth Larsen Bjarke Brink Buus Bohumir Jelinek Carsten Rostgaard Christian Glinsvad Christian Meisenbichler David Landis Felix Hanke Franz Knuth George Tritsaris Glen Jenness Heine Anton Hansen Hugo Strand Ivano Eligio Castelli Jakob Blomquist Jakob Gøttrup Nielsen Jakob Howalt Jakob Schiøtz Janne Blomqvist Janosch Michael Rauba Jens Jørgen Mortensen Jeppe Gavnholt Jesper Friis Jesper Kleis Jingzhe Chen John Kitchin John Sharp Jonas Bjork Jon Bergmann Maronsson Jun Yan Jussi Enkovaara Jörg Meyer Karsten Wedel Jacobsen Kristen Kaasbjerg Lars Grabow Lars Pastewka Lasse Vilhelmsen Marcin Dulak Marco Vanin Markus Kaukonen Martin Petisme Mathias List Mattias Slabanja Max Alberto Ramirez Max J. Hoffmann Michael Walter Miguel Marques Mikkel Strange Nicolai Rask Ondrej Marsalek Poul Georg Moses Reinhard Maurer Simon Brodersen Stephan Schenk Tao Jiang Thomas Bligaard Thomas Olsen Troels Kofoed Jacobsen Copyright: Copyright (C) 2007-2012 CAMD/CAMP, CSC, SINTEF, upstream authors License: This package is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This package 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 Lesser General Public License for more details. You should have received a copy of the GNU Lesser General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA A number of files have specific licenses as noted below. Copyright and license of ase/io/fortranfile.py: Copyright 2008-2010 Neil Martinsen-Burrell Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. The files ase/optimize/fmin_bfgs.py and ase/optimize/bfgslinesearch.py contain code from the scipy project. Copyright and license: Copyright (c) 2001, 2002 Enthought, Inc. All rights reserved. Copyright (c) 2003-2009 SciPy Developers. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: a. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. b. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. c. Neither the name of the Enthought nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Copyright and license of ase/tools/pep8.py: pep8.py - Check Python source code formatting, according to PEP 8 Copyright (C) 2006 Johann C. Rocholl Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. Copied from: https://github.com/jcrocholl/pep8/blob/ 8d2d68790b6931833277cd671dfb8158962fac0c/pep8.py on May 10, 2011. Copyright and license of ase/gui/gtkexcepthook.py: (c) 2003 Gustavo J A M Carneiro gjc at inescporto.pt 2004-2005 Filip Van Raemdonck http://www.daa.com.au/pipermail/pygtk/2003-August/005775.html Message-ID: <1062087716.1196.5.camel@emperor.homelinux.net> "The license is whatever you want." This file was downloaded from http://www.sysfs.be/downloads/ Minor adaptions 2009 by Martin Renold: - let KeyboardInterrupt through - print traceback to stderr before showing the dialog - nonzero exit code when hitting the "quit" button - suppress more dialogs while one is already active see also http://faq.pygtk.org/index.py?req=show&file=faq20.010.htp (The license is still whatever you want.) On Debian or Ubuntu systems, the complete text of the GNU Lesser General Public License can be found in `/usr/share/common-licenses/LGPL'. The Debian packaging is copyright 2009-2012, Ask Hjorth Larsen and is licensed under the GPL, see `/usr/share/common-licenses/GPL'. debian/source/0000755000000000000000000000000011757246226010502 5ustar debian/source/format0000644000000000000000000000001411757246226011710 0ustar 3.0 (quilt) debian/man/0000755000000000000000000000000011757246226007755 5ustar debian/man/ag.10000644000000000000000000000327111757246226010431 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.37.1. .TH AG "1" "May 2012" "ag 3.6.0" "User Commands" .SH NAME ag \- manual page for ag 3.6.0 .SH SYNOPSIS .B ag [\fIoptions\fR] [\fIfile\fR[\fI, file2, \fR...]] .SH DESCRIPTION See the online manual (https://wiki.fysik.dtu.dk/ase/ase/gui.html) for more information. .SH OPTIONS .TP \fB\-\-version\fR show program's version number and exit .TP \fB\-h\fR, \fB\-\-help\fR show this help message and exit .TP \fB\-n\fR NUMBER, \fB\-\-image\-number\fR=\fINUMBER\fR Pick image(s) from trajectory. NUMBER can be a single number (use a negative number to count from the back) or a range: start:stop:step, where the ":step" part can be left out \- default values are 0:nimages:1. .TP \fB\-u\fR I, \fB\-\-show\-unit\-cell\fR=\fII\fR 0: Don't show unit cell. 1: Show unit cell. 2: Show all of unit cell. .TP \fB\-r\fR REPEAT, \fB\-\-repeat\fR=\fIREPEAT\fR Repeat unit cell. Use "\-r 2" or "\-r 2,3,1". .TP \fB\-R\fR ROTATIONS, \fB\-\-rotations\fR=\fIROTATIONS\fR Examples: "\-R \fB\-90x\fR", "\-R 90z,\-30x". .TP \fB\-o\fR FILE, \fB\-\-output\fR=\fIFILE\fR Write configurations to FILE. .TP \fB\-g\fR EXPR, \fB\-\-graph\fR=\fIEXPR\fR Plot x,y1,y2,... graph from configurations or write data to sdtout in terminal mode. Use the symbols: i, s, d, fmax, e, ekin, A, R, E and F. See https://wiki.fysik.dtu.dk/ase/ase/gui.html#plottingdata for more details. .TP \fB\-t\fR, \fB\-\-terminal\fR Run in terminal window \- no GUI. .TP \fB\-\-aneb\fR Read ANEB data. .TP \fB\-\-interpolate\fR=\fIN\fR Interpolate N images between 2 given images. .TP \fB\-b\fR, \fB\-\-bonds\fR Draw bonds between atoms. .TP \fB\-s\fR FLOAT, \fB\-\-scale\fR=\fIFLOAT\fR Scale covalent radii. debian/man/ase.10000644000000000000000000000513311757246226010611 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.37.1. .TH ASE "1" "May 2012" "ase 3.6.0" "User Commands" .SH NAME ase \- manual page for ase 3.6.0 .SH SYNOPSIS .B ase [\fIoptions\fR] \fIsystem(s)\fR .SH DESCRIPTION Run EMT calculation. .SH OPTIONS .TP \fB\-h\fR, \fB\-\-help\fR show this help message and exit .IP General: .TP \fB\-t\fR TAG, \fB\-\-tag\fR=\fITAG\fR String tag added to filenames. .TP \fB\-M\fR M1,M2,..., \fB\-\-magnetic\-moment\fR=\fIM1\fR,M2,... Magnetic moment(s). Use "\-M 1" or "\-M 2.3,\-2.3". .TP \fB\-G\fR, \fB\-\-gui\fR Pop up ASE's GUI. .TP \fB\-s\fR, \fB\-\-write\-summary\fR Write summary. .TP \fB\-\-slice\fR=\fIstart\fR:stop:step Select subset of calculations using Python slice syntax. Use "::2" to do every second calculation and "\-5:" to do the last five. .TP \fB\-w\fR FILENAME, \fB\-\-write\-to\-file\fR=\fIFILENAME\fR Write configuration to file. .TP \fB\-i\fR, \fB\-\-interactive\-python\-session\fR Run calculation inside interactive Python session. A possible $PYTHONSTARTUP script will be imported and the "atoms" variable refers to the Atoms object. .TP \fB\-l\fR, \fB\-\-use\-lock\-files\fR Skip calculations where the json lock\-file or result file already exists. .TP \fB\-\-contains\fR=\fIELEMENT\fR Run only systems containing specific element. .TP \fB\-\-modify=\fR... Modify system with Python statement. Example: "system.positions[\-1,2]+=0.1". Warning: no spaces allowed! .TP \fB\-\-clean\fR Remove unfinished tasks from json file. .IP Optimize: .TP \fB\-R\fR FMAX, \fB\-\-relax\fR=\fIFMAX\fR Relax internal coordinates using L\-BFGS algorithm. .TP \fB\-\-constrain\-tags\fR=\fIT1\fR,T2,... Constrain atoms with tags T1, T2, ... .IP Molecule: .TP \fB\-v\fR VACUUM, \fB\-\-vacuum\fR=\fIVACUUM\fR Amount of vacuum to add around isolated systems (in Angstrom). .TP \fB\-\-unit\-cell\fR=\fIUNIT_CELL\fR Unit cell. Examples: "10.0" or "9,10,11" (in Angstrom). .TP \fB\-\-bond\-length\fR=\fIBOND_LENGTH\fR Bond length of dimer in Angstrom. .TP \fB\-F\fR N,x, \fB\-\-fit\fR=\fIN\fR,x Find optimal bondlength and vibration frequency using N points and displacements from \fB\-x\fR % to +x %. .TP \fB\-\-atomize\fR Calculate Atomization energies. .IP Calculator: .TP \fB\-k\fR K1,K2,K3, \fB\-\-monkhorst\-pack\fR=\fIK1\fR,K2,K3 Monkhorst\-Pack sampling of BZ. Example: "4,4,4": 4x4x4 k\-points, "4,4,4g": same set of k\-points shifted to include the Gamma point. .TP \fB\-\-k\-point\-density\fR=\fIK_POINT_DENSITY\fR Density of k\-points in Angstrom. .TP \fB\-p\fR key=value,..., \fB\-\-parameters\fR=\fIkey=value\fR,... Comma\-separated key=value pairs of calculator specific parameters. debian/man/testase.10000644000000000000000000000101211757246226011501 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.37.1. .TH TESTASE.PY "1" "May 2012" "testase.py 3.6.0" "User Commands" .SH NAME testase.py \- manual page for testase.py 3.6.0 .SH SYNOPSIS .B testase.py [\fIOPTION\fR] .SH DESCRIPTION Run ASE test suite. ***WARNING***: This will leave a large number of files in current working directory, so be sure to do it in a new directory! .SH OPTIONS .TP \fB\-h\fR, \fB\-\-help\fR show this help message and exit .TP \fB\-\-no\-display\fR do not open graphical windows debian/man/ASE2ase.10000644000000000000000000000067711757246226011234 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.37.1. .TH ASE2ASE.PY "1" "May 2012" "ASE2ase.py 3.6.0" "User Commands" .SH NAME ASE2ase.py \- manual page for ASE2ase.py 3.6.0 .SH SYNOPSIS .B ASE2ase.py \fIFILE\fR... .SH DESCRIPTION Convert ASE2 script FILEs to ase3. FILEs will be modified in\-place to be compatible with ase3. Original files are backed up. .SH OPTIONS .TP \fB\-h\fR, \fB\-\-help\fR show this help message and exit debian/manpages0000644000000000000000000000011311757246226010713 0ustar debian/man/ag.1 debian/man/ase.1 debian/man/ASE2ase.1 debian/man/testase.1