Changeset 49a136


Ignore:
Timestamp:
Aug 17, 2010, 12:43:46 PM (14 years ago)
Author:
Frederik Heber <heber@…>
Branches:
Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable
Children:
9cd807
Parents:
a19d73e (diff), 8e463e (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.
Message:

Merge branch 'FixMerge_TestSHBranch' into stable

Files:
2 edited

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  • COPYING

    ra19d73e r49a136  
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    487 not impose a license fee, royalty, or other charge for exercise of
    488 rights granted under this License, and you may not initiate litigation
    489 (including a cross-claim or counterclaim in a lawsuit) alleging that
    490 any patent claim is infringed by making, using, selling, offering for
    491 sale, or importing the Program or any portion of it.
    492 
    493   11. Patents.
    494 
    495   A "contributor" is a copyright holder who authorizes use under this
    496 License of the Program or a work on which the Program is based.  The
    497 work thus licensed is called the contributor's "contributor version".
    498 
    499   A contributor's "essential patent claims" are all patent claims
    500 owned or controlled by the contributor, whether already acquired or
    501 hereafter acquired, that would be infringed by some manner, permitted
    502 by this License, of making, using, or selling its contributor version,
    503 but do not include claims that would be infringed only as a
    504 consequence of further modification of the contributor version.  For
    505 purposes of this definition, "control" includes the right to grant
    506 patent sublicenses in a manner consistent with the requirements of
    507 this License.
    508 
    509   Each contributor grants you a non-exclusive, worldwide, royalty-free
    510 patent license under the contributor's essential patent claims, to
    511 make, use, sell, offer for sale, import and otherwise run, modify and
    512 propagate the contents of its contributor version.
    513 
    514   In the following three paragraphs, a "patent license" is any express
    515 agreement or commitment, however denominated, not to enforce a patent
    516 (such as an express permission to practice a patent or covenant not to
    517 sue for patent infringement).  To "grant" such a patent license to a
    518 party means to make such an agreement or commitment not to enforce a
    519 patent against the party.
    520 
    521   If you convey a covered work, knowingly relying on a patent license,
    522 and the Corresponding Source of the work is not available for anyone
    523 to copy, free of charge and under the terms of this License, through a
    524 publicly available network server or other readily accessible means,
    525 then you must either (1) cause the Corresponding Source to be so
    526 available, or (2) arrange to deprive yourself of the benefit of the
    527 patent license for this particular work, or (3) arrange, in a manner
    528 consistent with the requirements of this License, to extend the patent
    529 license to downstream recipients.  "Knowingly relying" means you have
    530 actual knowledge that, but for the patent license, your conveying the
    531 covered work in a country, or your recipient's use of the covered work
    532 in a country, would infringe one or more identifiable patents in that
    533 country that you have reason to believe are valid.
    534 
    535   If, pursuant to or in connection with a single transaction or
    536 arrangement, you convey, or propagate by procuring conveyance of, a
    537 covered work, and grant a patent license to some of the parties
    538 receiving the covered work authorizing them to use, propagate, modify
    539 or convey a specific copy of the covered work, then the patent license
    540 you grant is automatically extended to all recipients of the covered
    541 work and works based on it.
    542 
    543   A patent license is "discriminatory" if it does not include within
    544 the scope of its coverage, prohibits the exercise of, or is
    545 conditioned on the non-exercise of one or more of the rights that are
    546 specifically granted under this License.  You may not convey a covered
    547 work if you are a party to an arrangement with a third party that is
    548 in the business of distributing software, under which you make payment
    549 to the third party based on the extent of your activity of conveying
    550 the work, and under which the third party grants, to any of the
    551 parties who would receive the covered work from you, a discriminatory
    552 patent license (a) in connection with copies of the covered work
    553 conveyed by you (or copies made from those copies), or (b) primarily
    554 for and in connection with specific products or compilations that
    555 contain the covered work, unless you entered into that arrangement,
    556 or that patent license was granted, prior to 28 March 2007.
    557 
    558   Nothing in this License shall be construed as excluding or limiting
    559 any implied license or other defenses to infringement that may
    560 otherwise be available to you under applicable patent law.
    561 
    562   12. No Surrender of Others' Freedom.
    563 
    564   If conditions are imposed on you (whether by court order, agreement or
    565 otherwise) that contradict the conditions of this License, they do not
    566 excuse you from the conditions of this License.  If you cannot convey a
    567 covered work so as to satisfy simultaneously your obligations under this
    568 License and any other pertinent obligations, then as a consequence you may
    569 not convey it at all.  For example, if you agree to terms that obligate you
    570 to collect a royalty for further conveying from those to whom you convey
    571 the Program, the only way you could satisfy both those terms and this
    572 License would be to refrain entirely from conveying the Program.
    573 
    574   13. Use with the GNU Affero General Public License.
    575 
    576   Notwithstanding any other provision of this License, you have
    577 permission to link or combine any covered work with a work licensed
    578 under version 3 of the GNU Affero General Public License into a single
    579 combined work, and to convey the resulting work.  The terms of this
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    581 but the special requirements of the GNU Affero General Public License,
    582 section 13, concerning interaction through a network will apply to the
    583 combination as such.
    584 
    585   14. Revised Versions of this License.
    586 
    587   The Free Software Foundation may publish revised and/or new versions of
    588 the GNU General Public License from time to time.  Such new versions will
    589 be similar in spirit to the present version, but may differ in detail to
    590 address new problems or concerns.
    591 
    592   Each version is given a distinguishing version number.  If the
    593 Program specifies that a certain numbered version of the GNU General
    594 Public License "or any later version" applies to it, you have the
    595 option of following the terms and conditions either of that numbered
    596 version or of any later version published by the Free Software
    597 Foundation.  If the Program does not specify a version number of the
    598 GNU General Public License, you may choose any version ever published
    599 by the Free Software Foundation.
    600 
    601   If the Program specifies that a proxy can decide which future
    602 versions of the GNU General Public License can be used, that proxy's
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    604 to choose that version for the Program.
    605 
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    607 permissions.  However, no additional obligations are imposed on any
    608 author or copyright holder as a result of your choosing to follow a
    609 later version.
    610 
    611   15. Disclaimer of Warranty.
    612 
    613   THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
    614 APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
    615 HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
    616 OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
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    618 PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
    619 IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
    620 ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
    621 
    622   16. Limitation of Liability.
    623 
    624   IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
    625 WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
    626 THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
    627 GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
    628 USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
    629 DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
    630 PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
    631 EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
    632 SUCH DAMAGES.
    633 
    634   17. Interpretation of Sections 15 and 16.
    635 
    636   If the disclaimer of warranty and limitation of liability provided
    637 above cannot be given local legal effect according to their terms,
    638 reviewing courts shall apply local law that most closely approximates
    639 an absolute waiver of all civil liability in connection with the
    640 Program, unless a warranty or assumption of liability accompanies a
    641 copy of the Program in return for a fee.
    642 
    643                      END OF TERMS AND CONDITIONS
    644 
    645             How to Apply These Terms to Your New Programs
    646 =======
    64724this service if you wish), that you receive source code or can get it
    64825if you want it, that you can change the software or use pieces of it
    … …  
    909286
    910287            How to Apply These Terms to Your New Programs
    911 >>>>>>> FETCH_HEAD
    912288
    913289  If you develop a new program, and you want it to be of the greatest
    … …  
    917293  To do so, attach the following notices to the program.  It is safest
    918294to attach them to the start of each source file to most effectively
    919 <<<<<<< HEAD
    920 state the exclusion of warranty; and each file should have at least
    921 =======
    922295convey the exclusion of warranty; and each file should have at least
    923 >>>>>>> FETCH_HEAD
    924296the "copyright" line and a pointer to where the full notice is found.
    925297
    926     <one line to give the program's name and a brief idea of what it does.>
    927     Copyright (C) <year>  <name of author>
    928 
    929 <<<<<<< HEAD
    930     This program is free software: you can redistribute it and/or modify
    931     it under the terms of the GNU General Public License as published by
    932     the Free Software Foundation, either version 3 of the License, or
    933 =======
     298    MoleCuilder - to create and alter molecular systems
     299    Copyright (C) 2010  Frederik Heber
     300
    934301    This program is free software; you can redistribute it and/or modify
    935302    it under the terms of the GNU General Public License as published by
    936303    the Free Software Foundation; either version 2 of the License, or
    937 >>>>>>> FETCH_HEAD
    938304    (at your option) any later version.
    939305
    … …  
    944310
    945311    You should have received a copy of the GNU General Public License
    946 <<<<<<< HEAD
    947     along with this program.  If not, see <http://www.gnu.org/licenses/>.
    948 
    949 Also add information on how to contact you by electronic and paper mail.
    950 
    951   If the program does terminal interaction, make it output a short
    952 notice like this when it starts in an interactive mode:
    953 
    954     <program>  Copyright (C) <year>  <name of author>
    955     This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
    956 =======
    957312    along with this program; if not, write to the Free Software
    958313    Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
    … …  
    964319when it starts in an interactive mode:
    965320
    966     Gnomovision version 69, Copyright (C) year  name of author
    967     Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
    968 >>>>>>> FETCH_HEAD
     321    MoleCuilder version ??, Copyright (C) 2010  Frederik Heber
     322    MoleCuilder comes with ABSOLUTELY NO WARRANTY; for details type
     323    `molecuilder --help-warranty'.
    969324    This is free software, and you are welcome to redistribute it
    970     under certain conditions; type `show c' for details.
     325    under certain conditions; type `molecuilder --help-redistribute'
     326    for details.
    971327
    972328The hypothetical commands `show w' and `show c' should show the appropriate
    973 <<<<<<< HEAD
    974 parts of the General Public License.  Of course, your program's commands
    975 might be different; for a GUI interface, you would use an "about box".
    976 
    977   You should also get your employer (if you work as a programmer) or school,
    978 if any, to sign a "copyright disclaimer" for the program, if necessary.
    979 For more information on this, and how to apply and follow the GNU GPL, see
    980 <http://www.gnu.org/licenses/>.
    981 
    982   The GNU General Public License does not permit incorporating your program
    983 into proprietary programs.  If your program is a subroutine library, you
    984 may consider it more useful to permit linking proprietary applications with
    985 the library.  If this is what you want to do, use the GNU Lesser General
    986 Public License instead of this License.  But first, please read
    987 <http://www.gnu.org/philosophy/why-not-lgpl.html>.
    988 =======
    989329parts of the General Public License.  Of course, the commands you use may
    990330be called something other than `show w' and `show c'; they could even be
    … …  
    995335necessary.  Here is a sample; alter the names:
    996336
    997   Yoyodyne, Inc., hereby disclaims all copyright interest in the program
    998   `Gnomovision' (which makes passes at compilers) written by James Hacker.
    999 
    1000   <signature of Ty Coon>, 1 April 1989
    1001   Ty Coon, President of Vice
     337  University of Bonn, hereby disclaims all copyright interest in the program
     338  `MoleCuilder' (which creates molecular systems) written by Frederik Heber.
     339
     340  Frederik Heber, 17 Aug 2010
    1002341
    1003342This General Public License does not permit incorporating your program into
    … …  
    1006345library.  If this is what you want to do, use the GNU Library General
    1007346Public License instead of this License.
    1008 >>>>>>> FETCH_HEAD

  • README

    ra19d73e r49a136  
    1 <<<<<<< HEAD
    2 # Project: Molecuilder
     1# Project: MoleCuilder
    32#
    43# heber@ins.uni-bonn.de
    54
    6         Molecuilder
     5        MoleCuilder
    76
    8 ... is a tool that started as a mean to edit pcp configuration files (adding/remvoing groups of atoms, measuring bond lengths and so forth) and has grown into the many-body fragmentation test base of a new method coined BOSSANOVA (Bond Order diSSection in an ANOVA (ANalysis Of VAriance) -like fashion). It spills out configuration files for each fragment and includes joining and analyzing programs, to put together the partial energies and forces of each fragment to the total energy and forces. It allows for a complete Born-Oppenheimer molecular dynamics run.
    9 =======
    10 # Project: ParallelCarParrinello
    11 # Jan Hamaekers
    12 # Frederik Heber
    13 # 2005
    14 #
    15 # File: README
     7... is a tool that started as a mean to edit pcp configuration files (adding/
     8removing groups of atoms, measuring bond lengths and so forth), grew forth into
     9a many-body fragmentation test base of a new method coined BOSSANOVA (Bond
     10Order diSSection in an ANOVA (ANalysis Of VAriance) - like fashion). It spilled
     11out configuration files for each fragment and included joining and analyzing
     12programs, to put together the partial energies and forces of each fragment to
     13the total energy and forces. Since then it has evolved into a complete toolbox
     14for creating molecular systems and worlds.
    1615
    17         Electronic Structure PACKage
    18 
    19 Is a collection of mathematical-physical programs to calculate via various ab-initio methods
    20 such as density functional theory or Hartree-Fock electronic(-magnetic) properties including
    21 the molecular (Car&Parrinello) dynamics of a many electron system. Especially, the linear
    22 response of the system to a external magnetic field in a perturbation approach in terms of
    23 susceptibility and chemical shielding is implemented via the Density Functional Perturbation
    24 Theory. It was developed mainly by Jan Hamaekers (pcp) with additional code by Frederik Heber
    25 (dfpt part in pcp) and also Ralf Wildenhuis (Gauss) at the Institute for Numerical Simulation
    26 at the University of Bonn[1].
    27 
    28 
    29 >>>>>>> FETCH_HEAD
    3016
    3117INSTALLATION NOTES
    3218==================
    3319
    34 <<<<<<< HEAD
    3520The following packages are needed
    3621* GCC or alike
    3722* GSL (GNU Scientific Library, available at http://www.gnu.org/software/gsl)
    3823* Boost 1.4 or newer
    39 =======
    40 In general gcc or alike is needed to compile the sources, for more specific demands see the README files in the sub directory of each package part.
    4124
    4225LINKS
    4326=====
    4427[1] http://www.ins.uni-bonn.de/
    45 >>>>>>> FETCH_HEAD
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