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Commits (63)
 # compiled python files *.pyc # sphinx build folder _build _templates *.pyc *.DS_Store # OS generated files # ###################### .DS_Store? ehthumbs.db Icon? Thumbs.db # Editor backup files # ####################### *~
 image: umbrellium/sphinx-doc image: cloudcompass/docker-rtdsphinx spelling: script: - pip install codespell - codespell --skip=".git,_static,_build,Diff*" --quiet-level=2 - pip3 install codespell - codespell --skip=".git,_static,_build,Diff*,*.patch" --quiet-level=2 --ignore-words-list="adress" only: - master - merge_requests orphans: script: # Report all the orphans but ignore the exit code - find ./ -name "*.rst"|xargs -i grep -H orphan {} || true # Now handle the error code - if [ $(find ./ -name "*.rst"|xargs -i grep -H orphan {}|wc -l) -gt "1" ]; then$(exit 1); else $(exit 0); fi only: - master pages: script: - apt-get update - apt-get -y install dvipng - pip install pygments --upgrade - pip3 install pygments --upgrade - pip3 install Sphinx --upgrade - pip3 install sphinx-bootstrap-theme --upgrade - READTHEDOCS=True sphinx-build -nWT -b html . _build/html - mv _build/html/ public/ - echo -e "\n\n\e[1mYou can find your build of this documentation at \n\t\e[32m${CI_PAGES_URL}\e[0m\n\n" artifacts: paths: - public ... ...
 ... ... @@ -22,4 +22,5 @@ Add a brief description briefly here (which replaces this sentence), a line or t - [ ] Is there a description of any applications the module has? (This is a hard requirement for E-CAM PDRAs) *After Merging* - [ ] Make sure the module appears in a toctree - [ ] Add a link to the final result on https://e-cam.readthedocs.io
 ... ... @@ -242,5 +242,6 @@ August 2017. The following modules have been produced: ./modules/OpenPathSampling/ops_sr_shooter/readme ./modules/OpenPathSampling/ops_web_throwing/readme ./modules/OpenPathSampling/ops_plumed_wrapper/readme ./modules/OpenPathSampling/ops_s_shooting/readme .. _E-CAM: https://www.e-cam2020.eu/
 .. _ost_s_shooting: ############################## S-shooting in OpenPathSampling ############################## .. sidebar:: Software Technical Information The information in this section describes OpenPathSampling as a whole. Information specific to the additions in this module are in subsequent sections. Language Python (2.7) Documentation Tool Sphinx, numpydoc format (ReST) Application Documentation http://openpathsampling.org Relevant Training Material http://openpathsampling.org/latest/examples/ Licence LGPL, v. 2.1 or later .. contents:: :local: Authors: Andreas Singraber This module implements the S-shooting method [1]_ in OpenPathSampling. Purpose of Module _________________ S-shooting [1]_ is a recently developed method to determine rate constants of rare events. It is similar in spirit to the reactive flux method but its relaxed requirements help to overcome practical problems. The method is based on a simple shooting algorithm where trajectories are propagated forward and backward in time for a fixed number of timesteps. The starting points need to be provided and must lie in the saddle point region. This so-called S region (hence the name S-shooting) is defined via a suitable reaction coordinate and must to separate the stable states A and B in such a way that no trajectory can connect A with B without visiting S. In contrast to the reactive flux method the time derivative of the reaction coordinate is not required, which makes this approach applicable to systems exhibiting diffusive dynamics along the reaction coordinate. The S-shooting method can also be applied if the initial shooting points are taken from a biased simulation. Thus, it is a natural follow-up to free energy calculations like umbrella sampling and, in combination with free energy curves, allows the computation of rate constants. The implementation of the S-shooting method in OpenPathSampling (OPS) is split into two main parts: - Forward and backward trajectories started from initial snapshots are harvested and glued together calling the SShootingSimulation class. The user needs to provide the initial snapshots, a suitable definition of the S region and the desired trajectory length. - The S-shooting analysis is performed upon calling the SShootingAnalysis class. Mandatory arguments include the definition of the stable states (A and B) and of the S region. In case the initial snapshots are taken from a biased simulation a bias function may be provided as an optional argument. This module comes also with an IPython example notebook demonstrating the method by applying it to a one-dimensional system (a brownian walker in a double-well potential). .. [1] Menzl, G., Singraber, A. & Dellago, C. S-shooting: a Bennett–Chandler-like method for the computation of rate constants from committor trajectories. Faraday Discuss. 195, 345–364 (2017), https://doi.org/10.1039/C6FD00124F Background Information ______________________ This module builds on OpenPathSampling, a Python package for path sampling simulations. To learn more about OpenPathSampling, you might be interested in reading: * OPS documentation: http://openpathsampling.org * OPS source code: http://github.com/openpathsampling/openpathsampling Testing _______ Follow these steps to test the module: 1. Download and install OpenPathSampling (see http://openpathsampling.org/latest/install.html). .. caution:: This module has been developed alongside a specific OPS version available at that time. If incompatibilities arise as OPS is further enhanced, please use version 0.9.5 available here: https://github.com/openpathsampling/openpathsampling/releases/tag/v0.9.5 . 2. Install the nose_ package. 3. Download the source files of the module (see the Source Code_ section below). 4. Install the module: change to the S-Shooting directory and run python setup.py install. 5. Run the tests: execute nosetests in the S-Shooting directory. .. IF YOUR MODULE IS IN OPS CORE: .. This module has been included in the OpenPathSampling core. Its tests can .. be run by setting up a developer install of OpenPathSampling and running .. the command nosetests from the root directory of the repository. .. IF YOUR MODULE IS IN A SEPARATE REPOSITORY .. The tests for this module can be run by downloading its source code, .. installing its requirements, and running the command nosetests from the .. root directory of the repository. Examples ________ See the sshooting-example.ipynb IPython notebook in the source directory, here is the direct link: https://gitlab.e-cam2020.eu/singraber/S-Shooting/blob/master/ops_s_shooting/sshooting-example.ipynb To run the example execute jupyter notebook sshooting-example.ipynb in your terminal. Source Code ___________ .. link the source code .. IF YOUR MODULE IS IN OPS CORE .. This module has been merged into OpenPathSampling. It is composed of the .. following pull requests: .. * link PRs .. IF YOUR MODULE IS A SEPARATE REPOSITORY .. The source code for this module can be found in: URL. The source code for this module is located here: https://gitlab.e-cam2020.eu/singraber/S-Shooting .. tip:: Ultimately, this module will be merged into the official OPS code. Check the status of the corresponding pull request here: https://github.com/openpathsampling/openpathsampling/pull/787 . .. CLOSING MATERIAL ------------------------------------------------------- .. Here are the URL references used .. _nose: http://nose.readthedocs.io/en/latest/
 ... ... @@ -88,6 +88,7 @@ Modules not coming from ESDWs ./modules/SCDM_WFs/readme ./modules/flook/readme ./modules/MatrixSwitchDBCSR/readme Pilot Projects ============== ... ...
 ################## DBCSR@MatrixSwitch ################## .. sidebar:: Software Technical Information The information in this section describes DBCSR@MatrixSwitch as a whole. Information specific to the additions in this module are in subsequent sections. Language Fortran 2008 Documentation Tool Sphinx, ReStructuredText Application Documentation ESL wiki _ Relevant Training Material See a usage example in the omm/MatrixSwitch/examples directory of the source code. Software Module Developed by Alfio Lazzaro and David López-Durán Licence Simplified BSD .. contents:: :local: Purpose of Module _________________ MatrixSwitch is a module which acts as an intermediary interface layer between high-level and low-level routines dealing with matrix storage and manipulation. It allows a seamlessly switch between different software implementations of the matrix operations. DBCSR is an optimized library to deal with sparse matrices, which appear frequently in many kind of numerical simulations. In DBCSR@MatrixSwitch DBCSR capabilities have been added to MatrixSwitch as an *optional* library dependency. Background Information ______________________ MatrixSwitch, DBCSR, and DBCSR@MatrixSwitch are software libraries to be used within a calling code. MatrixSwitch has been developed within the same repository of other self-contained libraries, all them collected in the omm-bundle project (see the Source Code_ section below). As DBCSR has been added to MatrixSwitch in a modular way, all them can be used together or separated. To carry out calculations in serial mode may be too slow sometimes and a paralellisation strategy is needed. In serial/parallel MatrixSwitch employs Lapack/ScaLapack to perform matrix operations, irrespective of their dense or sparse character. The disadvantage of the Lapack/ScaLapack schemes is that they are not optimized for sparse matrices. DBCSR provides the necessary algorithms to solve this problem and in addition is specially suited to work in parallel. Installation ____________ The source code of the MatrixSwitch module is contained in a subdirectory of of the omm-bundle package with the same name, omm/MatrixSwitch. 'omm-bundle' is in a git repository and can be obtained in this way: git clone https://gitlab.e-cam2020.eu/esl/omm.git The DBCSR library was originally developed as part of the CP2K__ code, it is now available as a standalone library, and can be found in the CP2K releases directory: .. __: https://www.cp2k.org/ https://github.com/cp2k/dbcsr/releases/download/v1.0.0/dbcsr-1.0.0.tar.gz Build instructions for the DBCSR library _ are available on the project page. To enable DBCSR@MatrixSwitch in the omm-bundle package follow the steps below: 1. Enter the omm directory. 2. Copy make.inc.example to make.inc and modify it to suit your needs. To use DBCSR in MatrixSwitch include in your make.inc the path to the DBCSR library and add to FPPFLAGS the new flag -DHAVE_DBCSR (this requires that -DHAVE_MPI is also enabled). 3. Type make -f Makefile.manual. 4. Type make -f Makefile.manual install. Testing _______ The examples directory of MatrixSwitch contains example_pdcsr_pddbc.F90. It explains the use of DBCSR@MatrixSwitch and how DBCSR works. DBCSR results are compared to those obtained with Scapalack to check the validity of the new procedure. If this comparison fails, the program will exit immediately. To compile it: 1. Enter the omm/MatrixSwitch/examples directory. 2. Copy make.inc.example to make.inc and modify it to suit your needs. Be aware that make.inc in the src directory will also be used. 3. Type make -f Makefile.manual. As in the other examples in MatrixSwitch, example_pdcsr_pddbc.F90 contains a header explaining what the program does and provides a sample output to compare with. Source Code ___________ In the E-CAM Gitlab__ can be found all the source codes of MatrixSwitch__ and omm-bundle__, while DBCSR__ itself is in the set of CP2K__ Github__ repositories. .. __: https://gitlab.e-cam2020.eu/ .. __: https://gitlab.e-cam2020.eu/esl/omm/tree/master/MatrixSwitch/ .. __: https://gitlab.e-cam2020.eu/esl/omm/ .. __: https://github.com/cp2k/dbcsr/ .. __: https://github.com/cp2k/ .. __: https://github.com/
 :orphan: .. sidebar:: Software Technical Information Name ... ...
 ... ... @@ -67,7 +67,7 @@ The following modules connected to the DL_MESO_DPD code have been produced so fa ESPResSo++ ---------- The following modules connected to the ESPResSo++ code have been produced so far: The following modules connected to the ESPResSo++ code have been produced so far in the context of an associated Pilot Project _: .. toctree:: :glob: ... ... @@ -83,6 +83,14 @@ The following modules connected to the ESPResSo++ code have been produced so far ./modules/hierarchical-strategy/simple_one-component_melts/fine-graining/readme ./modules/hierarchical-strategy/simple_one-component_melts/coarse-graining/readme These modules have resulted in the final overarching module that captures the goal of the pilot project: .. toctree:: :glob: :maxdepth: 1 ./modules/hierarchical-strategy/simple_one-component_melts/readme ParaDiS ------- ... ... @@ -105,3 +113,16 @@ The first Meso- and Multi-scale ESDW was held in Barcelona, Spain, in July 2017. :maxdepth: 1 ./modules/DL_MESO_DPD/sionlib_dlmeso_dpd/readme GC-AdResS --------- Adaptive Resolution Simulation: Implementation in GROMACS .. toctree:: :glob: :maxdepth: 1 ./modules/GC-AdResS/Abrupt_AdResS/readme.rst ./modules/GC-AdResS/Abrupt_AdResS/abrupt_adress.rst
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 .. _abrupt_adress_patch: #################################### Patch file for module: Abrupt AdResS #################################### The patch for the abrupt AdResS code is: .. literalinclude:: ./abrupt_adress.patch :linenos: :download:Downloadable version of patch file
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 .. _simple_one-component_melts: .. _constrain_com: ########################################################################### Hierarchical Strategy for Simple One-Component Polymer Melts: constrain-com ... ...
 .. _simple_one-component_melts: ############################################################ Hierarchical Strategy for Simple One-Component Polymer Melts ############################################################ .. sidebar:: Software Technical Information The information in this section describes ESPResSo++ as a whole. Information specific to the additions in this module are in subsequent sections. Languages: Python (2.7) and C++ Documentation Tools: Sphinx and Doxygen Application Documentation: http://espressopp.github.io/ Relevant Training Material: https://github.com/espressopp/espressopp/tree/master/examples Licence GNU General Public License Author Hideki Kobayashi .. contents:: :local: The module is an implementation of the existing hierarchical strategy [1]_ for the equilibration of simple one-component polymer melts in ESPResSO++. .. Add technical info as a sidebar and allow text below to wrap around it Purpose of Module _________________ .. Give a brief overview of why the module is/was being created. To study the properties of polymer melts by numerical simulations, equilibrated configurations must be prepared. However, the relaxation time for high molecular weight polymer melts is huge and increases, according to reptation theory, with the third power of the molecular weight. Hence, an effective method for decreasing the equilibration time is required. The hierarchical strategy pioneered in Ref. [1]_ is a particularly suitable way to do this. The present module provides an integration of that method into the package ESPResSO++. To decrease the relaxation time, microscopic monomers are coarse-grained by mapping each subchain with :math:N_{b} monomers onto a soft blob. A polymer chain, originally consisting of :math:N monomers, is replaced by a coarse-grained (CG) chain consisting of :math:N/N_{b} soft blobs linked by a harmonic bond potential, :math:V_{bond}=3 k_{B}T d^{2}/2b_{CG}^2, and an angular bond-bending potential :math:V_{bend}=k_{B}T k_{bend}(1 + \cos(\theta))/2. Here :math:d is the distance and :math:\theta is the angle between consecutive bonds. The interactions between non-bonded soft blobs are taken into account by a repulsive pair potential :math:V_{nb}=k_{B}T \epsilon U_{G}(r_{ij}). Here :math:r_{ij} is the center-to-center distance between the two blobs, :math:U_{G}(r_{ij}) is a Gaussian function with variance :math:\overline{\sigma}^2 = \sigma_{i}^2 + \sigma_{j}^2 and :math:\sigma_{i} is the gyration radius of blob number :math:i. The gyration radius :math:\sigma is in turn fluctuating. This fluctuation is controlled by the potential :math:V_{sphere}=k_{B}T \, (a_{1}N_{b}^3\sigma^{-6} + a_{2}N_{b}^{-1}\sigma^{2} + a_{3}\sigma^{-3}). After equilibrating a configuration at very coarse resolution, each CG polymer chain is replaced with a more fine-grained (FG) chain. In this procedure, a CG blob is divided into several FG blobs. The center of mass (COM) of the FG blobs coincides with the position of the CG blob's center, and is being kept fixed during the relaxation of the local conformation of the FG monomers within the CG blob. To develop this module, the following classes have been implemented or modified (and may have been described in more detail elsewhere): * A VSpherePair class for calculating :math:V_{nb}=k_{B}T \epsilon U_{G}(r_{ij}) * A LangevinThermostatOnRadius class for simulating the fluctuations of the radii of the blobs * A VSphereSelf class for calculating :math:V_{sphere}=k_{B}T \, (a_{1}N_{b}^3\sigma^{-6} + a_{2}N_{b}^{-1}\sigma^{2} + a_{3}\sigma^{-3}) * A FixedLocalTupleList class for storing the N-tuple of particles consisting of both real and virtual particles * A ConstrainCOM class for conserving the COM of N FG blobs with the CG blob Background Information ______________________ The implementation of this module is based on ESPResSO++. You can learn about ESPResSO++ from the following links: * ESPResSO++ documentation: http://espressopp.github.io/ESPResSo++.pdf * ESPResSO++ source code: https://github.com/espressopp/espressopp Testing _______ Explanation of installation of ESPResSO++ can be found at: * https://github.com/espressopp/espressopp After installing this module, an example can be run from hierarchical_strategy_for_one-component subdirectory of the examples folder using the run_example script to be found there. * https://github.com/hidekb/espressopp/tree/hierarchical-strategy/examples/hierarchical-strategy/simple_one-component Source Code ___________ This module was merged into ESPResSo++ in the Pull Request: * https://github.com/espressopp/espressopp/pull/213 References ___________ .. Here are the URL references used .. [1] : http://pubs.acs.org/doi/abs/10.1021/mz5000015
 name = 'QuantumESPRESSO' version = '5.4.0' versionsuffix = '-hybrid' homepage = 'http://www.pwscf.org/' description = """Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'usempi': True, 'openmp': True} dependencies = [ # ('netCDF-Fortran','4.4.3'), # For Yambo, check if it is picked up # ('Libxc','2.2.2'), # For Yambo, check if it is picked up ] # Part of this list was determined from install/plugins_list sources = [ 'espresso-%(version)s.tar.gz', 'tddfpt-%(version)s.tar.gz', # Other sources # Common source 'atomic-%(version)s.tar.gz', 'neb-%(version)s.tar.gz', 'PHonon-%(version)s.tar.gz', 'pwcond-%(version)s.tar.gz', 'xspectra-%(version)s.tar.gz' , 'PWqui-%(version)s.tar.gz' , 'EPW-%(version)s.tar.gz' , 'test-suite-%(version)s.tar.gz' , 'GWW-%(version)s.tar.gz' , ] source_urls = [ 'http://files.qe-forge.org/index.php?file=', # Almost all 'http://www.qe-forge.org/gf/download/frsrelease/211/968/', # espresso-5.4.0.tar.gz # These will not be used because of the 404 signal not found from the previous link. 'http://www.qe-forge.org/gf/download/frsrelease/211/961/', # PWgui-5.4.0.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/211/956/', # tddfpt-5.4.0.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/211/954/', # atomic-5.4.0.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/211/959/', # neb-5.4.0.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/211/962/', # PHonon-5.4.0.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/211/960/', # pwcond-5.4.0.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/211/958/', # xspectra-5.4.0.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/211/969/', # EPW-5.4.0.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/211/963/', # test-suite-5.4.0.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/211/957/', # GWW-5.4.0.tar.gz ] # Hybrid option exist only for backward compatibility, use toolchain option openmp instead. #hybrid = True # Patch file to avoil the CPP problem generated by different OSes patches = ['QE_gfortran_f90rule.patch'] buildopts = 'all tddfpt neb xspectra ph ' # parallel build tends to fail parallel = 1 moduleclass = 'chem'
 ... ... @@ -4,11 +4,11 @@ Patch file for module ##################### :download:Downloadable version of patch file  To include a patch file do something like the following: .. literalinclude:: ./simple.patch :emphasize-lines: 2,9-11 :linenos: :download:Downloadable version of patch file
 ... ... @@ -3,6 +3,9 @@ template. Make sure that any time you use ReST syntax (such as for ".. sidebar::" below), it needs to be preceded and followed by white space (if you see warnings when this file is built they this is a common origin for problems). .. We allow the template to be standalone, so that the library maintainers add it in the right place :orphan: .. Firstly, let's add technical info as a sidebar and allow text below to wrap around it. This list is a work in progress, please help us improve it. We use *definition lists* of ReST_ to make this readable. ... ...