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Commits (5)
.. In ReStructured Text (ReST) indentation and spacing are very important (it is how ReST knows what to do with your
document). For ReST to understand what you intend and to render it correctly please to keep the structure of this
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).
.. 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.
.. sidebar:: Software Technical Information
Name
velocities_resolve_EVC
Language
C
Licence
`MIT <https://opensource.org/licenses/mit-license>`_
Documentation Tool
doxygen
Application Documentation
'https://gitlab.e-cam2020.eu/carrivain/velocities_resolve_evc/blob/master/refman.pdf'
Relevant Training Material
'https://gitlab.e-cam2020.eu/carrivain/velocities_resolve_evc/blob/master/velocities_resolve_EVC.pdf'
Software Module Developed by
Pascal Carrivain
.. In the next line you have the name of how this module will be referenced in the main documentation (which you can
reference, in this case, as ":ref:`example`"). You *MUST* change the reference below from "example" to something
unique otherwise you will cause cross-referencing errors. The reference must come right before the heading for the
reference to work (so don't insert a comment between).
.. _velocities_resolve_EVC:
###################################
E-CAM velocities_resolve_EVC module
###################################
.. Let's add a local table of contents to help people navigate the page
.. contents:: :local:
.. Add an abstract for a *general* audience here. Write a few lines that explains the "helicopter view" of why you are
creating this module. For example, you might say that "This module is a stepping stone to incorporating XXXX effects
into YYYY process, which in turn should allow ZZZZ to be simulated. If successful, this could make it possible to
produce compound AAAA while avoiding expensive process BBBB and CCCC."
The velocities_resolve_EVC is a module that resolve the excluded volume constraint with a velocity formulation (no potential
applied between two overlaped bonds).
The velocities_resolve_EVC uses the module minDist2segments_KKT to find the minimal distance between two bonds.
.. The E-CAM library is purely a set of documentation that describes software development efforts related to the project. A
.. *module* for E-CAM is the documentation of the single development of effort associated to the project.In that sense, a
.. module does not directly contain source code but instead contains links to source code, typically stored elsewhere. Each
.. module references the source code changes to which it direcctly applies (usually via a URL), and provides detailed
.. information on the relevant *application* for the changes as well as how to build and test the associated software.
.. The original source of this page (:download:`readme.rst`) contains lots of additional comments to help you create your
.. documentation *module* so please use this as a starting point. We use Sphinx_ (which in turn uses ReST_) to create this
.. documentation. You are free to add any level of complexity you wish (within the bounds of what Sphinx_ and ReST_ can
.. do). More general instructions for making your contribution can be found in ":ref:`contributing`".
.. Remember that for a module to be accepted into the E-CAM repository, your source code changes in the target application
.. must pass a number of acceptance criteria:
.. * Style *(use meaningful variable names, no global variables,...)*
.. * Source code documentation *(each function should be documented with each argument explained)*
.. * Tests *(everything you add should have either unit or regression tests)*
.. * Performance *(If what you introduce has a significant computational load you should make some performance optimisation
effort using an appropriate tool. You should be able to verify that your changes have not introduced unexpected
performance penalties, are threadsafe if needed,...)*
Purpose of Module
_________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
To study the long term memory of the initial conformation of a highly entangle polymer we need to preserve the topology.
It means that two bonds cannot cross. It is of great importance for the study of post-mitotic chromosome unfolding.
To resolve the excluded volume constraints you could use a soft or hard potential between the two points associated to the
minimal distance. Here, we propose to change the relative velocity between overlaped bonds to resolve the excluded volume
constraint in one time-step of molecular dynamics.
.. Give a brief overview of why the module is/was being created, explaining a little of the scientific background and how
.. it fits into the larger picture of what you want to achieve. The overview should be comprehensible to a scientist
.. non-expert in the domain area of the software module.
.. This section should also include the following (where appropriate):
* Polymer simulation.
* To resolve the excluded volume constraints.
* It is used in a scientific collaboration.
* Publications: not currently available.
.. note::
We would use the present module to avoid topology violation in entangle polymer system.
The present module uses the E-CAM module minDist2segments_KKT.
.. note::
This module is a part of a pilot project (E-CAM post-doc). We would use it to avoid topology violation in entangle polymer system.
url to the pilot project main page not currently available.
..
If needed you can include latex mathematics like
:math:`\frac{ \sum_{t=0}^{N}f(t,k) }{N}`
which won't show up on GitLab/GitHub but will in final online documentation.
If you want to add a citation, such as [CIT2009]_, please check the source code to see how this is done. Note that
citations may get rearranged, e.g., to the bottom of the "page".
.. [CIT2009] This is a citation (as often used in journals).
Background Information
______________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
.. If the modifications are to an existing code base (which is typical) then this would be the place to name that
.. application. List any relevant urls and explain how to get access to that code. There needs to be enough information
.. here so that the person reading knows where to get the source code for the application, what version this information is
.. relevant for, whether this requires any additional patches/plugins, etc.
.. Overall, this module is supposed to be self-contained, but linking to specific URLs with more detailed information is
.. encouraged. In other words, the reader should not need to do a websearch to understand the context of this module, all
.. the links they need should be already in this module.
You can find pdf file with a detailed derivation of the velocity-based method we use to resolve the excluded volume constraint
in one time-step of molecular dynamics at `GitLab E-CAM 2020 <https://gitlab.e-cam2020.eu/carrivain/velocities_resolve_EVC>`_.
Building and Testing
____________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
I provide a simple Makefile you can find at the same location that the source code.
You need C++11 in order to use pseudo-random number generator.
Before the compilation you can clean the previous build with "make mrproper" command.
The purpose of the module is to resolve excluded volume constraints.
Therefore, we provide a simple example of a system of N bonds with volume interactions.
We test every n iterations the average overlap over pairwize.
Source Code
___________
.. Notice the syntax of a URL reference below `Text <URL>`_ the backticks matter!
.. Here link the source code *that was created for the module*. If you are using Github or GitLab and the `Gitflow Workflow
<https://www.atlassian.com/git/tutorials/comparing-workflows#gitflow-workflow>`_ you can point to your feature branch.
Linking to your pull/merge requests is even better. Otherwise you can link to the explicit commits.
The source code and more informations can be find at `GitLab E-CAM 2020 <https://gitlab.e-cam2020.eu/carrivain/velocities_resolve_evc>`_.
.. In ReStructured Text (ReST) indentation and spacing are very important (it is how ReST knows what to do with your
document). For ReST to understand what you intend and to render it correctly please to keep the structure of this
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).
.. 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.
.. sidebar:: Software Technical Information
Name
OpenMM_Copolymer
Language
Python 3.7, OpenMM API
Licence
`MIT <https://opensource.org/licenses/mit-license>`_
Documentation Tool
'https://gitlab.e-cam2020.eu/carrivain/copolymer-using-openmm/blob/master/refman.pdf'
Application Documentation
Not currently available. Provide a link to any documentation for the application.
Relevant Training Material
Not currently available.
Software Module Developed by
Pascal Carrivain
.. In the next line you have the name of how this module will be referenced in the main documentation (which you can
reference, in this case, as ":ref:`example`"). You *MUST* change the reference below from "example" to something
unique otherwise you will cause cross-referencing errors. The reference must come right before the heading for the
reference to work (so don't insert a comment between).
.. _OpenMM_Copolymer:
#############################
E-CAM OpenMM_Copolymer module
#############################
.. Let's add a local table of contents to help people navigate the page
.. contents:: :local:
.. Add an abstract for a *general* audience here. Write a few lines that explains the "helicopter view" of why you are
creating this module. For example, you might say that "This module is a stepping stone to incorporating XXXX effects
into YYYY process, which in turn should allow ZZZZ to be simulated. If successful, this could make it possible to
produce compound AAAA while avoiding expensive process BBBB and CCCC."
The OpenMM_Copolymer is a module that sample conformation of a block-copolymer given a genome epigenetic state file.
This module takes advantage of the OpenMM software and GPU acceleration.
It builds a Kremer-Grest polymer model with uni-dimensionnal epigenetic informations and construct the epigenetic interactions
based on the model you design.
You simply need to feed the module with a epigenetic state file, the interaction model and the mechanical properties of the polymer.
.. The E-CAM library is purely a set of documentation that describes software development efforts related to the project. A
.. *module* for E-CAM is the documentation of the single development of effort associated to the project.In that sense, a
.. module does not directly contain source code but instead contains links to source code, typically stored elsewhere. Each
.. module references the source code changes to which it direcctly applies (usually via a URL), and provides detailed
.. information on the relevant *application* for the changes as well as how to build and test the associated software.
.. The original source of this page (:download:`readme.rst`) contains lots of additional comments to help you create your
.. documentation *module* so please use this as a starting point. We use Sphinx_ (which in turn uses ReST_) to create this
.. documentation. You are free to add any level of complexity you wish (within the bounds of what Sphinx_ and ReST_ can
.. do). More general instructions for making your contribution can be found in ":ref:`contributing`".
.. Remember that for a module to be accepted into the E-CAM repository, your source code changes in the target application
.. must pass a number of acceptance criteria:
.. * Style *(use meaningful variable names, no global variables,...)*
.. * Source code documentation *(each function should be documented with each argument explained)*
.. * Tests *(everything you add should have either unit or regression tests)*
.. * Performance *(If what you introduce has a significant computational load you should make some performance optimisation
effort using an appropriate tool. You should be able to verify that your changes have not introduced unexpected
performance penalties, are threadsafe if needed,...)*
Purpose of Module
_________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
Recently, the epigenetic and the tri-dimensionnal structure of a genome is studied by means of block-copolymer.
The epigenetic information is not present on the DNA but on the histone tails modifications.
This one dimensionnal information can be projected along the contour of a polymer.
Then, every pairwise interacts according to the epigenetic states leading to specific patterns of interactions.
However, the strength of the interactions between epigenetic states is not clearly known.
The module we propose uses the OpenMM software with the GPU acceleration to sample as many as possible epigenetic parameters.
.. Give a brief overview of why the module is/was being created, explaining a little of the scientific background and how
.. it fits into the larger picture of what you want to achieve. The overview should be comprehensible to a scientist
.. non-expert in the domain area of the software module.
.. This section should also include the following (where appropriate):
* Polymer physicist, epigenetic modelling.
* To understand the link between epigenetic and tri-dimensionnal structure of a genome. To estimate first-passage-time encounter of two locii.
* It is used in a scientific collaboration.
* Publications: not currently available.
..
.. note::
If the module is an ingredient for a more general workflow (e.g. the module was the necessary foundation for later
code; the module is part of a group of modules that will be used to calculate certain property or have certain
application, etc.) mention this, and point to the place where you specify the applications of the more general
workflow (that could be in another module, in another section of this repository, an application’s website, etc.).
.. note::
If you are a post-doc who works in E-CAM, an obvious application for the module (or for the group of modules that
this one is part of) is your pilot project. In this case, you could point to the pilot project page on the main
website (and you must ensure that this module is linked there).
..
If needed you can include latex mathematics like
:math:`\frac{ \sum_{t=0}^{N}f(t,k) }{N}`
which won't show up on GitLab/GitHub but will in final online documentation.
If you want to add a citation, such as [CIT2009]_, please check the source code to see how this is done. Note that
citations may get rearranged, e.g., to the bottom of the "page".
.. [CIT2009] This is a citation (as often used in journals).
Background Information
______________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
You can find pdf file with a detailed description on what we could do with this module at `GitLab E-CAM 2020 <https://gitlab.e-cam2020.eu/carrivain/copolymer-using-openmm>`_.
Building and Testing
____________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
We provide tests as python script for simple block copolymer model.
Source Code
___________
.. Notice the syntax of a URL reference below `Text <URL>`_ the backticks matter!
The source code and more informations can be find at `GitLab E-CAM 2020 <https://gitlab.e-cam2020.eu/carrivain/copolymer-using-openmm>`_.
.. In ReStructured Text (ReST) indentation and spacing are very important (it is how ReST knows what to do with your
document). For ReST to understand what you intend and to render it correctly please to keep the structure of this
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).
.. 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.
.. sidebar:: Software Technical Information
Name
OpenMM_KG_benchmark
Language
Python 3.7, OpenMM API
Licence
`MIT <https://opensource.org/licenses/mit-license>`_
Documentation Tool
sphynx
Application Documentation
`<https://gitlab.e-cam2020.eu/carrivain/openmm_kg_benchmark/blob/master/refman.pdf>`_
Relevant Training Material
Not currently available.
Software Module Developed by
Pascal Carrivain
.. In the next line you have the name of how this module will be referenced in the main documentation (which you can
reference, in this case, as ":ref:`example`"). You *MUST* change the reference below from "example" to something
unique otherwise you will cause cross-referencing errors. The reference must come right before the heading for the
reference to work (so don't insert a comment between).
.. _OpenMM_KG_benchmark:
################################
E-CAM OpenMM_KG_benchmark module
################################
.. Let's add a local table of contents to help people navigate the page
.. contents:: :local:
.. Add an abstract for a *general* audience here. Write a few lines that explains the "helicopter view" of why you are
creating this module. For example, you might say that "This module is a stepping stone to incorporating XXXX effects
into YYYY process, which in turn should allow ZZZZ to be simulated. If successful, this could make it possible to
produce compound AAAA while avoiding expensive process BBBB and CCCC."
The OpenMM_KG_benchmark is a module that sample conformation of Kremer-Grest polymer.
This module takes advantage of the OpenMM software and GPU acceleration.
It builds a Kremer-Grest polymer model from the OpenMM API, run it on different platforms.
It is designed to benchmark the performances of such a model.
.. The E-CAM library is purely a set of documentation that describes software development efforts related to the project. A
.. *module* for E-CAM is the documentation of the single development of effort associated to the project.In that sense, a
.. module does not directly contain source code but instead contains links to source code, typically stored elsewhere. Each
.. module references the source code changes to which it direcctly applies (usually via a URL), and provides detailed
.. information on the relevant *application* for the changes as well as how to build and test the associated software.
.. The original source of this page (:download:`readme.rst`) contains lots of additional comments to help you create your
.. documentation *module* so please use this as a starting point. We use Sphinx_ (which in turn uses ReST_) to create this
.. documentation. You are free to add any level of complexity you wish (within the bounds of what Sphinx_ and ReST_ can
.. do). More general instructions for making your contribution can be found in ":ref:`contributing`".
.. Remember that for a module to be accepted into the E-CAM repository, your source code changes in the target application
.. must pass a number of acceptance criteria:
.. * Style *(use meaningful variable names, no global variables,...)*
.. * Source code documentation *(each function should be documented with each argument explained)*
.. * Tests *(everything you add should have either unit or regression tests)*
.. * Performance *(If what you introduce has a significant computational load you should make some performance optimisation
effort using an appropriate tool. You should be able to verify that your changes have not introduced unexpected
performance penalties, are threadsafe if needed,...)*
Purpose of Module
_________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
The NVIDIA and AMD companies provide the market with new powerful GPUs.
The question then is to benchmark it on a simple polymer model.
The polymer field covers from tyres to chromosomes studies.
We need to know for each application what is the fastest and cheapest GPU to buy.
.. Give a brief overview of why the module is/was being created, explaining a little of the scientific background and how
.. it fits into the larger picture of what you want to achieve. The overview should be comprehensible to a scientist
.. non-expert in the domain area of the software module.
.. This section should also include the following (where appropriate):
* Polymer physicist.
* Numerical performances.
..
.. note::
If the module is an ingredient for a more general workflow (e.g. the module was the necessary foundation for later
code; the module is part of a group of modules that will be used to calculate certain property or have certain
application, etc.) mention this, and point to the place where you specify the applications of the more general
workflow (that could be in another module, in another section of this repository, an application’s website, etc.).
.. note::
If you are a post-doc who works in E-CAM, an obvious application for the module (or for the group of modules that
this one is part of) is your pilot project. In this case, you could point to the pilot project page on the main
website (and you must ensure that this module is linked there).
..
If needed you can include latex mathematics like
:math:`\frac{ \sum_{t=0}^{N}f(t,k) }{N}`
which won't show up on GitLab/GitHub but will in final online documentation.
If you want to add a citation, such as [CIT2009]_, please check the source code to see how this is done. Note that
citations may get rearranged, e.g., to the bottom of the "page".
.. [CIT2009] This is a citation (as often used in journals).
Background Information
______________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
You can find pdf file with a detailed description on what we could do with this module at `GitLab E-CAM 2020 <https://gitlab.e-cam2020.eu/carrivain/openmm_kg_benchmark>`_.
Building and Testing
____________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
We provide tests as a python script for simple Kremer-Grest model as well as unittest script.
We benchmark the model using /usr/bin/time command.
Source Code
___________
.. Notice the syntax of a URL reference below `Text <URL>`_ the backticks matter!
The source code and more informations can be find at `GitLab E-CAM 2020 <https://gitlab.e-cam2020.eu/carrivain/openmm_kg_benchmark>`_.
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