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1
Input files and parameters / Re: ChargeFromChargeEquilibration
« Last post by David Dubbeldam on January 28, 2019, 07:57:40 PM »
Check the format of the CIF file and compare it to the other ones to see where it goes wrong.
Usually, the error is printed to the console about what goes wrong with the reading.
2
General / Re: Parallelization of RASPA simulations with Golem
« Last post by nowakoww on January 25, 2019, 03:59:37 PM »
Hello,

It's Golem here. As mentioned in the post above, we have prepared a thin client. It hides all the complexity of Golem from RASPA users as much as possible. There's no need to install Golem on your computer. Now, you only have to install the thin client, provide connectivity details and run the example RASPA calculations provided within the installation pack to test the installation.

The thin client doesn't contain any Golem-specific components. It just sends computing tasks along with input data to a remote server that acts as a Golem requestor node. Currently this requestor node is hosted on AWS and managed by the Golem Team. The requestor node knows how to speak to the Golem network using the Golem protocol in order to find provider nodes which will actually do computational work in parallel. The more provider nodes there are in the Golem network, the better parallelization we can achieve and obtain results faster.

In the installation pack there are two main directories:
\golemrpc - contains thin client code,
\examples - contains example python script raspa_remote.py and \examples\cifs subfolder with input data.

We've tried to ensure that the code is well documented. To get familiar whit the thin client and the example, please read comments in the code. Also, don't hesitate to contact us either on this forum or via email or any other communication channel we use (see https://golem.network/).

How the example works

raspa_remote.py reads input .cif files and instructs remote requestor node to create computation tasks (one task per one input file) in the Golem network which can be then executed by provider nodes. The provided example runs get_helium_void_fraction() for two selected .cif files from \examples\cifs. After completing the calculations the results for each task are saved in \examples\cifs\<task_id>-output folder, e.g. \examples\cifs\40e0d906-20aa-11e9-8e1c-c772b47c74b3-output.

You can, of course, modify the example to perform your own RASPA calculations on your own input data.

The nature of the Golem network enables performing calculations of parallel tasks on virtually unlimited number of nodes (depending on how many independent subtasks your entire computational task can be divided). However, for the purpose of testing the RASPA thin client we have setup a test environment consisting of just several provider nodes. This means that you can perform calculations on several input files in parallel.

How to install the client and run the example?

The installation is very straightforward. Please follow the instructions here: https://github.com/golemfactory/golemrpc/blob/arbitrary_files/EXAMPLES.md

Note that the thin client connects with the remote Golem requestor node on AWS. To enable secure connection you need credential files: 'golemcli_aws.tck' and 'rpc_cert_aws.pem'. To obtain those files, please contact michal.plebanski@golem.network or wiktor.nowakowski@golem.network.



We would much appreciate your feedback about using the thin client. We would also appreciate if you spend a small quantum of time to answear our questions from the post above. We are open to any discussions on any time.

Best regards,
Wiktor
3
Input files and parameters / Re: (resolved)ChargeFromChargeEquilibration
« Last post by anne on January 21, 2019, 04:23:38 AM »
Hi David;

I have a followed-up question of this ChargeFromChargeEquilibriateion. It worked when I tried on MIL-53, MIL-100-primitive files which were in the share/raspa/structure/cif folder. However, it didn't work on the MIL-100-Fe.cif file I downloaded from CCDC (Link  https://www.ccdc.cam.ac.uk/structures/Search?Compound=MIL-100&DatabaseToSearch=Published). There is no output files/folders like Output, Movie, etc. after reading the cif file and force-field files. Here is the simulation.input file. I also attached the MIL-100-Fe.cif file.

SimulationType                   MC
NumberOfCycles                   0
NumberOfInitializationCycles     0
PrintEvery                       100
RestartFile                      no

Forcefield                       local
ChargeMethod                     Coulomb
CutOff                           12.0

ChargeFromChargeEquilibration    yes
ChargeEquilibrationPeriodic      yes
ChargeEquilibrationEwald         yes
SymmetrizeFrameworkCharges       no

Framework           0
FrameworkName       MIL-100-Fe
UnitCells           1 1 1
ExternalTemperature 298.0
ExternalPressure    0.0
InputFileType       cif

I am sure that the simulation.input file should be good and wondering if this is because there are no hydrogen atoms in the downloaded MIL-100-Fe.cif files (please see the attachment).

I appreciate it in advance.

Anne
4
Input files and parameters / Re: Single Point Energy Calculation?
« Last post by David Dubbeldam on January 17, 2019, 04:58:36 PM »
A single point is run by just using 0 cycles. To read in a configuration you can use the Restart-file (see manual).
A quick way of creating that file is to use 0 cycles and create a single molecule. That will write out the Restart-file containing (some) atomic positions of the molecule.
You can then edit this file, read it in, and run for 0 cycles to compute a 'single point' energy.
5
Input files and parameters / Single Point Energy Calculation?
« Last post by sen on January 15, 2019, 11:00:16 PM »
Hi all,

I'm a new user in raspa. Is it possible to for raspa to read in a configuration file that contains the MOF and one adsorbate coordinate, and then do a single point energy calculation? What I want is the energy of this system calculated from force filed.

Thanks!
6
RASPA Workshops: Molecular simulations for adsorption and diffusion in nanoporous materials, modeling of ionic liquids, and other applications

The workshops focus on a practical understanding of molecular simulations of fluids, ionic liquids, and nanoporous materials, and applying the RASPA software. The duration is 3.5 days, with lectures in the morning and exercises in the afternoon. The content of the Europe and US workshops is identical. Participants will learn the theoretical foundations of Molecular Dynamics (MD) and Monte Carlo (MC), as well as the practical side of performing molecular simulations: setting up the system, constructing input files for molecules and frameworks, setting up a force field, understanding input settings, and analyzing the output. We will use our publicly available code RASPA, but the gained knowledge and understanding are also directly applicable to other software. Participants will need to bring their own laptop (Mac, Linux, Windows).

Topics: (1) introduction to MD, MC; (2) studying adsorption and diffusion in porous materials (e.g. zeolites, MOFs); (3) Fluid and ionic liquid properties; (4) vapor-liquid equilibrium; (5) advanced simulation methods; (6) applying RASPA to industrial relevant systems.

Registration link:
RASPA Europe workshop at Wroclaw, Poland

More info:
Preliminary course schedule
7
Input files and parameters / Re: (resolved)ChargeFromChargeEquilibration
« Last post by anne on December 21, 2018, 04:02:10 PM »
Thanks, David. That's exactly what I need. It works.
8
Input files and parameters / Re: ChargeFromChargeEquilibration
« Last post by David Dubbeldam on December 20, 2018, 09:11:37 AM »
See the example in: RASPA-2.0/examples/Auxiliary/ChargeEquilibration/IRMOF-1
You do not need any cycles, it is run only once to compute the charges of the framework using charge-equilibration.
1 x 1 x 1 unit cells is sufficient.

The charges are then written as output in the file: Movies/System_0/Framework_0_final_1_1_1_P1.cif
This cif-file you can use as the new framework (copy it to your working directory) and then use:
UseChargesFromCIFFile yes
9
Input files and parameters / ChargeFromChargeEquilibration
« Last post by anne on December 19, 2018, 11:31:59 PM »
I have a problem with the ChargeFromChareEquilibration. This has been solved by referring to the example in the tutorial. Thank all!

10
General / Parallelization of RASPA simulations with Golem
« Last post by nowakoww on December 14, 2018, 11:13:29 AM »
Dear Professor Dubbeldam, Dear RASPA Users Community,

We are Golem. Golem is a project that aims at building the first truly decentralized supercomputer, creating a decentralized sharing economy of computing power. Golem connects computers in a peer-to-peer network, enabling users (requestors) to rent resources of other users' (providers) machines, from PCs to entire data centers. These resources can be used to complete computationally intensive tasks faster, cheaper and easier. Golem is capable of computing a wide variety of tasks, form CGI rendering, through machine learning to scientific computing. Apart from requestors and providers, an important part of Golem's ecosystem are software developers who use Golem as a channel for distribution  of their software. This software is intended to be used out-of-the-box by requestors and providers to submit and perform computing tasks. An example of such application could be a plug-in for an existing rendering software (like Blender or 3D Max) which enables its users to easily submit rendering of a 3D scene to hundreds or thousands of nodes in the Golem network and get things done much faster. Such a plug-in could hide all the complexity of task parallelization from the users. A Golem application doesn't have to be a plug-in. It could be a standalone application or python library as well. More about Golem you can find at our website: https://golem.network/

We are advanced on our way to make the above vision come true and rendering is the first use case we've implemented to demonstrate real Golem usage. We are now working hard on integrating a variety of new use cases to Golem in cooperation with our partners both from business and academia. We are especially interested in scientific computing, including molecular modelling, and so we came across RASPA which seems to be a good fit for Golem.

As a proof of concept we have implemented a python library that allows RASPA users to perform simulations using task-farming approach in the Golem network. With this library one can write workflows like the one described here (https://github.com/numat/RASPA2/wiki/Workflow). However, we are not experts in molecular modelling, thus we would need some advice from domain experts and RASPA users. We would appreciate if you could  help us with the two points below. Together we could work out a solution that, on one hand, would be useful for RASPA users and, on the other hand, would be another practical Golem use case.

  • Please give us some light on the domain and RASPA software itself by answering the following questions:

    • What are the most common usage scenarios for RASPA? Is the workflow described here (https://github.com/numat/RASPA2/wiki/Workflow) a typical one or maybe there's no common way of using RASPA and it heavily depends on particular problem at hand?
    • What is an average size of the input/output data? What are the biggest inputs/outputs that are used in pracitce (or RASPA is capable to deal with)?
    • What type of data (formats) RASPA produces as an output for different types of calculations/algorithms? Are these just numbers or target molecules that can be then visualised (in iRASPA for example)?
    • Could you please provide us with some real-world examples of input and resulting output data along with the desccription of workflows that were used to produce those results. This would give us a better understanding of real usage scenarios and would help us to consider best parallelization scenarios using Golem?
    • Is it possible to run simulations directly from iRASPA or is it intended only for building and visualizing models of molecules and simulations needs to be run separately using RASPA command line interface or from Python scripts?
    • Are there ways to verify if the RASPA simulation results are valid, e.g. using statistical methods? In Golem, in case a task is computed on an untrusted node, there should be a way to validate the results. It could be done by redundancy (computationally expensive) or using other less expensive methods.


  • We would also like to encourage you to play around with our Golem python client for RASPA. Basically we did all the heavy lifting so that the user can focus on doing his job. We appreciate trying out and giving us feedback. To help you get started we prepared installation manuals and example RASPA2 code.

    Our integration with this particular task is inspired by the workflow I mentioned above (https://github.com/numat/RASPA2/wiki/Workflow).

    In general we have two separate computation environments: testnet (rinkeby) and mainnet. RASPA2 integration is available only as a separate branch (‘glambda’) in our main repository. In other words it has no real adoption yet (in both environments). One has to set up his own workers on local computer to run the examples. We plan to merge it (or not) after receiving feedback.

    Installing from source is described here:

    https://github.com/golemfactory/golem/wiki/Installation#running-from-the-source

    Make sure you have checked out `glambda` branch.

    Now that we have Golem installed on our computer it’s time to try integrating our simulation glue code with it. We provided python library called 'golemrpc' (along with integration examples) to do so. For setup instructions please see both:

    https://github.com/golemfactory/golemrpc

    and the examples:

    https://github.com/golemfactory/golemrpc/tree/master/golemrpc/examples
    We are most interested in knowledge about user workflows. How can we do better to ease the process for RASPA2 users? Please ignore cumbersome local node’s setup for now. It will be solved by design if we decide to move forward with RASPA and allow it on testnet.

    More information about the project can be found here:

    https://golem.network/documentation/understanding-beta/

    We realize that the above installation process of the Golem client might not be very straightforward and we are working on a so called thin client installation of which would be as simple as possible. We will share it with you soon. In the meantime we encourage you to try out the current version.



Our future plans include also parallelization of RASPA simulations with MPI (e.g. using spatial or force decomposition) as we are currently working on implementation of MPI on Golem.

In case of any questions or problems from you regarding Golem, we will be more than happy to help you.

Best regards,
Wiktor Nowakowski
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