janus | Python library for adaptive QM/MM methods
kandi X-RAY | janus Summary
kandi X-RAY | janus Summary
A Python library for adaptive QM/MM methods Documentation can be found here.
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Top functions reviewed by kandi - BETA
- Define the buffer zone
- Compute the composition of atoms
- Compute qm center info
- Compute the buffer at the given qm_center
- Run QM
- Find all configurations
- Find the buffer zone associated with the buffer
- Compute the lambda function i e l_i
- Restart OpenMM simulation
- Create an OpenMM simulation
- Create a new OpenMM system for a given topology
- Calculates the energy and forces the effect of switching function
- Compute forces based on the shift function
- Compute the switching functions
- Calculate the Qmmmmm
- Get the switching function
- R Define buffer zone
- R Compute buffer atoms
- Calculate the energy and forces
- Compute the forces_sf gradient for each partition
- Run the QM process
- Find the system configurations
- Runsjan
- Run the qmm
- Find the system configurations
- Compute the energy and gradient of a trajectory
janus Key Features
janus Examples and Code Snippets
Community Discussions
Trending Discussions on janus
QUESTION
I am planning to use Janusgraph for building graph of different uses our team handles and I see that janus graph has option to use BigTable or Cassandra as storage backend. I am looking for any recommendation on which backend is more optimal/performant ( I am mainly talking about gremlin query performance on 2 hop neighbor of a node ) with JanusGraph.
I understand that performance is pretty subjective and varies based on datasize/graph connectivity and use case so best approach will be to try out myself, which I am planning to do. But has anyone else has done similar performance comparison ? Is there any general recommendation about storage backend here ?
...ANSWER
Answered 2021-Jun-10 at 18:14You're right in that performance is both:
- subjective
- depends largely on data size
I can tell you that I have done this exercise as well. To that end, I think it's important to share this comparison from DB-Engines.com.
In terms of performance, the biggest thing I'd be looking at is how each handles consistency. As a general rule, databases which enforce stronger levels of consistency typically have to sacrifice performance.
- BigTable == strong-consistent
- Cassandra == eventually consistent
Other factors worth considering, are the fact that BigTable limits you to Google Cloud (GCP). And if you don't want to lose performance over the network, you'll also need to pay for more (Janus) instances on GCP for data locality.
In terms of raw DB-Engine "score," Cassandra is currently at 114.112, while BigTable is at a paltry 3.582. These scores will change month-to-month, but in general this signifies that Cassandra has a much stronger community around it. Similarly, Cassandra has 18182 questions on this site, while BigTable only has 449. Bottom line, is that it'll be much easier to get support and answers to questions.
Just based on the underlying strength of the community, Cassandra is the better option here.
Having supported JanusGraph on Cassandra for the last few years, I can tell you that overall it's been solid. The difficulties tend to come into play with bulk data loading. But outside of that, things seem to run pretty well.
QUESTION
I am using following code to connect to gremlin (JanusGraph) server and execute addV in transaction. My code works fine and it add Vertex properly, but code shows following warnings: "The type GryoMessageSerializerV3d0 is deprecated" & The method getInstance() from the type JanusGraphIoRegistry is deprecated
So would like to know how can i get these warning resolved. Please find my code below:
...ANSWER
Answered 2021-May-19 at 15:57The warning message is just letting you know that features you are using have been deprecated. If you look at the TinkerPop javadoc you can see how to resolve this problem - simply, prefer GraphBinaryMessageSerializerV1 to Gryo. You can often find helpful information for these sorts of things in the TinkerPop Upgrade Documentation. That said, you are using JanusGraph and depending on the version you are using I'm not sure that their IoRegistry implementation is supporting GraphBinary yet. While their latest code on their master branch shows support I don't see that code in a tagged version. It may be best to stay on Gryo a while longer until GraphBinary is fully supported as depending on the Gremlin you write you may hit some serialization problems. The warnings are just warnings - they should not impact your usage.
As for the JanusGraphIoRegistry deprecation warning you can get rid of that pretty easily - simply prefer instance() rather than getInstance() (source code).
QUESTION
I am currently working on getting started with Janus Graph and Gremlin-Python. I am going through the following example:
https://old-docs.janusgraph.org/latest/connecting-via-python.html
In part 2 of the example, there is some strange syntax I have never seen in Python before:
...ANSWER
Answered 2021-Apr-07 at 17:38The identifier __ has no special meaning in Python, aside from not being imported by default when using from module import * like all identifiers of the form _*. See the Python documentation on Reserved Identifiers.
QUESTION
I'm trying to run apache atlas on my local. There are several problem I have faced to. First, for clearance of how I have build the apache atlas I will describe the steps:
- git clone https://github.com/apache/atlas
- cd atlas
- mvn clean install -DskipTests -X
- mvn clean package -Pdist -DskipTests
It has been built without any error. Here is the project structure:
...ANSWER
Answered 2021-Apr-03 at 17:06After struggling with Apache Atlas for a while, I found 3.0.0 Snapshot version very buggy! Therefore I have decided to build and install Apache Atlas 2.1.0 RC3.
Prerequisite:
Make sure you have installed java on your machine. In case it is not installed on your computer, you can install it using the following command in Linux:
sudo apt-get install openjdk-8-jre
Then JAVA_HOME should be set:
QUESTION
I've just set up janus and got it running.
I'm connecting to it, and can see in the janus logs:
[ERR] [transports/janus_http.c:janus_http_handler:1522] Invalid session (null)
I've looked online but can't find anything. Any ideas?
...ANSWER
Answered 2021-Mar-13 at 22:02ditched janus for a cloud service - eg Twilio - instead. IMO janus is not worth the hassle, and their dev community is detrimental to one's wellbeing. Avoid! – bionara just now Edit Delete
QUESTION
I'm trying to build Apache Atlas from the main repository. As it is described in the README.md file, after cloning the repository and changing the current directory to atlas, I am trying to build using mvn clean install command. Unfortunately, since they closed the issue part of the repository, I will explain my problem here.
Build Process
Do the following items in your terminal:
git clone https://github.com/apache/atlas.gitcd atlasexport MAVEN_OPTS="-Xms2g -Xmx2g"mvn clean install
After running the last command, I face to the following error:
...ANSWER
Answered 2021-Mar-07 at 13:43Since the community of Apache Atlas is quite small these days, I want to write the complete story of what has happened and how it works properly, now.
As it seems in the first error trace, the problem is with maven-surefire-plugin:2.18.1:test. In the root directory of project (repository) there is a file named pom.xml which contains the necessary libraries and frameworks to work with.
It seems that several tests are wrong and because of this problem, the building phase had error. In order to skip tests and not to exit from building process we have to add the -DskipTests when we want to build:
QUESTION
I am trying to make video calls with WebRTC and Janus. I am able to make calls using the video call demo page supplied by Janus as well as through an iOS app - this is all working perfectly fine.
However, when inspecting the network flow through both wireshark and chrome://webrtc-internals/ the connection does not seem to be directly to the public IP of the other device. Instead the data is directed to my Janus signaling server. It seems that the IP of the remoteIceCandidate is equal to the IP of my signaling server - shouldn't this should be equal to the public IP of device 2?
Is this correct behavior or not? If so, why is the remote IP not equal to the public IP of device 2? If not, what am I doing wrong?
...ANSWER
Answered 2021-Feb-23 at 08:18This is correct behavior and a mistake on my part. The Janus video call plugin documentation says the following:
The idea is to provide a similar service as the well known AppRTC demo (https://apprtc.appspot.com), but with the media flowing through a server rather than being peer-to-peer.
Therefore, the media data is supposed to go to the server instead of over a peer-to-peer connection.
QUESTION
I am trying to join 3 tables into a specific model using linq but I am getting incorrect results.
With my code below: ...ANSWER
Answered 2021-Feb-19 at 21:11I've tried using the method syntax because i'm not to great at the query syntax:
QUESTION
The question that my teacher gave me is : Create a Group Assignment that prompts the user for his or her name and then displays a group assignment. The group assignment depends on the FIRST LETTER OF THE STUDENT'S LAST NAME. Last names beginning with A through I are assigned to group 1, J through S are assigned to group 2 and T through Z are assigned to group 3.
example output: Enter you first and last name: Janus Smith You are assigned to group 2.
I don't know the code to get the first letter of the second word and if they are still code error please do fix it. Tnx.
...ANSWER
Answered 2021-Jan-03 at 07:32Use String#split to split the name by space to get two parts.
QUESTION
I try to make some customized routes for components with protected function but route is not working:
...ANSWER
Answered 2020-Dec-18 at 13:37Try this, it works.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
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Install janus
Go to folder where this is downloaded and run: bash Miniconda3-latest-OSX-x86_64.sh -b -p $HOME/miniconda
To set conda path to miniconda: echo PATH="\$HOME/miniconda/bin:\$PATH" >> ~/.bash_profile
Create environment in miniconda: conda create -n janus python=3.6 psi4 psi4-rt numpy openmm -c psi4 -c omnia
To activate the environment: source activate janus
To install locally: pip install -e .
For reading external datafiles with pytest within the janus environment: pip install pytest-datafiles
Adding mendeleev package: pip install mendeleev
To add MDtraj: conda install -c conda-forge mdtraj
To add sphinx : pip install Sphinx
To add napoleon extension to sphinx pip install sphinxcontrib-napoleon
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