Merge pull request #10 from GPUE-group/development

Merging development branch to master

Author: leios

README.md

@@ -1,60 +1,23 @@
-[![DOI](https://zenodo.org/badge/23153/mlxd/GPUE.svg)](https://zenodo.org/badge/latestdoi/23153/mlxd/GPUE)
-[![Code Climate](https://codeclimate.com/github/mlxd/GPUE/badges/gpa.svg)](https://codeclimate.com/github/mlxd/GPUE)
-![GPUE version](https://img.shields.io/badge/v-0.abs(exp(1i*pi))-blue.svg)
 --- 
-[logo]: https://github.com/mlxd/GPUE/blob/master/logo.png "GPUE"
+[logo]: https://github.com/gpue-group/GPUE/blob/master/logo.png "GPUE"
 ![GPUE - GPU Gross-Pitaevskii Equation solver][logo]
 
 ***
 
-[bb]: https://bitbucket.org/loriordan/gpue "Bitbucket"
-[gh]: https://github.com/mlxd/gpue "GitHub"
-
-## 0. Introduction
+[gh]: https://github.com/gpue-group/gpue "GitHub"
 
 Welcome to GPUE, the [fastest zero temperature BEC routines in the land](http://peterwittek.com/gpe-comparison.html) (the last time we checked).
-
-Runs on CUDA 7.0 (C++11 functionality needed) on both Linux and Mac OS X 
-(Nvidia GPU only). We have not tested on Windows. Other requirements are Python 
-2.6+ (though PyPy is MUCH faster), Numpy, Scipy, Matplotlib, Mencoder.
-
-To build, first check the predefined paths in the Makefile (CUDA lib/lib64, 
-bin, include, etc).
-
-Configuring the simulation parameters is as easy as editing the 
-bin/run_params.conf file, and entering them as specified. Each new line will 
-represent another simulation, with the maximum number of simultaneous
-simulations to be given in run.sh.
-
-To run the simulations:
-chmod +x ./run.sh; ./run.sh
-
-If the image generation fails, this can be rectified manually by editing the 
-file py/vis.py, and selecting the appropriate operation. Not all Python code 
-may currently not behave as expected, due to the switch over to vortex tracking
-entirely in C++.
-
-Many routines are also being converted from C host-code to C++11 host-code, 
-so if there is any strange behaviour then please let me know. Bug reports are 
-always welcome, as well as comments, improvements, cake, free-dinners and cold 
-weather.
-
-If you enjoy/use/learn from this code, please give me a citation, as it took a 
-long time to develop, and I'd appreciate it greatly! A nice email would suffice 
-too :)
+All documentation is available at [https://gpue-group.github.io](https://gpue-group.github.io).
 
 ## 1. What does this software do?
 
 This software is a CUDA-enabled non-linear Schrodinger (Gross-Pitaevskii) 
-equation solver. The primary use of this code was for my research on 
-rapidly rotating Bose-Einstein condensates. Due to the complexity and 
+equation solver. The primary use of this code was for research on 
+Bose-Einstein condensates. Due to the complexity and 
 timescales needed to simulate such system, it was essential to write some 
-accelerated code to understand the behaviour of such systems. If you would like 
-to know more, check my Google scholar profile 
-<https://scholar.google.com/citations?user=s-6jND0AAAAJ&hl=en>
-which will update as we finish some papers.
+accelerated code to understand the behaviour of such systems. 
 
-The premise is the following:
+As a short introduction of the use-case:
 We want to simulate how a Bose-Einstein condensate (BEC) behaves in a trap. 
 The trap is parabolic (harmonic), and for the lowest energy state of the 
 system (ground-state) the BEC will want to sit about the centre. Due to the
@@ -73,52 +36,33 @@ to enter with a singular unit of angular momentum (think 100x 1 unit vortices
 instead of 1x 100 unit vortex). This gives us a nice well arranged lattice if 
 performed correctly. It is this lattice that we have been researching (read as: 
 playing with). However, this code can be used in any trapping geometry, 
-rotation, etc. that you wish to use. Bear in mind, we have developed this for 
-a 2D system only. Extensions to 3D are currently in the works, and are in the
-beta branch lead by the amazing James Schloss (leois). When completed, these 
-will be merged into master.
+rotation, etc. that you wish to use. 
 
 ## 2. Great! How do I make a BEC?
-
-Well, first you need to look at the run_params.conf file, and give it some 
-necessary parameters to generate your favourite condensate.
-
-As an example
-./gpue -x 256 -y 256 -T 1e-3 -t 1e-3 -n 1e5 -g 1e3 -e 1e3 -p 1 -r 0 -w 0.3 -o 10 -d 0 -l 1 -s 1 -i 1.0 -P 0.0 -G 1.0 -L 0 -X 1 -Y 1 -k 0 -O 0.0 -W 1 -U 0 -V 0 -S 0.0
+See the [Building GPUE](https://gpue-group.github.io/build/) and [GPUE functionality](https://gpue-group.github.io/functionality/)
+sections of the documentation.
 
 As an example, here are some simulations performed with the code:
 https://www.youtube.com/playlist?list=PLiRboSbbz10s6cXxvYLFOn3QbmQpdtQVd
 
-The above parameters will be better explained when the papers have been 
-published (which is only fair). Comments will be added for relevant sections 
-too to allow for their use. 
-
-## 3. What do you see as the future of this?
-I would like this tool to be a suite for 1D, 2D and 3D simulations of both 
-Schrodinger and non-linear Schrodinger systems. 
-
-## 4. I have used your program and/or learned from the source. What now?
-A citation would be nice :) Feel free to cite as:
-
-Lee James O'Riordan et al., GPUE: Phasegineering release, Zenodo. (2016)
-\url{https://github.com/mlxd/GPUE} DOI:10.5281/zenodo.57968
-
-Otherwise, an email with a message, comments, or anything is appreciated. I'm 
-curious as to who is using this, so regardless of what you do with it, feel 
-free to get in touch. 
+## 3. Specific use-cases
+We would like this tool to be a suite for 1D, 2D and 3D simulations of both 
+Schrodinger and non-linear Schrodinger (Gross--Pitaevskii) systems. 
 
-If you would like to help, I am always looking for some additional improvements.
-There is a lot remaining to be done, but many hands make light work, after all.
+## 4. Works using GPUE
+If you have used GPUE, or any of the works using GPUE, please consider giving us a citation. 
+Previous versions of this code/works are citable as follows:
 
+- Lee James O'Riordan et al., GPUE: Phasegineering release, Zenodo. (2016), \url{https://github.com/mlxd/GPUE} DOI:10.5281/zenodo.57968
 
+More recent versions will be citable under the [GPUE Group](https://github.com/gpue-group/GPUE) repository. 
+Works which have used GPUE include (to-date):
+- [Moiré superlattice structures in kicked Bose-Einstein condensates](https://journals.aps.org/pra/abstract/10.1103/PhysRevA.93.023609)
+- [Topological defect dynamics of vortex lattices in Bose-Einstein condensates](https://journals.aps.org/pra/abstract/10.1103/PhysRevA.94.053603)
+- [Non-equilibrium vortex dynamics in rapidly rotating Bose-Einstein condensates](https://ci.nii.ac.jp/naid/500001054902/)
 
 ## 5. Acknowledgements
 We are greatly thankful to the support provided by Okinawa Institute of Science 
 and Technology Graduate University, without whom this research code would be a 
-fraction of what it currently has become. To the various people who have 
-contributed in ideas and parts to this project, in no particular order:
-Albert Benseney Cases, who assisted with the multivortex vortex tracking and
-various discussions; Angela White, who assisted with calculating the spectra
-and with a variety of physics discussions; Tadhg Morgan, for initial 
-discussions and works with simulating cold atoms; Thomas Busch, for guidance
-over the many areas of physics this code has touched upon.
+fraction of what it currently has become. A list of acknowledgements is given in [acknowledgements.md](https://github.com/GPUE-group/GPUE/blob/master/acknowledgements.md).
+ 

acknowledgements.md

@@ -0,0 +1,7 @@
+For their various contributions and discussions which made this work possible, the authors wish to thank (in no particular order):
+
+- Albert Benseney Cases, who assisted with the multivortex vortex tracking and various physics discussions.
+- Angela White, who assisted with calculating the spectra and with a variety of physics discussions.
+- Tadhg Morgan and Neil Crowley, for initial discussions and codes for simulating cold atoms.
+- Thomas Busch, for guidance over the many areas of physics this code has touched upon.
+

bin/RunTime.dat

@@ -14,9 +14,9 @@
          ╚═════╝ ╚═╝      ╚═════╝ ╚══════╝
 
    GPUE - GPU Gross-Pitaevskii Equation solver
-            Version 0.abs(exp(i*pi))
+            Version abs(exp(i*pi))
 
-       http:://bitbucket.org/loriordan/gpue
+       http:://github.com/gpue-group/gpue
 
 #################################################
 #################################################

bin/batch_run.sh

@@ -1,32 +1,3 @@
-#GPUE: Split Operator based GPU solver for Nonlinear 
-#Schrodinger Equation, Copyright (C) 2011-2015, Lee J. O'Riordan 
-#<loriordan@gmail.com>, Tadhg Morgan, Neil Crowley. All rights reserved.
-#Redistribution and use in source and binary forms, with or without 
-#modification, are permitted provided that the following conditions are 
-#met:
-#
-#1. Redistributions of source code must retain the above copyright 
-#notice, this list of conditions and the following disclaimer.
-#
-#2. Redistributions in binary form must reproduce the above copyright 
-#notice, this list of conditions and the following disclaimer in the 
-#documentation and/or other materials provided with the distribution.
-#
-#3. Neither the name of the copyright holder nor the names of its 
-#contributors may be used to endorse or promote products derived from 
-#this software without specific prior written permission.
-#
-#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS 
-#"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT 
-#LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A 
-#PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT 
-#HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, 
-#SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
-#TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
-#PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 
-#LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 
-#NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 
-#SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #!/bin/bash
 
 #SBATCH --job-name=

bin/path.sh

@@ -1,32 +1,2 @@
-#GPUE: Split Operator based GPU solver for Nonlinear 
-#Schrodinger Equation, Copyright (C) 2011-2015, Lee J. O'Riordan 
-#<loriordan@gmail.com>, Tadhg Morgan, Neil Crowley. All rights reserved.
-#Redistribution and use in source and binary forms, with or without 
-#modification, are permitted provided that the following conditions are 
-#met:
-#
-#1. Redistributions of source code must retain the above copyright 
-#notice, this list of conditions and the following disclaimer.
-#
-#2. Redistributions in binary form must reproduce the above copyright 
-#notice, this list of conditions and the following disclaimer in the 
-#documentation and/or other materials provided with the distribution.
-#
-#3. Neither the name of the copyright holder nor the names of its 
-#contributors may be used to endorse or promote products derived from 
-#this software without specific prior written permission.
-#
-#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS 
-#"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT 
-#LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A 
-#PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT 
-#HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, 
-#SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
-#TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
-#PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 
-#LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 
-#NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 
-#SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-#!/bin/bash
 export PATH=$PATH:/usr/local/cuda/bin:/usr/local/cuda/open64/bin
 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/lib64

bin/run.sh

@@ -1,32 +1,3 @@
-#GPUE: Split Operator based GPU solver for Nonlinear 
-#Schrodinger Equation, Copyright (C) 2011-2015, Lee J. O'Riordan 
-#<loriordan@gmail.com>, Tadhg Morgan, Neil Crowley. All rights reserved.
-#Redistribution and use in source and binary forms, with or without 
-#modification, are permitted provided that the following conditions are 
-#met:
-#
-#1. Redistributions of source code must retain the above copyright 
-#notice, this list of conditions and the following disclaimer.
-#
-#2. Redistributions in binary form must reproduce the above copyright 
-#notice, this list of conditions and the following disclaimer in the 
-#documentation and/or other materials provided with the distribution.
-#
-#3. Neither the name of the copyright holder nor the names of its 
-#contributors may be used to endorse or promote products derived from 
-#this software without specific prior written permission.
-#
-#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS 
-#"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT 
-#LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A 
-#PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT 
-#HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, 
-#SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
-#TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
-#PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 
-#LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 
-#NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 
-#SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #!/bin/bash
 i=0
 EMAIL=$1

bin/run_params.conf

@@ -1,33 +1,3 @@
-#GPUE: Split Operator based GPU solver for Nonlinear 
-#Schrodinger Equation, Copyright (C) 2011-2015, Lee J. O'Riordan 
-#<loriordan@gmail.com>, Tadhg Morgan, Neil Crowley. All rights reserved.
-#Redistribution and use in source and binary forms, with or without 
-#modification, are permitted provided that the following conditions are 
-#met:
-#
-#1. Redistributions of source code must retain the above copyright 
-#notice, this list of conditions and the following disclaimer.
-#
-#2. Redistributions in binary form must reproduce the above copyright 
-#notice, this list of conditions and the following disclaimer in the 
-#documentation and/or other materials provided with the distribution.
-#
-#3. Neither the name of the copyright holder nor the names of its 
-#contributors may be used to endorse or promote products derived from 
-#this software without specific prior written permission.
-#
-#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS 
-#"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT 
-#LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A 
-#PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT 
-#HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, 
-#SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
-#TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
-#PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 
-#LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 
-#NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 
-#SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-#
 # This files specifies the run-time parameters of the simulation(s).
 # Each new line represents a new simulation. The file run.sh reads each
 # line and creates a job until the maximum job number is reached.

bin/sanity_test.sh

@@ -1,33 +1,3 @@
-#GPUE: Split Operator based GPU solver for Nonlinear 
-#Schrodinger Equation, Copyright (C) 2011-2015, Lee J. O'Riordan 
-#<loriordan@gmail.com>, Tadhg Morgan, Neil Crowley. All rights reserved.
-#Redistribution and use in source and binary forms, with or without 
-#modification, are permitted provided that the following conditions are 
-#met:
-#
-#1. Redistributions of source code must retain the above copyright 
-#notice, this list of conditions and the following disclaimer.
-#
-#2. Redistributions in binary form must reproduce the above copyright 
-#notice, this list of conditions and the following disclaimer in the 
-#documentation and/or other materials provided with the distribution.
-#
-#3. Neither the name of the copyright holder nor the names of its 
-#contributors may be used to endorse or promote products derived from 
-#this software without specific prior written permission.
-#
-#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS 
-#"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT 
-#LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A 
-#PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT 
-#HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, 
-#SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
-#TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
-#PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 
-#LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 
-#NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 
-#SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
 #!/bin/bash
 FILE=$1
 COUNTER=0

bin/upload_vids.sh

@@ -1,32 +1,3 @@
-#GPUE: Split Operator based GPU solver for Nonlinear 
-#Schrodinger Equation, Copyright (C) 2011-2015, Lee J. O'Riordan 
-#<loriordan@gmail.com>, Tadhg Morgan, Neil Crowley. All rights reserved.
-#Redistribution and use in source and binary forms, with or without 
-#modification, are permitted provided that the following conditions are 
-#met:
-#
-#1. Redistributions of source code must retain the above copyright 
-#notice, this list of conditions and the following disclaimer.
-#
-#2. Redistributions in binary form must reproduce the above copyright 
-#notice, this list of conditions and the following disclaimer in the 
-#documentation and/or other materials provided with the distribution.
-#
-#3. Neither the name of the copyright holder nor the names of its 
-#contributors may be used to endorse or promote products derived from 
-#this software without specific prior written permission.
-#
-#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS 
-#"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT 
-#LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A 
-#PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT 
-#HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, 
-#SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
-#TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
-#PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 
-#LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 
-#NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 
-#SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #!/bin/bash
 OLDPWD=$(pwd)
 for i in $(cat ./ogg.txt | grep wfc);