diff --git a/html/src/README.rst b/html/src/README.rst
new file mode 100644
index 0000000..da2b10a
--- /dev/null
+++ b/html/src/README.rst
@@ -0,0 +1,23 @@
+Using GACODE
+============
+
+GACODE is free software released under the Apache 2.0 license. The developers of GACODE recommend the following **best practices**
+
+1. Compile/use the Software source code AS IS for publication purposes. You are welcome and encouraged to request changes through the `github issues system `_, to make code modifications for testing purposes, or to issue pull requests
+2. In published results or presentations, include the code name(s) and appropriate references in the table below
+
+.. csv-table:: **Appropriate References**
+ :header: "Physics code", "Topical Area", "Suitable citation"
+ :widths: 15,20,20
+
+ CGYRO, gyrokinetic simulation, `JCP2016 `_
+ GYRO, gyrokinetic simulation, `JCP2003 `_
+ NEO, neoclassical simulation, `PPCF2008 `_ | `PPCF2012 `_
+ TGLF, transport model, `POP2007 `_ | `POP2010 `_
+ TGYRO, profile evolution, `POP2009 `_
+
+Source code and documentation
+-----------------------------
+
+Source code is found in the `gacode repository `_.
+For technical documentation, please refer to the `GACODE website `_.
diff --git a/html/src/USER_AGREEMENT.txt b/html/src/USER_AGREEMENT.txt
deleted file mode 100644
index 23f8446..0000000
--- a/html/src/USER_AGREEMENT.txt
+++ /dev/null
@@ -1,27 +0,0 @@
-GACODE User Agreement
- Initial version (2013.07.02)
- Updated version (2018.11.06)
-
-GACODE development is funded by the US Department of Energy (DoE),
-and distribution is subject to DoE requirements and restrictions.
-
-By cloning, downloading or otherwise using the sources, the recipient
-agrees:
-
-1. The above copyright notice, this list of conditions and the
- following disclaimer shall be included in all copies or substantial
- portions of the Software.
-
-2. To compile/use the Software source code AS IS for publication
- purposes; users however are welcome to request changes, to make
- code modifications for testing purposes, or issue pull requests.
-
-3. If the authorized user’s copy of Software is made available to third
- parties, to ensure that the user agreement is followed by the third
- parties.
-
-4. To email a draft of any article/letter/note based on the Software
- use to gacode@fusion.gat.com
-
-5. To include in published results or presentations the code name(s)
- and appropriate references (see below)
diff --git a/html/src/cgyro.rst b/html/src/cgyro.rst
index 1842a6d..343c0c0 100644
--- a/html/src/cgyro.rst
+++ b/html/src/cgyro.rst
@@ -29,8 +29,8 @@ Simulation data courtesy Nathan Howard (MIT)
:width: 48 %
:alt: b1480
-Source Code
------------
+CGYRO Source Code
+-----------------
`CGYRO source code `_ is available at GitHub.
diff --git a/html/src/download.rst b/html/src/download.rst
deleted file mode 100644
index 605d716..0000000
--- a/html/src/download.rst
+++ /dev/null
@@ -1,27 +0,0 @@
-Download and user agreement
-===========================
-
-.. include:: USER_AGREEMENT.txt
- :literal:
-
-.. csv-table:: **Appropriate References**
- :header: "Physics code", "Topical Area", "Required citation"
- :widths: 15,20,20
-
- CGYRO, gyrokinetic simulation, ":cite:`candy:2016`"
- GYRO, gyrokinetic simulation, ":cite:`candy:2003`"
- NEO, neoclassical simulation, ":cite:`belli:2008,belli:2012`"
- TGLF, transport model, ":cite:`staebler:2007,staebler:2010`"
- TGYRO, profile evolution, ":cite:`candy:2009`"
-
-Source code
------------
-
-Sources are found in the `gacode repository `_ on GitHub.
-
-
-Repository access
------------------
-
-Get a (free) account at `GitHub `_ and send your GitHub username to **gacode-AT-fusion.gat.com** with a request for user or developer access.
-
diff --git a/html/src/index.rst b/html/src/index.rst
index 6889808..3d5d9a3 100644
--- a/html/src/index.rst
+++ b/html/src/index.rst
@@ -35,8 +35,7 @@ GACODE software works with the :ref:`input.gacode` format.
:maxdepth: 4
:caption: Software
- license
- download
+ README
setup
build
zreferences
diff --git a/html/src/license.rst b/html/src/license.rst
deleted file mode 100644
index 099a4b1..0000000
--- a/html/src/license.rst
+++ /dev/null
@@ -1,35 +0,0 @@
-GACODE License
-==============
-
-Copyright 2018, "Turbulence and Transport Group"
-
-Permission is hereby granted, free of charge, to any person obtaining a copy of this software
-and associated documentation files (the "Software"), to deal in the Software without restriction,
-including without limitation the rights to use, copy and/or modify the Software,
-and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
-
-1. The above copyright notice, this list of conditions and the following disclaimer
- shall be included in all copies or substantial portions of the Software.
-
-2. To compile/use the Software source code AS IS for publication
- purposes; users however are welcome to request changes, to make
- code modifications for testing purposes, or issue pull requests.
-
-3. If the authorized user’s copy of Software is made available to third
- parties, to ensure that the user agreement is followed by the third
- parties.
-
-4. To email a draft of any article/letter/note based on the Software use to
- gacode@fusion.gat.com
-
-5. To include in published results or presentations the proper code
- name(s) and appropriate references.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
-INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
-PARTICULAR PURPOSE AND NONINFRINGEMENT.
-IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
-DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-
-
diff --git a/html/src/references.bib b/html/src/references.bib
index 64870ca..ddd8017 100644
--- a/html/src/references.bib
+++ b/html/src/references.bib
@@ -82,11 +82,12 @@ @Article{ beer:1996b
@Article{ belli:2005,
author = {E.A. Belli and G.W. Hammett},
- title = {{{A numerical instability in an ADI algorithm for
- gyrokinetics}}},
+ title = {A numerical instability in an {{ADI}} algorithm for
+ gyrokinetics},
journal = cpc,
volume = 172,
pages = 119,
+ doi = {doi.org/10.1016/j.cpc.2005.06.007},
year = 2005
}
@@ -98,8 +99,8 @@ @Article{ belli:2008
journal = ppcf,
volume = 50,
pages = 095010,
- year = 2008,
- doi = {10.1088/0741-3335/50/9/095010}
+ doi = {doi.org/10.1088/0741-3335/50/9/095010},
+ year = 2008
}
@Article{ belli:2008b,
@@ -109,16 +110,18 @@ @Article{ belli:2008b
journal = pop,
volume = 15,
pages = 092303,
+ doi = {doi.org/10.1063/1.2972160},
year = 2008
}
@Article{ belli:2009,
author = {E.A. Belli and J. Candy},
- title = {{{An Eulerian method for the solution of the
- multi-species drift-kinetic equation}}},
+ title = {An {{Eulerian}} method for the solution of the
+ multi-species drift-kinetic equation},
journal = ppcf,
volume = 51,
pages = 075018,
+ doi = {doi.org/10.1088/0741-3335/51/7/075018},
year = 2009
}
@@ -129,68 +132,131 @@ @Article{ belli:2010
journal = pop,
volume = 17,
pages = 112314,
+ doi = {doi.org/10.1063/1.3495976},
year = 2010
}
@Article{ belli:2012,
author = {E.A. Belli and J. Candy},
- title = {{{Full linearized Fokker-Planck collisions in
- neoclassical transport simulations}}},
+ title = {Full linearized {{Fokker-Planck}} collisions in
+ neoclassical transport simulations},
journal = ppcf,
volume = 54,
pages = 015015,
+ doi = {doi.org/10.1088/0741-3335/54/1/015015},
year = 2012
}
@Article{ belli:2014,
author = {E.A. Belli and J. Candy},
- title = {{{Limitations of bootstrap current models}}},
+ title = {Limitations of bootstrap current models},
journal = ppcf,
volume = 56,
pages = 045006,
+ doi = {doi.org/10.1088/0741-3335/56/4/045006},
year = 2014
}
-@Article{ belli:2014b,
+@Article{ belli:2014b,
author = {E.A. Belli and J. Candy},
- title = {{{Pfirsch-Schl\"uter Neoclassical Impurity Transport
- in a Rotating Plasma}}},
+ title = {{{Pfirsch-Schl\"uter}} Neoclassical Impurity
+ Transport in a Rotating Plasma},
journal = ppcf,
volume = 56,
pages = 124005,
+ doi = {doi.org/10.1088/0741-3335/56/12/124002},
year = 2014
}
-@Article{ belli:2015,
+@Article{ belli:2015,
author = {E.A. Belli and J. Candy},
- title = {{{Neoclassical transport in toroidal plasmas with
- nonaxisymmetric flux surfaces}}},
+ title = {Neoclassical transport in toroidal plasmas with
+ nonaxisymmetric flux surfaces},
journal = ppcf,
volume = 57,
pages = 054012,
+ doi = {doi.org/10.1088/0741-3335/57/5/054012},
year = 2015
}
-@Article{ belli:2017,
+@Article{ belli:2017,
author = {E.A. Belli and J. Candy},
title = {Implications of advanced collision operators for
gyrokinetic simulation},
journal = ppcf,
volume = 59,
pages = 045005,
+ doi = {doi.org/10.1088/1361-6587/aa5c94},
year = 2017
}
-@Article{ belli:2018,
+@Article{ belli:2018,
author = {E.A. Belli and J. Candy},
title = {Impact of centrifugal drifts on ion turbulent
transport},
journal = pop,
volume = 25,
pages = 032301,
+ doi = {doi.org/10.1063/1.5020298},
year = 2018
}
+@Article{ belli:2019,
+ author = {E.A. Belli and J. Candy and R.E. Waltz},
+ title = {Reversal of turbulent {{GyroBohm}} isotope scaling
+ due to nonadiabatic electron drive},
+ journal = pop,
+ volume = 26,
+ pages = 082305,
+ doi = {doi.org/10.1063/1.5110401},
+ year = 2019
+}
+
+@Article{ belli:2020,
+ author = {E.A. Belli and J. Candy and R.E. Waltz},
+ title = {Reversal of simple hydrogenic isotope scaling laws
+ in tokamak edge turbulence},
+ journal = prl,
+ volume = 125,
+ pages = 015001,
+ doi = {doi.org/10.1103/PhysRevLett.125.015001},
+ year = 2020
+}
+
+@Article{ belli:2021,
+ author = {E.A. Belli and J. Candy},
+ title = {Asymmetry between deuterium and tritium turbulent
+ particle flows},
+ journal = pop,
+ volume = 28,
+ pages = 062301,
+ doi = {doi.org/10.1063/5.0048620},
+ year = 2021
+}
+
+@Article{ belli:2022,
+ author = {E.A. Belli and J. Candy and I. Sfiligoi and
+ F. W\"urthwein},
+ title = {Comparing single-node and multi-node performance of
+ an important fusion {{HPC}} code benchmark},
+ journal = {PEARC '22: Practice and Experience in Advanced
+ Research Computing},
+ pages = 1,
+ doi = {doi.org/10.1145/3491418.3535130},
+ year = 2022
+}
+
+@article{belli:2023,
+ author = {E.A. Belli and J. Candy and I. Sfiligoi},
+ journal = {Plasma Phys. Control. Fusion},
+ pages = 024001,
+ title = {Spectral transition of multiscale turbulence in the
+ tokamak pedestal},
+ volume = 65,
+ year = 2023,
+ doi = {doi.org/10.1088/1361-6587/aca9fa},
+}
+
@Article{ bravenec:2011,
author = {R.V. Bravenec and J. Candy and M. Barnes and
C. Holland},
@@ -202,55 +268,55 @@ @Article{ bravenec:2011
year = 2011
}
-@Article{ candy:1997,
- author = {J. Candy and D. Borba and H.L. Berk and
- G.T.A. Huysmans and W. Kerner},
- title = {Nonlinear interaction of fast particles with
- {{Alfv\en}} waves in toroidal plasmas},
- journal = pop,
- volume = 4,
- pages = 2597,
- year = 1997
-}
-
@Article{ candy:2003,
author = {J. Candy and R.E. Waltz},
- title = {{{An Eulerian gyrokinetic-Maxwell solver}}},
+ title = {An {E}ulerian gyrokinetic-{M}axwell solver},
journal = jcp,
volume = 186,
pages = 545,
- year = 2003,
- doi = {10.1016/S0021-9991(03)00079-2}
+ doi = {doi.org/10.1016/S0021-9991(03)00079-2},
+ year = 2003
}
@Article{ candy:2003b,
author = {J. Candy and R.E. Waltz},
- title = {Anomalous Transport Scaling in the {{DIII-D}}
- Tokamak Matched by Supercomputer Simulation},
+ title = {Anomalous Transport in the {{DIII-D}} Tokamak
+ Matched by Supercomputer Simulation},
journal = prl,
volume = 91,
- pages = 045001,
- year = 2003,
- doi = {10.1103/PhysRevLett.91.045001}
+ pages = {045001-1},
+ doi = {doi.org/10.1103/PhysRevLett.91.045001},
+ year = 2003
}
-@Article{ candy:2004a,
+@Article{ candy:2004,
author = {J. Candy and R.E. Waltz and W. Dorland},
title = {The local limit of global gyrokinetic simulations},
journal = pop,
volume = 11,
pages = {L25},
year = 2004,
- doi = {10.1063/1.1695358}
+ doi = {doi.org/10.1063/1.1695358}
+}
+
+@Article{ candy:2004a,
+ author = {J. Candy and R.E. Waltz and W. Dorland},
+ title = {The local limit of global gyrokinetic simulations},
+ journal = pop,
+ volume = 11,
+ pages = {L25},
+ doi = {doi.org/10.1063/1.1695358},
+ year = 2004
}
@Article{ candy:2004b,
author = {J. Candy and R.E. Waltz and M.N. Rosenbluth},
title = {Smooothness of turbulent transport across a
- {{minimum-q}} surface},
+ {{minimum-$q$}} surface},
journal = pop,
volume = 11,
pages = 1879,
+ doi = {doi.org/10.1063/1.1689967},
year = 2004
}
@@ -261,6 +327,7 @@ @Article{ candy:2005
journal = pop,
volume = 12,
pages = 072307,
+ doi = {doi.org/10.1063/1.1954123},
year = 2005
}
@@ -272,6 +339,7 @@ @Article{ candy:2006
journal = pop,
volume = 13,
pages = 032310,
+ doi = {doi.org/10.1063/1.2184069},
year = 2006
}
@@ -282,6 +350,7 @@ @Article{ candy:2006b
journal = pop,
volume = 13,
pages = 074501,
+ doi = {doi.org/10.1063/1.2220536},
year = 2006
}
@@ -301,6 +370,7 @@ @Article{ candy:2007
journal = ppcf,
volume = 49,
pages = 1209,
+ doi = {doi.org/10.1088/0741-3335/49/8/008},
year = 2007
}
@@ -312,6 +382,7 @@ @Article{ candy:2007b
journal = jpcon,
volume = 78,
pages = 012008,
+ doi = {doi.org/10.1088/1742-6596/78/1/012008},
year = 2007
}
@@ -323,6 +394,7 @@ @Article{ candy:2009
journal = pop,
volume = 16,
pages = 060704,
+ doi = {doi.org/10.1063/1.3167820},
year = 2009
}
@@ -333,6 +405,7 @@ @Article{ candy:2009b
journal = ppcf,
volume = 51,
pages = 105009,
+ doi = {doi.org/10.1088/0741-3335/51/10/105009},
year = 2009
}
@@ -351,47 +424,60 @@ @Article{ candy:2011
journal = prl,
volume = 106,
pages = 235003,
+ doi = {doi.org/10.1103/PhysRevLett.106.235003},
year = 2011
}
-@Article{ candy:2013,
+@Article{ candy:2013,
author = {J. Candy},
title = {Turbulent energy exchange: Calculation and relevance
for profile prediction},
- journal = POP,
+ journal = pop,
volume = 20,
pages = 082503,
+ doi = {doi.org/10.1063/1.4817820},
year = 2013
}
@Article{ candy:2015,
author = {J. Candy and E.A. Belli},
- title = {{{Nonaxisymmetric local magnetostatic equilibrium}}},
+ title = {Nonaxisymmetric local magnetostatic equilibrium},
journal = jpp,
volume = 81,
pages = 905810323,
+ doi = {doi.org/10.1017/S0022377815000264},
+ year = 2015
+}
+
+@Article{ candy:2015b,
+ author = {J. Candy and G. Staebler and C.H. Holland and P.B.
+ Snyder},
+ title = {{TGLF Recalibration for ITER Standard Case
+ Parameters}},
+ journal = {General Atomics Internal Report},
+ volume = {GA-A28239},
year = 2015
}
@Article{ candy:2016,
author = {J. Candy and E.A. Belli and R.V. Bravenec},
- title = {{{A high-accuracy Eulerian gyrokinetic solver for
- collisional plasmas}}},
+ title = {A high-accuracy {{Eulerian}} gyrokinetic solver for
+ collisional plasmas},
journal = jcp,
volume = 324,
pages = 73,
- year = 2016,
- doi = {10.1016/j.jcp.2016.07.039}
+ doi = {doi.org/10.1016/j.jcp.2016.07.039},
+ year = 2016
}
@Article{ candy:2018,
author = {J. Candy and E.A. Belli},
- title = {{{Spectral treatment of gyrokinetic shear flow}}},
+ title = {Spectral treatment of gyrokinetic shear flow},
journal = jcp,
volume = 356,
pages = 448,
- year = 2018,
- doi = {10.1016/j.jcp.2017.12.020}
+ doi = {doi.org/10.1016/j.jcp.2017.12.020},
+ year = 2018
}
@Article{ candy:2019,
@@ -399,11 +485,11 @@ @Article{ candy:2019
K. Hallatschek and C. Holland and N. Howard and
E.D`Azevedo},
title = {Multiscale-optimized plasma turbulence simulation on
- petascale architechtures},
+ petascale architectures},
journal = cf,
volume = 188,
pages = 125,
- doi = {10.1016/j.compfluid.2019.04.016},
+ doi = {doi.org/10.1016/j.compfluid.2019.04.016},
year = 2019
}
@@ -413,7 +499,7 @@ @Article{ candy:2020
journal = ppcf,
volume = 62,
pages = 042001,
- doi = {10.1088/1361-6587/ab759c},
+ doi = {doi.org/10.1088/1361-6587/ab759c},
year = 2020
}