diff --git a/Makefile b/Makefile deleted file mode 100644 index 7515d21401..0000000000 --- a/Makefile +++ /dev/null @@ -1,9 +0,0 @@ -%.html: %.md template.html metadata.yml assets/css/style.css - pandoc "$<" --template "$<" --metadata-file=metadata.yml | pandoc --template "template.html" --metadata-file=metadata.yml -c "assets/css/style.css" --write=html5 -o "$@" - @sed -i 's/<\/a> | |\n + + + + + + + + + + + +ESPResSo documentation | ESPResSo + + + + + + + + + + + + + + + +
+
+ View on GitHub + +

ESPResSo

+

Extensible Simulation Package for Research on Soft Matter Systems

+ +
+ Download this project as a tar.gz file +
+ +
+
+ + +
+
+ +

ESPResSo documentation

+

These GitHub Pages provide the user manuals of every ESPResSo release +since 4.0.0 as well as the user guide, tutorials and doxygen +documentation of the development branch of ESPResSo (updated during +nightly builds). When adding a new release, update the +latest_release variable in file +metadata.yml.

+

The material is generated automatically from ESPResSo sources +licensed under the GNU GPL 3, +unless stated otherwise. The theme files were obtained from +jekyll-theme-slate, available at pages-themes/slate and +licensed under the CC0 1.0 +Universal. The Jekyll template was generated with Jekyll 3.9.0.

+ +
+
+ + + + + + + diff --git a/Readme.md b/Readme.md deleted file mode 100644 index de464b91a1..0000000000 --- a/Readme.md +++ /dev/null @@ -1,13 +0,0 @@ -# ESPResSo documentation - -These GitHub Pages provide the user manuals of every ESPResSo release since -4.0.0 as well as the user guide, tutorials and doxygen documentation of the -development branch of ESPResSo (updated during nightly builds). When adding -a new release, update the `latest_release` variable in file `metadata.yml`. - -The material is generated automatically from ESPResSo sources licensed under -the [GNU GPL 3](https://www.gnu.org/licenses/gpl-3.0.en.html), unless stated -otherwise. The theme files were obtained from jekyll-theme-slate, available -at [pages-themes/slate](https://github.com/pages-themes/slate) and licensed -under the [CC0 1.0 Universal](http://creativecommons.org/publicdomain/zero/1.0/). -The Jekyll template was generated with Jekyll 3.9.0. diff --git a/index.html b/index.html new file mode 100644 index 0000000000..3905911f09 --- /dev/null +++ b/index.html @@ -0,0 +1,102 @@ + + + + + + + + + + + + +ESPResSo documentation | ESPResSo + + + + + + + + + + + + + + + +
+
+ View on GitHub + +

ESPResSo

+

Extensible Simulation Package for Research on Soft Matter Systems

+ +
+ Download this project as a tar.gz file +
+ +
+
+ + +
+
+ +

User guide

+ +

Tutorials

+ +

Development

+ +

Further documentation

+ + +
+
+ + + + + + + diff --git a/index.md b/index.md deleted file mode 100644 index 9950bed453..0000000000 --- a/index.md +++ /dev/null @@ -1,28 +0,0 @@ -# User guide - -* For [ESPResSo devel](doc/index.html) -$if(latest_release)$ -* For [ESPResSo $latest_release$](doc$latest_release$/index.html) -$endif$ - -# Tutorials - -* For [ESPResSo devel](tutorials.html) -$if(latest_release)$ -* For [ESPResSo $latest_release$](tutorials$latest_release$.html) -$endif$ -* [Online videos](videos.html) - -# Development - -* [Developer's Guide](https://github.com/espressomd/espresso/wiki) -* [Doxygen documentation](dox/index.html) - -# Further documentation - -* [Quickstart](quickstart.html) -* [Installation FAQ](https://github.com/espressomd/espresso/wiki/Installation-FAQ) -* [Filing bug reports](https://github.com/espressomd/espresso/wiki/Filing-bug-reports) -* [User's Mailing List](http://espressomd.org/wordpress/?page_id=79) - ([archives](http://lists.nongnu.org/archive/html/espressomd-users/)) -* [ESPResSo official website](http://espressomd.org/wordpress/) diff --git a/quickstart.html b/quickstart.html new file mode 100644 index 0000000000..c5f93a28f3 --- /dev/null +++ b/quickstart.html @@ -0,0 +1,82 @@ + + + + + + + + + + + + +ESPResSo documentation | ESPResSo + + + + + + + + + + + + + + + +
+
+ View on GitHub + +

ESPResSo

+

Extensible Simulation Package for Research on Soft Matter Systems

+ +
+ Download this project as a tar.gz file +
+ +
+
+ + +
+
+ +

Quickstart

+

New users should follow these steps to get ESPResSo +running:

+
    +
  1. Check the installation +requirements for your operating system
    2. +
  2. Download +ESPResSo
    3. +
  3. Build +ESPResSo
    4. +
  4. Run your script with ./pypresso my_script.py
    5. +
+ +
+
+ + + + + + + diff --git a/quickstart.md b/quickstart.md deleted file mode 100644 index 7f4dd3a658..0000000000 --- a/quickstart.md +++ /dev/null @@ -1,8 +0,0 @@ -# Quickstart - -New users should follow these steps to get **ESPResSo** running: - -1. Check the [installation requirements](doc/installation.html#requirements) for your operating system -2. [Download **ESPResSo**](https://espressomd.org/wordpress/download/) -3. [Build **ESPResSo**](doc/installation.html#quick-installation) -4. Run your script with `./pypresso my_script.py` diff --git a/tutorials.html b/tutorials.html new file mode 100644 index 0000000000..c057fe6cec --- /dev/null +++ b/tutorials.html @@ -0,0 +1,159 @@ + + + + + + + + + + + + +ESPResSo documentation | ESPResSo + + + + + + + + + + + + + + + +
+
+ View on GitHub + +

ESPResSo

+

Extensible Simulation Package for Research on Soft Matter Systems

+ +
+ Download this project as a tar.gz file +
+ +
+
+ + +
+
+ +

Tutorials

+

All tutorials are available as Jupyter notebooks and can be found in +doc/tutorials/ in the source code and on +GitHub.

+

+

Introductory tutorials

+ +

Intermediate tutorials

+ +

Advanced tutorials

+ + +
+
+ + + + + + + diff --git a/tutorials.py b/tutorials.py deleted file mode 100644 index 4365da5cf1..0000000000 --- a/tutorials.py +++ /dev/null @@ -1,41 +0,0 @@ -# -# Copyright (C) 2021 The ESPResSo project -# -# This file is part of ESPResSo. -# -# ESPResSo is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. -# -# ESPResSo is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program. If not, see . -# -""" -This script generates the landing page for tutorials. -""" - -import re - -marker_begin = '[comment]: # (Begin of tutorials landing page)' -marker_end = '[comment]: # (End of tutorials landing page)' - -with open('build/doc/tutorials/Readme.md') as f: - content = f.read() - -assert marker_begin in content, f'Readme.md is missing "{marker_begin}"' -assert marker_end in content, f'Readme.md is missing "{marker_end}"' -tutorial_descriptions = content.split(marker_begin)[1].split(marker_end)[0] -tutorial_descriptions = tutorial_descriptions.replace('.ipynb', '.html') -tutorial_descriptions = re.sub(r"\]\((?!https?://)", '](tutorials/', tutorial_descriptions) - -with open('tutorials_header.md', 'r') as f: - tutorial_header = f.read() - -with open('tutorials.md', 'w') as f: - f.write(tutorial_header + tutorial_descriptions) diff --git a/tutorials4.1.4.html b/tutorials4.1.4.html new file mode 100644 index 0000000000..2d6962e1a7 --- /dev/null +++ b/tutorials4.1.4.html @@ -0,0 +1,146 @@ + + + + + + + + + + + + +ESPResSo documentation | ESPResSo + + + + + + + + + + + + + + + +
+
+ View on GitHub + +

ESPResSo

+

Extensible Simulation Package for Research on Soft Matter Systems

+ +
+ Download this project as a tar.gz file +
+ +
+
+ + +
+
+ +

Tutorials for ESPResSo 4.1.4

+

All tutorials are available as Jupyter notebooks and can be found in +doc/tutorials/ in the source code and on +GitHub.

+

Introductory tutorials

+
    +
  • Simulate a simple Lennard-Jones liquid
    +Modelling of a single-component and a two-component Lennard-Jones +liquid.
    +Guide
    • +
  • Visualization
    +Using the online visualizers of ESPResSo.
    +Guide
    • +
+

Intermediate tutorials

+
    +
  • Charged systems
    +Modelling of charged systems such as ionic crystals.
    +Guide Part +1 Part +2
    • +
  • Ferrofluid
    +Modelling of a monolayer ferrofluid system.
    +Guide Part 1 +| Part +2 | Part +3
    • +
  • Lattice-Boltzmann
    +Simulations including hydrodynamic interactions using the +Lattice-Boltzmann method.
    +Guide Part +1 | Part +2 | Part +3 | Part +4
    • +
  • Raspberry electrophoresis
    +Extended objects in a Lattice-Boltzmann fluid, raspberry +particles.
    +Guide
    • +
+

Advanced tutorials

+
    +
  • Active matter
    +Modelling of self-propelling particles.
    +Guide | +Exercises +| Solutions
    • +
  • Electrokinetics
    +Modelling electrokinetics together with hydrodynamic interactions.
    +Guide
    • +
  • Constant pH method
    +Modelling an acid dissociation curve using the constant pH method.
    +Guide
    • +
  • Reaction Ensemble method
    +Modelling an acid dissociation curve using the reaction ensemble +method.
    +Guide
    • +
+ +
+
+ + + + + + + diff --git a/tutorials4.1.4.md b/tutorials4.1.4.md deleted file mode 100644 index 3b37b27d3b..0000000000 --- a/tutorials4.1.4.md +++ /dev/null @@ -1,55 +0,0 @@ -# Tutorials for ESPResSo 4.1.4 - -All tutorials are available as Jupyter notebooks and can be found in `doc/tutorials/` in the -source code and [on GitHub](https://github.com/espressomd/espresso/tree/4.1.4/doc/tutorials). - -#### Introductory tutorials - -* **Simulate a simple Lennard-Jones liquid** - Modelling of a single-component and a two-component Lennard-Jones liquid. - [Guide](tutorials4.1.4/01-lennard_jones/01-lennard_jones.html) -* **Visualization** - Using the online visualizers of ESPResSo. - [Guide](tutorials4.1.4/08-visualization/08-visualization.html) - -#### Intermediate tutorials - -* **Charged systems** - Modelling of charged systems such as ionic crystals. - Guide - [Part 1](tutorials4.1.4/02-charged_system/02-charged_system-1.html) - [Part 2](tutorials4.1.4/02-charged_system/02-charged_system-2.html) -* **Ferrofluid** - Modelling of a monolayer ferrofluid system. - Guide - [Part 1](tutorials4.1.4/11-ferrofluid/11-ferrofluid_part1.html) | - [Part 2](tutorials4.1.4/11-ferrofluid/11-ferrofluid_part2.html) | - [Part 3](tutorials4.1.4/11-ferrofluid/11-ferrofluid_part3.html) -* **Lattice-Boltzmann** - Simulations including hydrodynamic interactions using the Lattice-Boltzmann method. - Guide - [Part 1](tutorials4.1.4/04-lattice_boltzmann/04-lattice_boltzmann_part1.html) | - [Part 2](tutorials4.1.4/04-lattice_boltzmann/04-lattice_boltzmann_part2.html) | - [Part 3](tutorials4.1.4/04-lattice_boltzmann/04-lattice_boltzmann_part3.html) | - [Part 4](tutorials4.1.4/04-lattice_boltzmann/04-lattice_boltzmann_part4.html) -* **Raspberry electrophoresis** - Extended objects in a Lattice-Boltzmann fluid, raspberry particles. - [Guide](tutorials4.1.4/05-raspberry_electrophoresis/05-raspberry_electrophoresis.html) - -#### Advanced tutorials - -* **Active matter** - Modelling of self-propelling particles. - [Guide](tutorials4.1.4/06-active_matter/06-active_matter.html) | - [Exercises](https://github.com/espressomd/espresso/tree/4.1.4/doc/tutorials/06-active_matter/EXERCISES) | - [Solutions](https://github.com/espressomd/espresso/tree/4.1.4/doc/tutorials/06-active_matter/SOLUTIONS) -* **Electrokinetics** - Modelling electrokinetics together with hydrodynamic interactions. - [Guide](tutorials4.1.4/07-electrokinetics/07-electrokinetics.html) -* **Constant pH method** - Modelling an acid dissociation curve using the constant pH method. - [Guide](tutorials4.1.4/12-constant_pH/12-constant_pH.html) -* **Reaction Ensemble method** - Modelling an acid dissociation curve using the reaction ensemble method. - [Guide](tutorials4.1.4/10-reaction_ensemble/10-reaction_ensemble.html) - diff --git a/tutorials4.2.0.html b/tutorials4.2.0.html new file mode 100644 index 0000000000..a4a53d6df9 --- /dev/null +++ b/tutorials4.2.0.html @@ -0,0 +1,141 @@ + + + + + + + + + + + + +ESPResSo documentation | ESPResSo + + + + + + + + + + + + + + + +
+
+ View on GitHub + +

ESPResSo

+

Extensible Simulation Package for Research on Soft Matter Systems

+ +
+ Download this project as a tar.gz file +
+ +
+
+ + +
+
+ +

Tutorials

+

All tutorials are available as Jupyter notebooks and can be found in +doc/tutorials/ in the source code and on +GitHub.

+

Introductory tutorials

+
    +
  • Simulate a simple Lennard-Jones liquid
    +Modelling of a single-component and a two-component Lennard-Jones +liquid.
    +Guide
    • +
  • Error analysis
    +Statistical analysis of simulation results
    +Guide Part +1 | Part +2
    • +
  • Visualization
    +Using the online visualizers of ESPResSo.
    +Guide
    • +
+

Intermediate tutorials

+
    +
  • Charged systems
    +Modelling of ion condensation around a charged rod.
    +Guide
    • +
  • Langevin dynamics
    +Modelling of Brownian motion and measurement of diffusion +coefficients.
    +Guide
    • +
  • Ferrofluid
    +Modelling of a monolayer ferrofluid system.
    +Guide Part +1 | +Part +2 | +Part +3
    • +
  • Lattice-Boltzmann
    +Simulations including hydrodynamic interactions using the +Lattice-Boltzmann method.
    +Guide Part +1 | Part +2
    • +
  • Polymers
    +Modelling polymers with hydrodynamic interactions.
    +Guide
    • +
  • Raspberry electrophoresis
    +Extended objects in a Lattice-Boltzmann fluid, raspberry +particles.
    +Guide
    • +
+

Advanced tutorials

+
    +
  • Active matter
    +Modelling of self-propelling particles.
    +Guide
    • +
  • Electrokinetics
    +Modelling electrokinetics together with hydrodynamic interactions.
    +Guide
    • +
  • Constant pH method
    +Modelling an acid dissociation curve using the constant pH method.
    +Guide
    • +
+ +
+
+ + + + + + + diff --git a/tutorials4.2.0.md b/tutorials4.2.0.md deleted file mode 100644 index 454baff301..0000000000 --- a/tutorials4.2.0.md +++ /dev/null @@ -1,58 +0,0 @@ -# Tutorials - -All tutorials are available as Jupyter notebooks and can be found in `doc/tutorials/` in the -source code and [on GitHub](https://github.com/espressomd/espresso/tree/4.2.0/doc/tutorials). - - -### Introductory tutorials - -* **Simulate a simple Lennard-Jones liquid** - Modelling of a single-component and a two-component Lennard-Jones liquid. - [Guide](tutorials4.2.0/lennard_jones/lennard_jones.html) -* **Error analysis** - Statistical analysis of simulation results - Guide - [Part 1](tutorials4.2.0/error_analysis/error_analysis_part1.html) | - [Part 2](tutorials4.2.0/error_analysis/error_analysis_part2.html) -* **Visualization** - Using the online visualizers of ESPResSo. - [Guide](tutorials4.2.0/visualization/visualization.html) - -### Intermediate tutorials - -* **Charged systems** - Modelling of ion condensation around a charged rod. - [Guide](tutorials4.2.0/charged_system/charged_system.html) -* **Langevin dynamics** - Modelling of Brownian motion and measurement of diffusion coefficients. - [Guide](tutorials4.2.0/langevin_dynamics/langevin_dynamics.html) -* **Ferrofluid** - Modelling of a monolayer ferrofluid system. - Guide - [Part 1](tutorials4.2.0/ferrofluid/ferrofluid_part1.html) | - [Part 2](tutorials4.2.0/ferrofluid/ferrofluid_part2.html) | - [Part 3](tutorials4.2.0/ferrofluid/ferrofluid_part3.html) -* **Lattice-Boltzmann** - Simulations including hydrodynamic interactions using the Lattice-Boltzmann method. - Guide - [Part 1](tutorials4.2.0/lattice_boltzmann/lattice_boltzmann_theory.html) | - [Part 2](tutorials4.2.0/lattice_boltzmann/lattice_boltzmann_poiseuille_flow.html) -* **Polymers** - Modelling polymers with hydrodynamic interactions. - [Guide](tutorials4.2.0/polymers/polymers.html) -* **Raspberry electrophoresis** - Extended objects in a Lattice-Boltzmann fluid, raspberry particles. - [Guide](tutorials4.2.0/raspberry_electrophoresis/raspberry_electrophoresis.html) - -### Advanced tutorials - -* **Active matter** - Modelling of self-propelling particles. - [Guide](tutorials4.2.0/active_matter/active_matter.html) -* **Electrokinetics** - Modelling electrokinetics together with hydrodynamic interactions. - [Guide](tutorials4.2.0/electrokinetics/electrokinetics.html) -* **Constant pH method** - Modelling an acid dissociation curve using the constant pH method. - [Guide](tutorials4.2.0/constant_pH/constant_pH.html) - diff --git a/tutorials4.2.1.html b/tutorials4.2.1.html new file mode 100644 index 0000000000..07526c953a --- /dev/null +++ b/tutorials4.2.1.html @@ -0,0 +1,141 @@ + + + + + + + + + + + + +ESPResSo documentation | ESPResSo + + + + + + + + + + + + + + + +
+
+ View on GitHub + +

ESPResSo

+

Extensible Simulation Package for Research on Soft Matter Systems

+ +
+ Download this project as a tar.gz file +
+ +
+
+ + +
+
+ +

Tutorials

+

All tutorials are available as Jupyter notebooks and can be found in +doc/tutorials/ in the source code and on +GitHub.

+

Introductory tutorials

+
    +
  • Simulate a simple Lennard-Jones liquid
    +Modelling of a single-component and a two-component Lennard-Jones +liquid.
    +Guide
    • +
  • Error analysis
    +Statistical analysis of simulation results
    +Guide Part +1 | Part +2
    • +
  • Visualization
    +Using the online visualizers of ESPResSo.
    +Guide
    • +
+

Intermediate tutorials

+
    +
  • Charged systems
    +Modelling of ion condensation around a charged rod.
    +Guide
    • +
  • Langevin dynamics
    +Modelling of Brownian motion and measurement of diffusion +coefficients.
    +Guide
    • +
  • Ferrofluid
    +Modelling of a monolayer ferrofluid system.
    +Guide Part +1 | +Part +2 | +Part +3
    • +
  • Lattice-Boltzmann
    +Simulations including hydrodynamic interactions using the +Lattice-Boltzmann method.
    +Guide Part +1 | Part +2
    • +
  • Polymers
    +Modelling polymers with hydrodynamic interactions.
    +Guide
    • +
  • Raspberry electrophoresis
    +Extended objects in a Lattice-Boltzmann fluid, raspberry +particles.
    +Guide
    • +
+

Advanced tutorials

+
    +
  • Active matter
    +Modelling of self-propelling particles.
    +Guide
    • +
  • Electrokinetics
    +Modelling electrokinetics together with hydrodynamic interactions.
    +Guide
    • +
  • Constant pH method
    +Modelling an acid dissociation curve using the constant pH method.
    +Guide
    • +
+ +
+
+ + + + + + + diff --git a/tutorials4.2.1.md b/tutorials4.2.1.md deleted file mode 100644 index d7a704cb18..0000000000 --- a/tutorials4.2.1.md +++ /dev/null @@ -1,57 +0,0 @@ -# Tutorials - -All tutorials are available as Jupyter notebooks and can be found in `doc/tutorials/` in the -source code and [on GitHub](https://github.com/espressomd/espresso/tree/4.2.1/doc/tutorials). - - -### Introductory tutorials - -* **Simulate a simple Lennard-Jones liquid** - Modelling of a single-component and a two-component Lennard-Jones liquid. - [Guide](tutorials4.2.1/lennard_jones/lennard_jones.html) -* **Error analysis** - Statistical analysis of simulation results - Guide - [Part 1](tutorials4.2.1/error_analysis/error_analysis_part1.html) | - [Part 2](tutorials4.2.1/error_analysis/error_analysis_part2.html) -* **Visualization** - Using the online visualizers of ESPResSo. - [Guide](tutorials4.2.1/visualization/visualization.html) - -### Intermediate tutorials - -* **Charged systems** - Modelling of ion condensation around a charged rod. - [Guide](tutorials4.2.1/charged_system/charged_system.html) -* **Langevin dynamics** - Modelling of Brownian motion and measurement of diffusion coefficients. - [Guide](tutorials4.2.1/langevin_dynamics/langevin_dynamics.html) -* **Ferrofluid** - Modelling of a monolayer ferrofluid system. - Guide - [Part 1](tutorials4.2.1/ferrofluid/ferrofluid_part1.html) | - [Part 2](tutorials4.2.1/ferrofluid/ferrofluid_part2.html) | - [Part 3](tutorials4.2.1/ferrofluid/ferrofluid_part3.html) -* **Lattice-Boltzmann** - Simulations including hydrodynamic interactions using the Lattice-Boltzmann method. - Guide - [Part 1](tutorials4.2.1/lattice_boltzmann/lattice_boltzmann_theory.html) | - [Part 2](tutorials4.2.1/lattice_boltzmann/lattice_boltzmann_poiseuille_flow.html) -* **Polymers** - Modelling polymers with hydrodynamic interactions. - [Guide](tutorials4.2.1/polymers/polymers.html) -* **Raspberry electrophoresis** - Extended objects in a Lattice-Boltzmann fluid, raspberry particles. - [Guide](tutorials4.2.1/raspberry_electrophoresis/raspberry_electrophoresis.html) - -### Advanced tutorials - -* **Active matter** - Modelling of self-propelling particles. - [Guide](tutorials4.2.1/active_matter/active_matter.html) -* **Electrokinetics** - Modelling electrokinetics together with hydrodynamic interactions. - [Guide](tutorials4.2.1/electrokinetics/electrokinetics.html) -* **Constant pH method** - Modelling an acid dissociation curve using the constant pH method. - [Guide](tutorials4.2.1/constant_pH/constant_pH.html) diff --git a/tutorials4.2.2.html b/tutorials4.2.2.html new file mode 100644 index 0000000000..76237655ca --- /dev/null +++ b/tutorials4.2.2.html @@ -0,0 +1,141 @@ + + + + + + + + + + + + +ESPResSo documentation | ESPResSo + + + + + + + + + + + + + + + +
+
+ View on GitHub + +

ESPResSo

+

Extensible Simulation Package for Research on Soft Matter Systems

+ +
+ Download this project as a tar.gz file +
+ +
+
+ + +
+
+ +

Tutorials

+

All tutorials are available as Jupyter notebooks and can be found in +doc/tutorials/ in the source code and on +GitHub.

+

Introductory tutorials

+
    +
  • Simulate a simple Lennard-Jones liquid
    +Modelling of a single-component and a two-component Lennard-Jones +liquid.
    +Guide
    • +
  • Error analysis
    +Statistical analysis of simulation results
    +Guide Part +1 | Part +2
    • +
  • Visualization
    +Using the online visualizers of ESPResSo.
    +Guide
    • +
+

Intermediate tutorials

+
    +
  • Charged systems
    +Modelling of ion condensation around a charged rod.
    +Guide
    • +
  • Langevin dynamics
    +Modelling of Brownian motion and measurement of diffusion +coefficients.
    +Guide
    • +
  • Ferrofluid
    +Modelling of a monolayer ferrofluid system.
    +Guide Part +1 | +Part +2 | +Part +3
    • +
  • Lattice-Boltzmann
    +Simulations including hydrodynamic interactions using the +Lattice-Boltzmann method.
    +Guide Part +1 | Part +2
    • +
  • Polymers
    +Modelling polymers with hydrodynamic interactions.
    +Guide
    • +
  • Raspberry electrophoresis
    +Extended objects in a Lattice-Boltzmann fluid, raspberry +particles.
    +Guide
    • +
+

Advanced tutorials

+
    +
  • Active matter
    +Modelling of self-propelling particles.
    +Guide
    • +
  • Electrokinetics
    +Modelling electrokinetics together with hydrodynamic interactions.
    +Guide
    • +
  • Constant pH method
    +Modelling an acid dissociation curve using the constant pH method.
    +Guide
    • +
+ +
+
+ + + + + + + diff --git a/tutorials4.2.2.md b/tutorials4.2.2.md deleted file mode 100644 index 7d6fa2bfcd..0000000000 --- a/tutorials4.2.2.md +++ /dev/null @@ -1,58 +0,0 @@ -# Tutorials - -All tutorials are available as Jupyter notebooks and can be found in `doc/tutorials/` in the -source code and [on GitHub](https://github.com/espressomd/espresso/tree/python/doc/tutorials). - - -### Introductory tutorials - -* **Simulate a simple Lennard-Jones liquid** - Modelling of a single-component and a two-component Lennard-Jones liquid. - [Guide](tutorials4.2.2/lennard_jones/lennard_jones.html) -* **Error analysis** - Statistical analysis of simulation results - Guide - [Part 1](tutorials4.2.2/error_analysis/error_analysis_part1.html) | - [Part 2](tutorials4.2.2/error_analysis/error_analysis_part2.html) -* **Visualization** - Using the online visualizers of ESPResSo. - [Guide](tutorials4.2.2/visualization/visualization.html) - -### Intermediate tutorials - -* **Charged systems** - Modelling of ion condensation around a charged rod. - [Guide](tutorials4.2.2/charged_system/charged_system.html) -* **Langevin dynamics** - Modelling of Brownian motion and measurement of diffusion coefficients. - [Guide](tutorials4.2.2/langevin_dynamics/langevin_dynamics.html) -* **Ferrofluid** - Modelling of a monolayer ferrofluid system. - Guide - [Part 1](tutorials4.2.2/ferrofluid/ferrofluid_part1.html) | - [Part 2](tutorials4.2.2/ferrofluid/ferrofluid_part2.html) | - [Part 3](tutorials4.2.2/ferrofluid/ferrofluid_part3.html) -* **Lattice-Boltzmann** - Simulations including hydrodynamic interactions using the Lattice-Boltzmann method. - Guide - [Part 1](tutorials4.2.2/lattice_boltzmann/lattice_boltzmann_theory.html) | - [Part 2](tutorials4.2.2/lattice_boltzmann/lattice_boltzmann_poiseuille_flow.html) -* **Polymers** - Modelling polymers with hydrodynamic interactions. - [Guide](tutorials4.2.2/polymers/polymers.html) -* **Raspberry electrophoresis** - Extended objects in a Lattice-Boltzmann fluid, raspberry particles. - [Guide](tutorials4.2.2/raspberry_electrophoresis/raspberry_electrophoresis.html) - -### Advanced tutorials - -* **Active matter** - Modelling of self-propelling particles. - [Guide](tutorials4.2.2/active_matter/active_matter.html) -* **Electrokinetics** - Modelling electrokinetics together with hydrodynamic interactions. - [Guide](tutorials4.2.2/electrokinetics/electrokinetics.html) -* **Constant pH method** - Modelling an acid dissociation curve using the constant pH method. - [Guide](tutorials4.2.2/constant_pH/constant_pH.html) - diff --git a/tutorials_header.md b/tutorials_header.md deleted file mode 100644 index 0ff547becb..0000000000 --- a/tutorials_header.md +++ /dev/null @@ -1,4 +0,0 @@ -# Tutorials - -All tutorials are available as Jupyter notebooks and can be found in `doc/tutorials/` in the -source code and [on GitHub](https://github.com/espressomd/espresso/tree/python/doc/tutorials). diff --git a/videos.html b/videos.html new file mode 100644 index 0000000000..1c83f6a4c6 --- /dev/null +++ b/videos.html @@ -0,0 +1,97 @@ + + + + + + + + + + + + +ESPResSo documentation | ESPResSo + + + + + + + + + + + + + + + +
+
+ View on GitHub + +

ESPResSo

+

Extensible Simulation Package for Research on Soft Matter Systems

+ +
+ Download this project as a tar.gz file +
+ +
+
+ + +
+
+ +

Online videos

+

Video lectures about ESPResSo are available on +YouTube. Follow ESPResSo +Simulation Package channel to get the latest updates!

+ + +
+
+ + + + + + + diff --git a/videos.py b/videos.py deleted file mode 100644 index b138d6e75c..0000000000 --- a/videos.py +++ /dev/null @@ -1,37 +0,0 @@ -# -# Copyright (C) 2021 The ESPResSo project -# -# This file is part of ESPResSo. -# -# ESPResSo is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. -# -# ESPResSo is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program. If not, see . -# -""" -This script generates the landing page for video lectures. -""" - -marker_begin = '[comment]: # (Begin of videos landing page)' -marker_end = '[comment]: # (End of videos landing page)' - -with open('build/doc/tutorials/Readme.md') as f: - content = f.read() - -assert marker_begin in content, f'Readme.md is missing "{marker_begin}"' -assert marker_end in content, f'Readme.md is missing "{marker_end}"' -video_descriptions = content.split(marker_begin)[1].split(marker_end)[0] - -with open('videos_header.md', 'r') as f: - video_header = f.read() - -with open('videos.md', 'w') as f: - f.write(video_header + video_descriptions) diff --git a/videos_header.md b/videos_header.md deleted file mode 100644 index 8cf07502e3..0000000000 --- a/videos_header.md +++ /dev/null @@ -1,5 +0,0 @@ -# Online videos - -Video lectures about **ESPResSo** are available on YouTube. -Follow [ESPResSo Simulation Package](https://www.youtube.com/channel/UC6yzqhq2KrT-aDhPjcL-VNw/) -channel to get the latest updates!