docs: secure and modernize http external reference links to https

doc/blog/epidemiology-final.md

@@ -45,7 +45,7 @@ Clear separation between the frameworks and a flexible workflow allows the user
 
 As the OpenLB simulation is time and resource consuming we did spent a large amount of time in researching aerosol parametrization methods that should allow much faster evaluation of the viral loads in the observed spaces. However, during the this of this project we did not find a proper parametrization code.
 
-The technical paper and all codes of this project can be found in the following Zenodo online repository: [http://doi.org/10.5281/zenodo.5534456](http://doi.org/10.5281/zenodo.5534456).
+The technical paper and all codes of this project can be found in the following Zenodo online repository: [https://doi.org/10.5281/zenodo.5534456](https://doi.org/10.5281/zenodo.5534456).
 
 This work is sponsored by a grant from the [European Open Science Cloud](https://www.eoscsecretariat.eu) (EOSC).
 EOSCsecretariat.eu has received funding from the European Union's Horizon Programme call H2020-INFRAEOSC-05-2018-2019, grant Agreement number 831644.

doc/blog/epidemiology.md

@@ -7,7 +7,7 @@ meta_description: ""
 
 In addition to cellular studies (tumour growth modelling or neural development), BioDynaMo can be used to simulate different systems, such as groups of people and their interactions. As BioDynaMo has been developed to simulate billions of cells, it should be able to handle fairly easily simulations of up to millions of people.
 
-In one of these types of simulation, BioDynaMo is used to study the spreading of viruses in indoor spaces, specifically COVID-19 in droplets and aerosols. We are investigating several scenarios, such as public transportation (bus, metro) and buildings (supermarkets, offices). In these simulations BioDynaMo is in charge of simulating the behaviour and characteristics of individuals, while the [ROOT](http://root.cern) geometrical modeller is used to define the precise environmental geometry. Each individual can then independently move around in these environments where infected individuals can possibly contaminate healthy ones through the spreading of droplets and aerosols. By studying different geometries, airflows, distancing, masks and other parameters we can hopefully determine which environments are best to avoid virus buildup and prevent people from getting infected.
+In one of these types of simulation, BioDynaMo is used to study the spreading of viruses in indoor spaces, specifically COVID-19 in droplets and aerosols. We are investigating several scenarios, such as public transportation (bus, metro) and buildings (supermarkets, offices). In these simulations BioDynaMo is in charge of simulating the behaviour and characteristics of individuals, while the [ROOT](https://root.cern) geometrical modeller is used to define the precise environmental geometry. Each individual can then independently move around in these environments where infected individuals can possibly contaminate healthy ones through the spreading of droplets and aerosols. By studying different geometries, airflows, distancing, masks and other parameters we can hopefully determine which environments are best to avoid virus buildup and prevent people from getting infected.
 
 We are working closely together with the epidemiological department of the University of Geneva to make sure that our simulations reflect correctly the many observed cases of virus outbreaks in closed spaces.
 

doc/dev_guide/code_quality.md

@@ -42,11 +42,11 @@ More information:
 
 ### Git Workflow
 
-We are following the Git workflow proposed by Vincent Driessen in his blog post: [A successful Git branching model](http://nvie.com/posts/a-successful-git-branching-model/) with the modification that his `develop` branch is our `master` branch.
+We are following the Git workflow proposed by Vincent Driessen in his blog post: [A successful Git branching model](https://nvie.com/posts/a-successful-git-branching-model/) with the modification that his `develop` branch is our `master` branch.
 
 ### Git Commit Message
 
-Taken from a great blog post from [Chris Beams](http://chris.beams.io/posts/git-commit/)
+Taken from a great blog post from [Chris Beams](https://chris.beams.io/posts/git-commit/)
 
 1. Separate subject from body with a blank line
 2. Capitalize the subject line

doc/user_guide/faq.md

@@ -42,4 +42,4 @@ real_t A = pow(25.0 , 0.5);
 
 ## General C ++ tutorial
 
-If you are unfamiliar with the basics of the C++ language in general or simply need a refresher there are a plethora of useful guides online. For example cplusplus provides and excellent guide http://www.cplusplus.com/doc/tutorial/ , from entry level to more adept concepts for C++ including compilation, data types and much more.
+If you are unfamiliar with the basics of the C++ language in general or simply need a refresher there are a plethora of useful guides online. For example cplusplus provides and excellent guide https://cplusplus.com/doc/tutorial/ , from entry level to more adept concepts for C++ including compilation, data types and much more.

third_party/nanoflann/nanoflann.hpp

@@ -40,7 +40,7 @@
  *  See:
  *   - <a href="modules.html" >C++ API organized by modules</a>
  *   - <a href="https://github.com/jlblancoc/nanoflann" >Online README</a>
- *   - <a href="http://jlblancoc.github.io/nanoflann/" >Doxygen
+ *   - <a href="https://jlblancoc.github.io/nanoflann/" >Doxygen
  * documentation</a>
  */
 

third_party/opencl/cl2.hpp

@@ -55,7 +55,7 @@
  *
  *   Doxygen documentation for this header is available here:
  *
- *       http://khronosgroup.github.io/OpenCL-CLHPP/
+ *       https://khronosgroup.github.io/OpenCL-CLHPP/
  *
  *   The latest version of this header can be found on the GitHub releases page:
  *