Merge branch 'master' of https://github.com/lorenzo-rovigatti/oxDNA

docs/docs_requirements.txt

@@ -4,3 +4,4 @@ myst_parser==0.17.2
 docutils==0.16
 Jinja2<3.1
 sphinx-argparse>=0.3.1
+ipython>=7.26.0

docs/source/configurations.md

@@ -29,6 +29,10 @@ $\vec{a}_1$, $\vec{a}_2 = \vec{a}_3 \times \vec{a}_1$ and $\vec{a}_3$ define the
   * stacking site $ = \vec{r} + 0.34 \, \vec{a}_1$;
   * backbone repulsion site $ = \vec{r} - 0.34 \, \vec{a}_1 + 0.3408 \, \vec{a}_2$.
 
+```{warning}
+The position of the centre of mass of the nucleotides in oxDNA1 (0.4 length units away from the backbone site) is different from what the PhD thesis of T. E. Ouldridge specifies (0.24 length units away from the backbone site). This change has no effect on the thermodynamics, and the extent to which it changes the dynamics is arguably very small.
+```
+
 ```{note}
 When simulating very large structures the size of the trajectory files stored on disk may become very large. In this case it may be convenient to avoid printing the last six columns by setting `trajectory_print_momenta = false` in the input file, thus decreasing the size of the trajectory by $\approx 40\%$. 
 ```

docs/source/index.md

@@ -2,7 +2,7 @@
 
 oxDNA is a simulation code that was initially conceived as an implementation of the coarse-grained DNA model introduced by [T. E. Ouldridge, J. P. K. Doye and A. A. Louis](http://dx.doi.org/10.1063/1.3552946). It has been since reworked and it is now an extensible simulation+analysis framework. 
 
-oxDNA can perform both molecular dynamics (MD) and Monte Carlo (MC) simulations of the oxDNA and oxRNA models. MD simulations can be run on single CPUs or single CUDA-enabled GPUs, while MC simulations, which can only be run serially, can exploit the Virtual Move Monte Carlo algorithm[@VMMC] to greatly speed-up equilibration and sampling, and Umbrella Sampling biasing to efficiently obtain free-energy profiles. The package also features a Forward-Flux Sampling interface to study the kinetics of rare events, and makes it possible to alter the behaviour of the systems by adding *external forces* that can be used, for instance, to pull on or apply torques to strands or confine nucleotides within semi-planes or spheres.
+oxDNA can perform both molecular dynamics (MD) and Monte Carlo (MC) simulations of the oxDNA and oxRNA models. MD simulations can be run on single CPUs or single CUDA-enabled GPUs, while MC simulations, which can only be run serially, can exploit the Virtual Move Monte Carlo algorithm to greatly speed-up equilibration and sampling, and Umbrella Sampling biasing to efficiently obtain free-energy profiles. The package also features a Forward-Flux Sampling interface to study the kinetics of rare events, and makes it possible to alter the behaviour of the systems by adding *external forces* that can be used, for instance, to pull on or apply torques to strands or confine nucleotides within semi-planes or spheres.
 
 The package also includes `oxpy`, a Python library which makes it possible to control the behavior of the simulation using Python scripts. The repository contains examples that demonstrate how to leverage `oxpy` to write backends to run replica-exchange and well-tempered metadynamics simulations, which are popular techniques in modern molecular dynamics to improve sampling efficiency.
 

docs/source/install.md

@@ -28,6 +28,19 @@ At the end of the compilation three executables (*oxDNA*, *DNAnalysis* and *conf
 
 Compiling with Python bindings will also generate an `oxpy` package in the `build/oxpy` directory that can be imported in Python. Running `make install` will attempt to copy the package (as well as `oxDNA_analysis_tools`) to the `pip`'s module directory. The specific location will depend on your system's settings. We advise you to use [virtual environments](https://docs.python.org/3/tutorial/venv.html) (see *e.g.* [pipenv](https://docs.pipenv.org/)) to avoid conflicts with other packages and/or dependency and permission issues.
 
+### Updating a local copy
+
+If you cloned the repository to install oxDNA, your local copy can be updated with the following commands:
+
+```bash
+cd oxDNA        # enter the oxDNA folder
+git pull        # use git to synchronize your repo with the online one
+cd build        # enter the build folder (see above)
+make -j4        # compile the updated source
+```
+
+If you also want to update `oxpy` don't forget to run `make install` after the compilation.
+
 ### CMake options
 
 * `-DCUDA=ON` Enables CUDA support

src/Utilities/Utils.cpp

@@ -202,7 +202,7 @@ number get_temperature(std::string raw_T) {
 			}
 			break;
 		default:
-			throw oxDNAException("Unrecognizable temperature '%s'", raw_T);
+			throw oxDNAException("Unrecognizable temperature '%s'", raw_T.c_str());
 			/* no break */
 		}
 	}