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6 changes: 3 additions & 3 deletions _sources/input.md.txt
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Expand Up @@ -36,7 +36,7 @@ These are the options that control the overall behaviour of the simulation and o
* `time_scale = linear/log_lin`: a linear time_scale will make oxDNA print linearly-spaced configurations. a log_lin will make it print linearly-spaced cycles of logarithmically-spaced configurations.
* `print_conf_interval = <int>`: if the time scale is linear, this is the number of time steps between the outputing of configurations, otherwise this is just the first point of the logarithmic part of the log_lin time scale.
* `print_energy_every = <int>`: number of time steps between the outputing of the energy (and of the other default observables such as acceptance ratios in Monte Carlo simulations).
* `[interaction_type = DNA|DNA2|RNA|RNA2|DRH|LJ|...]`: Particle-particle interaction of choice. Check the documentation relative to the specific interaction for more details and the supported interaction-specific options. Defaults to `DNA`.
* `[interaction_type = DNA|DNA2|RNA|RNA2|NA|LJ|...]`: Particle-particle interaction of choice. Check the documentation relative to the specific interaction for more details and the supported interaction-specific options. Defaults to `DNA`.
* `[max_io = <float>]`: the maximum rate at which the output is printed, in MB/s. This is a useful option to avoid filling up the disk too quickly. Increase the default value (1 MB/s) at your own risk!
* `[fix_diffusion = <bool>]`: if true, particles that leave the simulation box are brought back in via periodic boundary conditions. Defaults to `true`.
* `[fix_diffusion_every = <int>]`: number of time steps every which the diffusion is fixed. Used only if `fix_diffusion = true`, defaults to 100000 ({math}`10^5`).
Expand Down Expand Up @@ -173,12 +173,12 @@ The following options control the behaviour of MC simulations.
* `[mismatch_repulsion = <bool>]`: if `true`, add a repulsion between mismatches. Defaults to `false`.
* `[mismatch_repulsion_strength = <float>]`: set the strength of the repulsion between mismatches. Used only if `mismatch_repulsion = true`, defaults to `1`.

## Options for `DRH` simulations
## Options for `NA` simulations

* `[use_average_seq = <bool>]`: use the average-sequence parameters. Defaults to `true`.
* `[seq_dep_file_DNA = <path>]`: path to the location of the file containing the DNA sequence-dependent parameters. Mandatory if `use_average_seq = false`.
* `[seq_dep_file_RNA = <path>]`: path to the location of the file containing the DNA sequence-dependent parameters. Mandatory if `use_average_seq = false`.
* `[seq_dep_file_DRH = <path>]`: path to the location of the file containing the DNA-RNA sequence-dependent parameters. Mandatory if `use_average_seq = false`.
* `[seq_dep_file_NA = <path>]`: path to the location of the file containing the DNA-RNA sequence-dependent parameters. Mandatory if `use_average_seq = false`.


## Options for `LJ` (Lennard-Jones) simulations
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4 changes: 4 additions & 0 deletions _sources/usage.md.txt
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Expand Up @@ -36,6 +36,10 @@ confGenerator <input_file> <box|density> [key1=value1] [key2=value2] [...]

In addition to the input file, *confGenerator* takes another mandatory argument whose meaning depends on its value. It specifies the simulation box if it is a single number larger than 2 (in which case the simulation box is assumed to be cubic) or if it is an x-separated triplet of numbers that specify the length of the edges of the box (which is assumed to be a cuboid). By contrast, the second mandatory argument is interpreted as a number density if it is smaller than 2.

```{warning}
This tool generates a configuration by inserting one particle (nucleotide) at a time, provided that its interaction energy does not exceed some predetermined value (which can be set with `energy_threshold`). It does so by placing each nucleotide randomly, but close to its neighbours, so that it is not too unlikely to end up with a non-overstretched bond. Unfortunately, this procedure makes it extremely unlikely to successfully generate a circular strand.
```

The following examples generate random initial configurations in a cubic box of size 10, in a cuboid of sizes 10x5x15 and in a cubic box with edge $L$ such that $N / L^3 = 0.1$, where $N$ is the total number of nucleotides specified in the topology file.

```text
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2 changes: 1 addition & 1 deletion index.html
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Expand Up @@ -202,7 +202,7 @@ <h1>oxDNA<a class="headerlink" href="#oxdna" title="Permalink to this headline">
<li class="toctree-l2"><a class="reference internal" href="input.html#options-for-dna2-simulations">Options for <code class="docutils literal notranslate"><span class="pre">DNA2</span></code> simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="input.html#options-for-rna-and-rna2-simulations">Options for <code class="docutils literal notranslate"><span class="pre">RNA</span></code> and <code class="docutils literal notranslate"><span class="pre">RNA2</span></code> simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="input.html#options-for-rna2-simulations">Options for <code class="docutils literal notranslate"><span class="pre">RNA2</span></code> simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="input.html#options-for-drh-simulations">Options for <code class="docutils literal notranslate"><span class="pre">DRH</span></code> simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="input.html#options-for-na-simulations">Options for <code class="docutils literal notranslate"><span class="pre">NA</span></code> simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="input.html#options-for-lj-lennard-jones-simulations">Options for <code class="docutils literal notranslate"><span class="pre">LJ</span></code> (Lennard-Jones) simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="input.html#forward-flux-sampling-ffs-options">Forward Flux Sampling (FFS) options</a></li>
<li class="toctree-l2"><a class="reference internal" href="input.html#dnanalysis-options"><em>DNAnalysis</em> options</a></li>
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Expand Up @@ -103,7 +103,7 @@
<li class="toctree-l2"><a class="reference internal" href="#options-for-dna2-simulations">Options for <code class="docutils literal notranslate"><span class="pre">DNA2</span></code> simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="#options-for-rna-and-rna2-simulations">Options for <code class="docutils literal notranslate"><span class="pre">RNA</span></code> and <code class="docutils literal notranslate"><span class="pre">RNA2</span></code> simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="#options-for-rna2-simulations">Options for <code class="docutils literal notranslate"><span class="pre">RNA2</span></code> simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="#options-for-drh-simulations">Options for <code class="docutils literal notranslate"><span class="pre">DRH</span></code> simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="#options-for-na-simulations">Options for <code class="docutils literal notranslate"><span class="pre">NA</span></code> simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="#options-for-lj-lennard-jones-simulations">Options for <code class="docutils literal notranslate"><span class="pre">LJ</span></code> (Lennard-Jones) simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="#forward-flux-sampling-ffs-options">Forward Flux Sampling (FFS) options</a></li>
<li class="toctree-l2"><a class="reference internal" href="#dnanalysis-options"><em>DNAnalysis</em> options</a></li>
Expand Down Expand Up @@ -230,7 +230,7 @@ <h2>Core options<a class="headerlink" href="#core-options" title="Permalink to t
<li><p><code class="docutils literal notranslate"><span class="pre">time_scale</span> <span class="pre">=</span> <span class="pre">linear/log_lin</span></code>: a linear time_scale will make oxDNA print linearly-spaced configurations. a log_lin will make it print linearly-spaced cycles of logarithmically-spaced configurations.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">print_conf_interval</span> <span class="pre">=</span> <span class="pre">&lt;int&gt;</span></code>: if the time scale is linear, this is the number of time steps between the outputing of configurations, otherwise this is just the first point of the logarithmic part of the log_lin time scale.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">print_energy_every</span> <span class="pre">=</span> <span class="pre">&lt;int&gt;</span></code>: number of time steps between the outputing of the energy (and of the other default observables such as acceptance ratios in Monte Carlo simulations).</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">[interaction_type</span> <span class="pre">=</span> <span class="pre">DNA|DNA2|RNA|RNA2|DRH|LJ|...]</span></code>: Particle-particle interaction of choice. Check the documentation relative to the specific interaction for more details and the supported interaction-specific options. Defaults to <code class="docutils literal notranslate"><span class="pre">DNA</span></code>.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">[interaction_type</span> <span class="pre">=</span> <span class="pre">DNA|DNA2|RNA|RNA2|NA|LJ|...]</span></code>: Particle-particle interaction of choice. Check the documentation relative to the specific interaction for more details and the supported interaction-specific options. Defaults to <code class="docutils literal notranslate"><span class="pre">DNA</span></code>.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">[max_io</span> <span class="pre">=</span> <span class="pre">&lt;float&gt;]</span></code>: the maximum rate at which the output is printed, in MB/s. This is a useful option to avoid filling up the disk too quickly. Increase the default value (1 MB/s) at your own risk!</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">[fix_diffusion</span> <span class="pre">=</span> <span class="pre">&lt;bool&gt;]</span></code>: if true, particles that leave the simulation box are brought back in via periodic boundary conditions. Defaults to <code class="docutils literal notranslate"><span class="pre">true</span></code>.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">[fix_diffusion_every</span> <span class="pre">=</span> <span class="pre">&lt;int&gt;]</span></code>: number of time steps every which the diffusion is fixed. Used only if <code class="docutils literal notranslate"><span class="pre">fix_diffusion</span> <span class="pre">=</span> <span class="pre">true</span></code>, defaults to 100000 (<span class="math notranslate nohighlight">\(10^5\)</span>).</p></li>
Expand Down Expand Up @@ -387,13 +387,13 @@ <h2>Options for <code class="docutils literal notranslate"><span class="pre">RNA
<li><p><code class="docutils literal notranslate"><span class="pre">[mismatch_repulsion_strength</span> <span class="pre">=</span> <span class="pre">&lt;float&gt;]</span></code>: set the strength of the repulsion between mismatches. Used only if <code class="docutils literal notranslate"><span class="pre">mismatch_repulsion</span> <span class="pre">=</span> <span class="pre">true</span></code>, defaults to <code class="docutils literal notranslate"><span class="pre">1</span></code>.</p></li>
</ul>
</div>
<div class="section" id="options-for-drh-simulations">
<h2>Options for <code class="docutils literal notranslate"><span class="pre">DRH</span></code> simulations<a class="headerlink" href="#options-for-drh-simulations" title="Permalink to this headline"></a></h2>
<div class="section" id="options-for-na-simulations">
<h2>Options for <code class="docutils literal notranslate"><span class="pre">NA</span></code> simulations<a class="headerlink" href="#options-for-na-simulations" title="Permalink to this headline"></a></h2>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">[use_average_seq</span> <span class="pre">=</span> <span class="pre">&lt;bool&gt;]</span></code>: use the average-sequence parameters. Defaults to <code class="docutils literal notranslate"><span class="pre">true</span></code>.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">[seq_dep_file_DNA</span> <span class="pre">=</span> <span class="pre">&lt;path&gt;]</span></code>: path to the location of the file containing the DNA sequence-dependent parameters. Mandatory if <code class="docutils literal notranslate"><span class="pre">use_average_seq</span> <span class="pre">=</span> <span class="pre">false</span></code>.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">[seq_dep_file_RNA</span> <span class="pre">=</span> <span class="pre">&lt;path&gt;]</span></code>: path to the location of the file containing the DNA sequence-dependent parameters. Mandatory if <code class="docutils literal notranslate"><span class="pre">use_average_seq</span> <span class="pre">=</span> <span class="pre">false</span></code>.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">[seq_dep_file_DRH</span> <span class="pre">=</span> <span class="pre">&lt;path&gt;]</span></code>: path to the location of the file containing the DNA-RNA sequence-dependent parameters. Mandatory if <code class="docutils literal notranslate"><span class="pre">use_average_seq</span> <span class="pre">=</span> <span class="pre">false</span></code>.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">[seq_dep_file_NA</span> <span class="pre">=</span> <span class="pre">&lt;path&gt;]</span></code>: path to the location of the file containing the DNA-RNA sequence-dependent parameters. Mandatory if <code class="docutils literal notranslate"><span class="pre">use_average_seq</span> <span class="pre">=</span> <span class="pre">false</span></code>.</p></li>
</ul>
</div>
<div class="section" id="options-for-lj-lennard-jones-simulations">
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4 changes: 4 additions & 0 deletions usage.html
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Expand Up @@ -203,6 +203,10 @@ <h2>confGenerator<a class="headerlink" href="#confgenerator" title="Permalink to
</pre></div>
</div>
<p>In addition to the input file, <em>confGenerator</em> takes another mandatory argument whose meaning depends on its value. It specifies the simulation box if it is a single number larger than 2 (in which case the simulation box is assumed to be cubic) or if it is an x-separated triplet of numbers that specify the length of the edges of the box (which is assumed to be a cuboid). By contrast, the second mandatory argument is interpreted as a number density if it is smaller than 2.</p>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p>This tool generates a configuration by inserting one particle (nucleotide) at a time, provided that its interaction energy does not exceed some predetermined value (which can be set with <code class="docutils literal notranslate"><span class="pre">energy_threshold</span></code>). It does so by placing each nucleotide randomly, but close to its neighbours, so that it is not too unlikely to end up with a non-overstretched bond. Unfortunately, this procedure makes it extremely unlikely to successfully generate a circular strand.</p>
</div>
<p>The following examples generate random initial configurations in a cubic box of size 10, in a cuboid of sizes 10x5x15 and in a cubic box with edge <span class="math notranslate nohighlight">\(L\)</span> such that <span class="math notranslate nohighlight">\(N / L^3 = 0.1\)</span>, where <span class="math notranslate nohighlight">\(N\)</span> is the total number of nucleotides specified in the topology file.</p>
<div class="highlight-text notranslate"><div class="highlight"><pre><span></span>confGenerator input 10
confGenerator input 10x5x15
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