Difference between revisions of "Documentation"
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* Defining atomic <code>[[supergroups file|supergroups]]</code>. | * Defining atomic <code>[[supergroups file|supergroups]]</code>. | ||
| − | * Providing <code>[[masses file| | + | * Providing <code>[[masses file|masses]]</code> information for the atoms involved in the MD. |
* Containing all the <code>[[input file|input]]</code> options and other miscellaneous information pertaining your simulation, such as time step, etc. The <code>[[input]]</code> file can contain minimal input parameters or it can contain special keywords that allow you to fine tune the simulation parameters, e.g., allow you to switch on pre- and post-processing of trajectory data or to choose between different available implementations of the hard-sphere formalism. | * Containing all the <code>[[input file|input]]</code> options and other miscellaneous information pertaining your simulation, such as time step, etc. The <code>[[input]]</code> file can contain minimal input parameters or it can contain special keywords that allow you to fine tune the simulation parameters, e.g., allow you to switch on pre- and post-processing of trajectory data or to choose between different available implementations of the hard-sphere formalism. | ||
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These input files should all be present within the directory where DoSPT is to be executed. Read through the description of each input file to familiarize yourself with the expected format and the scope/effect of the different input parameters accepted by DoSPT. | These input files should all be present within the directory where DoSPT is to be executed. Read through the description of each input file to familiarize yourself with the expected format and the scope/effect of the different input parameters accepted by DoSPT. | ||
| − | An optional input file is the <code>[[topology file|topology]]</code> file. The <code>[[topology]]</code> file contains bond and molecule information that allows DoSPT to handle bond breaking and bond formation dynamically (that is, as it happens during the MD run). | + | An optional input file is the <code>[[topology file|topology]]</code> file. The <code>[[topology file|topology]]</code> file contains bond and molecule information that allows DoSPT to handle bond breaking and bond formation dynamically (that is, as it happens during the MD run). |
{| class="wikitable" | {| class="wikitable" | ||
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|- | |- | ||
| <code>[[input]]</code>, <code>[[groups]]</code>, <code>[[supergroups]]</code>, <code>[[masses]]</code>, <code>[[traj.***]]</code> | | <code>[[input]]</code>, <code>[[groups]]</code>, <code>[[supergroups]]</code>, <code>[[masses]]</code>, <code>[[traj.***]]</code> | ||
| − | | <code>[[topology]]</code> | + | | <code>[[topology file|topology]]</code> |
|} | |} | ||
| − | You can also check out the [[ | + | You can also check out the [[wishlist]], which summarizes wanted and planned functionality to be (hopefully) incorporated to DoSPT. |
Latest revision as of 06:54, 16 April 2021
The DoSPT code is structured around several input files that serve the purpose of:
- Providing the MD trajectory information, that is atomic positions (and possibly velocities). This info is contained in a trajectory file, that can be supplied in a variety of popular formats (e.g.,
traj.groortraj.xyz).
- Defining atomic
groups.
- Defining atomic
supergroups.
- Providing
massesinformation for the atoms involved in the MD.
- Containing all the
inputoptions and other miscellaneous information pertaining your simulation, such as time step, etc. Theinputfile can contain minimal input parameters or it can contain special keywords that allow you to fine tune the simulation parameters, e.g., allow you to switch on pre- and post-processing of trajectory data or to choose between different available implementations of the hard-sphere formalism.
These input files should all be present within the directory where DoSPT is to be executed. Read through the description of each input file to familiarize yourself with the expected format and the scope/effect of the different input parameters accepted by DoSPT.
An optional input file is the topology file. The topology file contains bond and molecule information that allows DoSPT to handle bond breaking and bond formation dynamically (that is, as it happens during the MD run).
| Required | Optional |
|---|---|
input, groups, supergroups, masses, traj.***
|
topology
|
You can also check out the wishlist, which summarizes wanted and planned functionality to be (hopefully) incorporated to DoSPT.
