docs: refresh reference manual#269
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| | DFTB+ | ||
| | Turbomole | ||
| | PySCF | ||
| | MACE-MP and MACE-OFF | ||
| | ASE-DFTB+ | ||
| | ASE-xTB |
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I suggest adding links, just like in the reference manual of the input file
| Integrator: | ||
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| | Velocity Verlet | ||
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| 1) Velocity Verlet | ||
| Thermostats: | ||
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| Thermostats | ||
| =========== | ||
| | Langevin | ||
| | Berendsen | ||
| | stochastic velocity rescaling | ||
| | Nose-Hoover chain | ||
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| 1) Langevin Thermostat | ||
| 2) Berendsen Thermostat | ||
| 3) Velocity Rescaling Thermostat | ||
| 4) Nose-Hoover Thermostat | ||
| Manostats: | ||
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| Manostats | ||
| ========= | ||
| | Berendsen | ||
| | stochastic cell rescaling | ||
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| 1) Berendsen Manostat | ||
| 2) Stochastic Rescaling Manostat | ||
| Cell coupling modes: | ||
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| Isotropicity | ||
| ============ | ||
| | isotropic | ||
| | semi-isotropic | ||
| | anisotropic cell lengths | ||
| | full anisotropic cell lengths and angles | ||
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| All calculation schemes of any MD runner can be performed with triclinic cells | ||
| Constraints: | ||
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| 1) Isotropic | ||
| 2) Semi-Isotropic | ||
| 3) Anisotropic (only cell lengths) | ||
| 4) Full Anisotropic (cell lengths and angles) | ||
| | SHAKE/RATTLE | ||
| | M-SHAKE | ||
| | distance constraints |
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When looking at the rendered html file I don't like that the spacing before and after the category are the same, e.g. white space before and after Manostats. I would also like more highlighting/differentiation between the category (e.g. Manostats) and the associated items (e.g. Berendsen stochastic cell rescaling)
either with explicit bullet points or bold font or font size
| Planned Items | ||
| ************* | ||
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| The following items are not documented as supported features in this release: |
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I would somehow add that these items are planned, because phrasing it like this sounds just like an info that they are not featured, however they are indeed planned;
example suggestion:
The following items are planned for future releases.
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| | ``jobtype = mm-md`` for a molecular-mechanics MD simulation | ||
| | ``start_file = input_h2o.rst`` for the initial structure | ||
| | default ``moldescriptor_file`` and ``guff_file`` setup names |
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I would suggest "setup files" instead of "setup names"
| The first line of each block is the number of atoms in the reference geometry. | ||
| The second line must contain ``moltype = <id>;`` and is parsed with the same | ||
| command syntax as the input file. It is followed by one atom line per reference | ||
| atom: atom name and Cartesian coordinates. The atom names must match the atom | ||
| names of the referenced molecule type. |
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please add that the moltype comes from the moldescriptor.dat file and also link it
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please add a note that when the force-field keyword in the input file is set to on or bonded, the topology file and the parameter file become mandatory; also add corresponding links
Moreover, the topology file becomes mandatory if the shake keyword is set to on --> add link
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| Some setup files are only required for specific modes: | ||
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| | ``topology_file`` is required when topology-defined constraints or bonded force-field terms are used. |
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is required if force-field is set to bonded or on; or shake is set to on
| Some setup files are only required for specific modes: | ||
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| | ``topology_file`` is required when topology-defined constraints or bonded force-field terms are used. | ||
| | ``parameter_file`` is required for force-field simulations. |
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is required if force-field is set to bonded or on
| | ``qm-rpmd`` | ||
| | ``mm-opt`` | ||
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| These values are case-insensitive and dashes are treated like underscores. |
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omit this remark here and instead add this information as a general info to the referenceManual->InputFile
| 2. **on** - SHAKE for bond constraints defined in the :ref:`topologyFile` will be applied. | ||
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| 3. **shake** - SHAKE for bond constraints defined in the :ref:`topologyFile` will be applied. |
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please fuse these two options into one bullet point
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Summary
Validation