Files::TARGETS: Difference between revisions
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| Line 14: | Line 14: | ||
| off | | off | ||
| [[Control key types|logical]] | | [[Control key types|logical]] | ||
| | | optimize geometry at each optimization step | ||
|- style="vertical-align: top;" | |- style="vertical-align: top;" | ||
| | | keepoptgeo | ||
| off | | off | ||
| [[Control key types|logical]] | | [[Control key types|logical]] | ||
| | | keep optimized geometries for the next optimization step | ||
|- style="vertical-align: top; background-color: #f6f6f6;" | |- style="vertical-align: top; background-color: #f6f6f6;" | ||
| | | nofreqs | ||
| off | | off | ||
| [[Control key types|logical]] | | [[Control key types|logical]] | ||
| | | do not calculate TRG vibrational frequencies when a point contains TRG Hessian | ||
|- style="vertical-align: top;" | |- style="vertical-align: top;" | ||
| savegeo | | savegeo | ||
| off | | off | ||
| [[Control key types|logical]] | | [[Control key types|logical]] | ||
| | | save geometries of all points at the end of each {FFOPT} group | ||
|- style="vertical-align: top; background-color: #f6f6f6;" | |- style="vertical-align: top; background-color: #f6f6f6;" | ||
| savepath | | savepath | ||
| "points" | | "points" | ||
| [[Control key types|string]] | | [[Control key types|string]] | ||
| | | path name for saved points | ||
|- style="vertical-align: top;" | |- style="vertical-align: top;" | ||
| | | optprogress | ||
| off | | off | ||
| [[Control key types|logical]] | | [[Control key types|logical]] | ||
| | | show geometry optimization progress at each FF optimization step | ||
|} | |} | ||
| Line 59: | Line 54: | ||
| name of the set. The name is mandatory for reference sets otherwise it is optional. | | name of the set. The name is mandatory for reference sets otherwise it is optional. | ||
|- | |- | ||
| colspan="4" style="vertical-align: top; background-color: #d6d6d6; text-align:center;" | ''Topology | | colspan="4" style="vertical-align: top; background-color: #d6d6d6; text-align:center;" | ''Topology'' | ||
|- style="vertical-align: top;" | |- style="vertical-align: top;" | ||
| topology | | topology | ||
| | | | ||
| [[Control key types|string]] | | [[Control key types|string]] | ||
| Line 76: | Line 71: | ||
| 0 | | 0 | ||
| [[Control key types|integer]] | | [[Control key types|integer]] | ||
| number of atoms in a vdW probe. The probe must be at the end of the structure. | | number of atoms in a vdW probe. The probe must be at the end of the structure and cannot be covalently bound to the rest of the structure. | ||
|- style="vertical-align: top; background-color: #f6f6f6;" | |- style="vertical-align: top; background-color: #f6f6f6;" | ||
| unique_probe_types | | unique_probe_types | ||
| off | | off | ||
| [[Control key types|logical]] | | [[Control key types|logical]] | ||
| | | if ''on'' then ensure that the probe atom types are not part of the rest of structure (probed part of the structure). | ||
|- | |- | ||
| colspan="4" style="vertical-align: top; background-color: #d6d6d6; text-align:center;" | ''Reference setup'' | | colspan="4" style="vertical-align: top; background-color: #d6d6d6; text-align:center;" | ''Reference setup'' | ||
| Line 88: | Line 83: | ||
| off | | off | ||
| [[Control key types|logical]] | | [[Control key types|logical]] | ||
| set the set as a reference. In the reference mode, the set can contain only one point. | | set the set as a reference. In the reference mode, the set can contain only one point. This option is mutually exclusive with ''references'' and ''shift2zero''. | ||
|- style="vertical-align: top; background-color: #f6f6f6;" | |- style="vertical-align: top; background-color: #f6f6f6;" | ||
| references | | references | ||
| | | | ||
| [[Control key types|list]] | | [[Control key types|list]] | ||
| names of sets, which are references for this set. This option is mutually exclusive with ''isreference' and 'shift2zero'. | | names of sets, which are references for this set. This option is mutually exclusive with ''isreference'' and ''shift2zero''. | ||
|- style="vertical-align: top | |- style="vertical-align: top;" | ||
| shift2zero | | shift2zero | ||
| off | | off | ||
| [[Control key types|logical]] | | [[Control key types|logical]] | ||
| make TRG energies relative to the global minima. This option is mutually exclusive with ''isreference' and 'reference'. | | make TRG energies relative to the global minima. This option is mutually exclusive with ''isreference'' and ''reference''. | ||
|- | |- | ||
| colspan="4" style="vertical-align: top; background-color: #d6d6d6; text-align:center;" | ''Points'' | | colspan="4" style="vertical-align: top; background-color: #d6d6d6; text-align:center;" | ''Points'' | ||
| Line 108: | Line 103: | ||
|- style="vertical-align: top; background-color: #f6f6f6;" | |- style="vertical-align: top; background-color: #f6f6f6;" | ||
| keepoptgeo | | keepoptgeo | ||
| | | off | ||
| [[Control key types|logical]] | | [[Control key types|logical]] | ||
| keep optimized geometries for the next optimization step | | keep optimized geometries for the next optimization step | ||
| Line 117: | Line 112: | ||
| save geometries of all points at the end of each [[Files::FFOPT|{FFOPT}]] group | | save geometries of all points at the end of each [[Files::FFOPT|{FFOPT}]] group | ||
|- style="vertical-align: top; background-color: #f6f6f6;" | |- style="vertical-align: top; background-color: #f6f6f6;" | ||
| nofreqs | |||
| off | |||
| [[Control key types|logical]] | |||
| do not calculate TRG vibrational frequencies when a point contains TRG Hessian | |||
|- style="vertical-align: top;" | |||
| wmode | | wmode | ||
| "auto" | |||
| [[Control key types|string]] | |||
| weight mode. Supported modes: auto and ire2 | |||
|- style="vertical-align: top; background-color: #f6f6f6;" | |||
| point | |||
| | |||
| [[Control key types|string]] | |||
| file name of point optionally followed by its weight. Multiple number of ''point'' specifications can be provided. | |||
|- style="vertical-align: top;" | |||
| points | |||
| | |||
| [[Control key types|string]] | |||
| file name of stream with points optionally followed by their weight. Multiple number of ''points'' specifications can be provided. | |||
|- style="vertical-align: top; background-color: #f6f6f6;" | |||
| final_drvene | |||
| | | | ||
| [[Control key types|string]] | | [[Control key types|string]] | ||
| | | file name with final energies of points saved at the end of each [[Files::FFOPT|{FFOPT}]] group. The file will also contain values of associated collective variables. | ||
|- style="vertical-align: top;" | |||
| final_drvxyz | |||
| | |||
| [[Control key types|string]] | |||
| file name with final structures of points saved at the end of each [[Files::FFOPT|{FFOPT}]] group as multi-xyz stream. | |||
|} | |} | ||
Latest revision as of 18:33, 5 March 2019
Navigation: Documentation / Files / Control files / {TARGETS}
The {TARGETS} group is employed by the ffoptimize program for definition of training data. The group can obtain one [setup] section and several [set] sections. The [setup] section is processed first and it alters default values for keys in the [set] sections with the same name.
[setup]
| Key | Default value | Type | Description |
| optgeo | off | logical | optimize geometry at each optimization step |
| keepoptgeo | off | logical | keep optimized geometries for the next optimization step |
| nofreqs | off | logical | do not calculate TRG vibrational frequencies when a point contains TRG Hessian |
| savegeo | off | logical | save geometries of all points at the end of each {FFOPT} group |
| savepath | "points" | string | path name for saved points |
| optprogress | off | logical | show geometry optimization progress at each FF optimization step |
[set]
| Key | Default value | Type | Description |
| name | string | name of the set. The name is mandatory for reference sets otherwise it is optional. | |
| Topology | |||
| topology | string | input topology in the STOP format | |
| final_topology | string | optimized FF parameters will be saved as topology in the STOP format | |
| Probe mode | |||
| probesize | 0 | integer | number of atoms in a vdW probe. The probe must be at the end of the structure and cannot be covalently bound to the rest of the structure. |
| unique_probe_types | off | logical | if on then ensure that the probe atom types are not part of the rest of structure (probed part of the structure). |
| Reference setup | |||
| isreference | off | logical | set the set as a reference. In the reference mode, the set can contain only one point. This option is mutually exclusive with references and shift2zero. |
| references | list | names of sets, which are references for this set. This option is mutually exclusive with isreference and shift2zero. | |
| shift2zero | off | logical | make TRG energies relative to the global minima. This option is mutually exclusive with isreference and reference. |
| Points | |||
| optgeo | off | logical | optimize geometry at each optimization step |
| keepoptgeo | off | logical | keep optimized geometries for the next optimization step |
| savegeo | off | logical | save geometries of all points at the end of each {FFOPT} group |
| nofreqs | off | logical | do not calculate TRG vibrational frequencies when a point contains TRG Hessian |
| wmode | "auto" | string | weight mode. Supported modes: auto and ire2 |
| point | string | file name of point optionally followed by its weight. Multiple number of point specifications can be provided. | |
| points | string | file name of stream with points optionally followed by their weight. Multiple number of points specifications can be provided. | |
| final_drvene | string | file name with final energies of points saved at the end of each {FFOPT} group. The file will also contain values of associated collective variables. | |
| final_drvxyz | string | file name with final structures of points saved at the end of each {FFOPT} group as multi-xyz stream. | |