FFDevel Wiki

Files::TARGETS: Difference between revisions

← Older edit
No edit summary
No edit summary
 
(8 intermediate revisions by the same user not shown)
Line 2: Line 2:
Navigation: [[Documentation]] / [[Files]] / [[Control files]] / [[Files::TARGETS | {TARGETS}]]
Navigation: [[Documentation]] / [[Files]] / [[Control files]] / [[Files::TARGETS | {TARGETS}]]
----
----
The [[Files::TARGETS | {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 process first and it alters default values for [set] sections.   
The [[Files::TARGETS | {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.   


==[set]==
==[setup]==
{| style="width: 100%;"
{| style="width: 100%;"
| style="width: 10em;" | '''Key'''  
| style="width: 10em;" | '''Key'''  
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;"  
| optprogress
| 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;"
| keepoptgeo
| 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;"
| optprogress
| off
| [[Control key types|logical]]
| show geometry optimization progress at each FF optimization step
|}
==[set]==
{| style="width: 100%;"
| style="width: 10em;" | '''Key'''
| style="width: 10em;" | '''Default value'''
| style="width: 5em;" | '''Type'''
| '''Description'''
|- style="vertical-align: top; background-color: #f6f6f6;"
| name
|
| [[Control key types|string]]
| 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''
|- style="vertical-align: top;"
| topology
|
| [[Control key types|string]]
| input topology in the [[Files::STOP|STOP]] format
|- style="vertical-align: top; background-color: #f6f6f6;"
| final_topology
|  
|  
| [[Control key types|string]]
| optimized FF parameters will be saved as topology in the [[Files::STOP|STOP]] format
|-
| colspan="4" style="vertical-align: top; background-color: #d6d6d6; text-align:center;" | ''Probe mode''
|- style="vertical-align: top;"
| probesize
| 0
| [[Control key types|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.
|- style="vertical-align: top; background-color: #f6f6f6;"
| unique_probe_types
| off
| [[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''
|- style="vertical-align: top;"
|- style="vertical-align: top;"
| nofreqs
| isreference
| 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. This option is mutually exclusive with ''references'' and ''shift2zero''.
|- style="vertical-align: top; background-color: #f6f6f6;"
| references
|  
|  
| [[Control key types|list]]
| names of sets, which are references for this set. This option is mutually exclusive with ''isreference'' and ''shift2zero''.
|- style="vertical-align: top;"
| shift2zero
| off
| [[Control key types|logical]]
| 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''
|- style="vertical-align: top;"
| optgeo
| off
| [[Control key types|logical]]
| optimize geometry at each optimization step
|- style="vertical-align: top; background-color: #f6f6f6;"
| keepoptgeo
| off
| [[Control key types|logical]]
| keep optimized geometries for the next optimization step
|- style="vertical-align: top;"
| savegeo
| off
| [[Control key types|logical]]
| 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;"
| comb_rules
| 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;"
| 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]]
| 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.
|}
|}
Retrieved from "https://ffdevel.ncbr.muni.cz/wiki/index.php/Files::TARGETS"