Files::TARGETS: Difference between revisions

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| 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;"
|- style="vertical-align: top;"
| nofreqs
| optprogress
| off
| [[Control key types|logical]]
|
|- style="vertical-align: top; background-color: #f6f6f6;"
| comb_rules
| off
| off
| [[Control key types|logical]]
| [[Control key types|logical]]
|  
| show geometry optimization progress at each FF optimization step
|}
|}


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|  
|  
| [[Control key types|string]]
| [[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;"
|- style="vertical-align: top;"
| topology
| topology
|  
|  
| [[Control key types|string]]
| [[Control key types|string]]
|  
| input topology in the [[Files::STOP|STOP]] format
|- style="vertical-align: top; background-color: #f6f6f6;"
|- style="vertical-align: top; background-color: #f6f6f6;"
| final
| final_topology
|  
|  
| [[Control key types|string]]
| [[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;"
|- style="vertical-align: top;"
| probesize
| probesize
| 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 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''
|- style="vertical-align: top;"
|- style="vertical-align: top;"
| isreference
| 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;"
|- 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''.
|- 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;"
|- style="vertical-align: top;"
| optgeo
| optgeo
| off
| off
| [[Control key types|logical]]
| [[Control key types|logical]]
|  
| optimize geometry at each optimization step
|- 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
|- 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 [[Files::FFOPT|{FFOPT}]] group
|- 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
| "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;"
|- style="vertical-align: top; background-color: #f6f6f6;"
| wmode
| 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;"
|- style="vertical-align: top;"
| shift2zero
| final_drvxyz
| off
| [[Control key types|logical]]
|  
|  
| [[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.
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