Difference between revisions of "Phaser: Manual"
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| + | <div style="margin-left: 25px; float: right;">__TOC__</div> | ||
| + | ===Phaser Executable=== | ||
| + | |||
| + | The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the [[#MODE | MODE]] keyword. The different modes and the keywords relevant to each mode are described in [[Modes]]. | ||
| + | |||
| + | Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. However, some keywords are meaningful when entered multiple times. The order may or may not be important. | ||
| + | |||
| + | *[[Image:User1.gif|link=]] [[#Basic Keywords | Basic Keywords]] | ||
| + | |||
| + | *[[Image:Output.png|link=]] [[#Output Control Keywords | Output Control Keywords]] | ||
| + | |||
| + | *[[Image:User2.gif|link=]] [[#Advanced Keywords |Advanced Keywords ]] | ||
| + | |||
| + | *[[Image:Expert.gif|link=]] [[#Expert Keywords | Expert Keywords]] | ||
| + | |||
| + | *[[Image:Developer.gif|link=]] [[#Developer Keywords | Developer Keywords]] | ||
| + | |||
| + | str string | ||
| + | int integer | ||
| + | float double precision floating point | ||
| + | dvect3 array of 3 doubles | ||
| + | |||
| + | |||
| + | ===Python Interface=== | ||
| + | |||
| + | Phaser can be compiled as a python library. The python interface takes a phaser keyword string as input. | ||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | ==Basic Keywords== | ||
| + | ===[[Image:User1.gif|link=]]ATOM=== | ||
| + | |||
| + | |||
| + | |||
| + | |||
| + | ==Output Control Keywords== | ||
| + | ===[[Image:Output.png|link=]]DEBUG=== | ||
| + | ; DEBUG [ON|OFF] | ||
| + | : Extra verbose output for debugging | ||
| + | * Default: DEBUG OFF | ||
| + | |||
| + | ==Advanced Keywords== | ||
| + | ===[[Image:User2.gif|link=]]ELLG=== | ||
| + | ; ELLG TARGET <TARGET> | ||
| + | : Target value for expected LLG for determining resolution limits and search order | ||
| + | <!--; ELLG HIRES <HIRES> Internal control only--> | ||
| + | * Default: ELLG TARGET 225 | ||
| + | |||
| + | |||
| + | |||
| + | |||
| + | ==Expert Keywords== | ||
| + | |||
| + | ===[[Image:Expert.gif|link=]]MACANO=== | ||
| + | ; MACANO PROTOCOL [DEFAULT|CUSTOM|OFF|ALL] | ||
| + | : Protocol for the refinement of SigmaN in the anisotropy correction | ||
| + | ; MACANO ANISO [ON|OFF] BINS [ON|OFF] SOLK [ON|OFF] SOLB [ON|OFF] ''{NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}'' | ||
| + | : Macrocycle for the custom refinement of SigmaN in the anisotropy correction. Macrocycles are performed in the order in which they are entered. | ||
| + | * Default: MACANO PROTOCOL DEFAULT | ||
| + | |||
| + | |||
| + | |||
| + | ==Developer Keywords== | ||
| + | ===[[Image:Developer.gif|link=]]BINS=== | ||
| + | ; BINS DATA [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ] | ||
| + | : The binning of the data. | ||
| + | : <sup>1</sup> L = minimum number of bins | ||
| + | : <sup>2</sup> H = maximum number of bins. | ||
| + | : <sup>3</sup> W = width of the bins in number of reflections | ||
Revision as of 11:39, 9 March 2018
Phaser Executable
The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the MODE keyword. The different modes and the keywords relevant to each mode are described in Modes.
Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. However, some keywords are meaningful when entered multiple times. The order may or may not be important.
str string int integer float double precision floating point dvect3 array of 3 doubles
Python Interface
Phaser can be compiled as a python library. The python interface takes a phaser keyword string as input.
Basic Keywords
ATOM
Output Control Keywords
DEBUG
- DEBUG [ON|OFF]
- Extra verbose output for debugging
- Default: DEBUG OFF
Advanced Keywords
ELLG
- ELLG TARGET <TARGET>
- Target value for expected LLG for determining resolution limits and search order
- Default: ELLG TARGET 225
Expert Keywords
MACANO
- MACANO PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]
- Protocol for the refinement of SigmaN in the anisotropy correction
- MACANO ANISO [ON|OFF] BINS [ON|OFF] SOLK [ON|OFF] SOLB [ON|OFF] {NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}
- Macrocycle for the custom refinement of SigmaN in the anisotropy correction. Macrocycles are performed in the order in which they are entered.
- Default: MACANO PROTOCOL DEFAULT
Developer Keywords
BINS
- BINS DATA [ 1MIN <L> | 2MAX <H> | 3WIDTH <W> ]
- The binning of the data.
- 1 L = minimum number of bins
- 2 H = maximum number of bins.
- 3 W = width of the bins in number of reflections
