From e139dba003fc67352de1f2c96462efbf00e22455 Mon Sep 17 00:00:00 2001 From: Tristan Youngs Date: Tue, 3 Sep 2024 09:42:39 +0100 Subject: [PATCH] refactor: Update docs to reflect Generators rather than Procedures (#1947) --- web/docs/examples/benzene/step2.md | 2 +- .../{procedures => generators}/_index.md | 18 +++---- .../{procedures => generators}/expressions.md | 0 .../nodes/_index.md | 0 .../nodes/addnode.md | 0 .../nodes/addpairnode.md | 0 .../nodes/boxnode.md | 0 .../nodes/coordinatesetsnode.md | 0 .../{procedures => generators}/nodes/copy.md | 0 .../nodes/customregion.md | 0 .../nodes/cylindricalglobalpotential.md | 0 .../nodes/cylindricalregion.md | 0 .../nodes/generalregion.md | 0 .../nodes/importcoordinates.md | 0 .../nodes/parametersnode.md | 2 +- .../nodes/picknode.md | 0 .../nodes/pickproximity.md | 0 .../nodes/pickregion.md | 0 .../nodes/regionalglobalpotential.md | 0 .../nodes/removenode.md | 0 .../nodes/restraintpotential.md | 0 .../nodes/rotatefragment.md | 0 .../nodes/selectnode.md | 0 .../nodes/sizefactornode.md | 0 .../nodes/sphericalglobalpotential.md | 0 .../nodes/temperaturenode.md | 0 .../nodes/transmutenode.md | 0 web/docs/userguide/gui/configurationtab.md | 2 +- web/docs/userguide/guide/workflow.md | 2 +- .../userguide/inputfile/configurationblock.md | 16 +++--- .../modules/analysis/analyse/_index.md | 17 ------ .../procedures/nodes/calculateanglenode.md | 39 -------------- .../nodes/calculateaxisanglenode.md | 40 -------------- .../procedures/nodes/calculatedistancenode.md | 32 ------------ .../procedures/nodes/calculateexpression.md | 29 ----------- .../procedures/nodes/calculatevectornode.md | 38 -------------- .../procedures/nodes/collect1dnode.md | 36 ------------- .../procedures/nodes/collect2dnode.md | 38 -------------- .../procedures/nodes/collect3dnode.md | 40 -------------- .../procedures/nodes/integercollect1d.md | 37 ------------- .../userguide/procedures/nodes/integrate1d.md | 33 ------------ .../procedures/nodes/operatedividenode.md | 31 ----------- .../procedures/nodes/operateexpressionnode.md | 31 ----------- .../procedures/nodes/operatemultiplynode.md | 31 ----------- .../procedures/nodes/operatenormalisenode.md | 32 ------------ .../operatenumberdensitynormalisenode.md | 32 ------------ .../operatesitepopulationnormalisenode.md | 31 ----------- .../operatesphericalshellnormalisenode.md | 23 -------- .../procedures/nodes/process1dnode.md | 51 ------------------ .../procedures/nodes/process2dnode.md | 51 ------------------ .../procedures/nodes/process3dnode.md | 52 ------------------- .../userguide/procedures/nodes/sum1dnode.md | 42 --------------- 52 files changed, 19 insertions(+), 809 deletions(-) rename web/docs/userguide/{procedures => generators}/_index.md (50%) rename web/docs/userguide/{procedures => generators}/expressions.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/_index.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/addnode.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/addpairnode.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/boxnode.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/coordinatesetsnode.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/copy.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/customregion.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/cylindricalglobalpotential.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/cylindricalregion.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/generalregion.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/importcoordinates.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/parametersnode.md (89%) rename web/docs/userguide/{procedures => generators}/nodes/picknode.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/pickproximity.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/pickregion.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/regionalglobalpotential.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/removenode.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/restraintpotential.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/rotatefragment.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/selectnode.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/sizefactornode.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/sphericalglobalpotential.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/temperaturenode.md (100%) rename web/docs/userguide/{procedures => generators}/nodes/transmutenode.md (100%) delete mode 100644 web/docs/userguide/modules/analysis/analyse/_index.md delete mode 100644 web/docs/userguide/procedures/nodes/calculateanglenode.md delete mode 100644 web/docs/userguide/procedures/nodes/calculateaxisanglenode.md delete mode 100644 web/docs/userguide/procedures/nodes/calculatedistancenode.md delete mode 100644 web/docs/userguide/procedures/nodes/calculateexpression.md delete mode 100644 web/docs/userguide/procedures/nodes/calculatevectornode.md delete mode 100644 web/docs/userguide/procedures/nodes/collect1dnode.md delete mode 100644 web/docs/userguide/procedures/nodes/collect2dnode.md delete mode 100644 web/docs/userguide/procedures/nodes/collect3dnode.md delete mode 100644 web/docs/userguide/procedures/nodes/integercollect1d.md delete mode 100644 web/docs/userguide/procedures/nodes/integrate1d.md delete mode 100644 web/docs/userguide/procedures/nodes/operatedividenode.md delete mode 100644 web/docs/userguide/procedures/nodes/operateexpressionnode.md delete mode 100644 web/docs/userguide/procedures/nodes/operatemultiplynode.md delete mode 100644 web/docs/userguide/procedures/nodes/operatenormalisenode.md delete mode 100644 web/docs/userguide/procedures/nodes/operatenumberdensitynormalisenode.md delete mode 100644 web/docs/userguide/procedures/nodes/operatesitepopulationnormalisenode.md delete mode 100644 web/docs/userguide/procedures/nodes/operatesphericalshellnormalisenode.md delete mode 100644 web/docs/userguide/procedures/nodes/process1dnode.md delete mode 100644 web/docs/userguide/procedures/nodes/process2dnode.md delete mode 100644 web/docs/userguide/procedures/nodes/process3dnode.md delete mode 100644 web/docs/userguide/procedures/nodes/sum1dnode.md diff --git a/web/docs/examples/benzene/step2.md b/web/docs/examples/benzene/step2.md index 752e7c3c31..6455c0127f 100644 --- a/web/docs/examples/benzene/step2.md +++ b/web/docs/examples/benzene/step2.md @@ -20,7 +20,7 @@ In anticipation of some bad contacts: {{< action type="tabs">}}Go to the {{< gui-tab type="configuration" text="Liquid" >}} configuration tab{{< /action >}} {{< action type="groups">}}Click the {{< gui-button icon="palette" text="Show Available Nodes" >}} on the bottom-left of the window{{< /action >}} -{{< action type="mouse">}}Drag the {{< node "SizeFactor" >}} node into the **Procedure** section to add it{{< /action >}} +{{< action type="mouse">}}Drag the {{< node "SizeFactor" >}} node into the **Generator** section to add it{{< /action >}} {{< action type="edit" text="Set the value for the _Size Factor_ to 10.0" />}} Finally, before we move on, we will have to reduce our pair potential range from the default of 15 Å since this is larger than the half the maximum width of our simulation box. diff --git a/web/docs/userguide/procedures/_index.md b/web/docs/userguide/generators/_index.md similarity index 50% rename from web/docs/userguide/procedures/_index.md rename to web/docs/userguide/generators/_index.md index ec276f212f..0971c94f4b 100644 --- a/web/docs/userguide/procedures/_index.md +++ b/web/docs/userguide/generators/_index.md @@ -1,28 +1,24 @@ --- -title: 8. Procedures -description: Defining procedures to create, analyse, and edit +title: 8. Generators +description: Creating Configurations with Generators weight: 8 --- ## Overview -Procedures are used within Dissolve to allow user-defined tasks to be created and used for various jobs - e.g. generating the contents for a configuration, performing a specific analysis etc. They are simple sequences of steps or "nodes" that are run when required, with each node having a focussed and specific purpose. Combined, the actions of these simplistic nodes can generate and manipulate complex coordinate ensembles, and analyse complicated structural patterns. +Generators are a flexible way of describing how a configuration should be created. They are sequences of simple steps or "nodes" that are run when required, with each node having a focussed and specific purpose. Combined, the actions of these simplistic nodes can generate basic disordered systems through to complex coordinate ensembles. -There are three stages to any procedure and its constituent nodes, with each stage performed every time the procedure is run: +There are three stages to any generator and its constituent nodes, with each stage performed every time the generator is run: #### Set Up -Before the procedure is executed, every node present within it is permitted a set-up stage during which any critical values can be retrieved for use, or any data structures (e.g. to hold results) can be initialised. +Before the generator is executed, every node present within it is permitted a set-up stage during which any critical values can be retrieved for use, or any data structures (e.g. to hold results) can be initialised. #### Execute -The main work of the procedure is performed within the execution stages of the nodes, which are run according to the structure and sequence defined in the procedure. - -#### Finalise -Once the procedure has completed its execution stage, every node present within it is permitted a final operation during which data can be retrieved, normalised, processed, saved etc. -, or printing out a final summary of the node's work over the entire procedure. +The main work of the generator is performed within the execution stages of the nodes, which are run according to the structure and sequence defined in the generator. ## Nodes -A procedure is made up of one or more "nodes", each of which performs a specific task on or with some defined objects in a simulation (e.g. species or configuration boxes), generates data from the simulation, or manipulates data generated by other nodes. +A generator is made up of one or more "nodes", each of which performs a specific task on or with some defined objects in a simulation (e.g. species or configuration boxes), generates data from the simulation, or manipulates data generated by other nodes. ## Branches diff --git a/web/docs/userguide/procedures/expressions.md b/web/docs/userguide/generators/expressions.md similarity index 100% rename from web/docs/userguide/procedures/expressions.md rename to web/docs/userguide/generators/expressions.md diff --git a/web/docs/userguide/procedures/nodes/_index.md b/web/docs/userguide/generators/nodes/_index.md similarity index 100% rename from web/docs/userguide/procedures/nodes/_index.md rename to web/docs/userguide/generators/nodes/_index.md diff --git a/web/docs/userguide/procedures/nodes/addnode.md b/web/docs/userguide/generators/nodes/addnode.md similarity index 100% rename from web/docs/userguide/procedures/nodes/addnode.md rename to web/docs/userguide/generators/nodes/addnode.md diff --git a/web/docs/userguide/procedures/nodes/addpairnode.md b/web/docs/userguide/generators/nodes/addpairnode.md similarity index 100% rename from web/docs/userguide/procedures/nodes/addpairnode.md rename to web/docs/userguide/generators/nodes/addpairnode.md diff --git a/web/docs/userguide/procedures/nodes/boxnode.md b/web/docs/userguide/generators/nodes/boxnode.md similarity index 100% rename from web/docs/userguide/procedures/nodes/boxnode.md rename to web/docs/userguide/generators/nodes/boxnode.md diff --git a/web/docs/userguide/procedures/nodes/coordinatesetsnode.md b/web/docs/userguide/generators/nodes/coordinatesetsnode.md similarity index 100% rename from web/docs/userguide/procedures/nodes/coordinatesetsnode.md rename to web/docs/userguide/generators/nodes/coordinatesetsnode.md diff --git a/web/docs/userguide/procedures/nodes/copy.md b/web/docs/userguide/generators/nodes/copy.md similarity index 100% rename from web/docs/userguide/procedures/nodes/copy.md rename to web/docs/userguide/generators/nodes/copy.md diff --git a/web/docs/userguide/procedures/nodes/customregion.md b/web/docs/userguide/generators/nodes/customregion.md similarity index 100% rename from web/docs/userguide/procedures/nodes/customregion.md rename to web/docs/userguide/generators/nodes/customregion.md diff --git a/web/docs/userguide/procedures/nodes/cylindricalglobalpotential.md b/web/docs/userguide/generators/nodes/cylindricalglobalpotential.md similarity index 100% rename from web/docs/userguide/procedures/nodes/cylindricalglobalpotential.md rename to web/docs/userguide/generators/nodes/cylindricalglobalpotential.md diff --git a/web/docs/userguide/procedures/nodes/cylindricalregion.md b/web/docs/userguide/generators/nodes/cylindricalregion.md similarity index 100% rename from web/docs/userguide/procedures/nodes/cylindricalregion.md rename to web/docs/userguide/generators/nodes/cylindricalregion.md diff --git a/web/docs/userguide/procedures/nodes/generalregion.md b/web/docs/userguide/generators/nodes/generalregion.md similarity index 100% rename from web/docs/userguide/procedures/nodes/generalregion.md rename to web/docs/userguide/generators/nodes/generalregion.md diff --git a/web/docs/userguide/procedures/nodes/importcoordinates.md b/web/docs/userguide/generators/nodes/importcoordinates.md similarity index 100% rename from web/docs/userguide/procedures/nodes/importcoordinates.md rename to web/docs/userguide/generators/nodes/importcoordinates.md diff --git a/web/docs/userguide/procedures/nodes/parametersnode.md b/web/docs/userguide/generators/nodes/parametersnode.md similarity index 89% rename from web/docs/userguide/procedures/nodes/parametersnode.md rename to web/docs/userguide/generators/nodes/parametersnode.md index e396328982..fba1ce7080 100644 --- a/web/docs/userguide/procedures/nodes/parametersnode.md +++ b/web/docs/userguide/generators/nodes/parametersnode.md @@ -14,7 +14,7 @@ description: Store numerical reference parameters ## Overview -The `Parameters` node stores zero or more named numerical values that may be referenced in [expressions]({{< ref "expressions" >}}) within nodes contained in the same encompassing [procedure]({{< ref "procedures" >}}). +The `Parameters` node stores zero or more named numerical values that may be referenced in [expressions]({{< ref "expressions" >}}) within nodes contained in the same encompassing [generator]({{< ref "generators" >}}). ## Description diff --git a/web/docs/userguide/procedures/nodes/picknode.md b/web/docs/userguide/generators/nodes/picknode.md similarity index 100% rename from web/docs/userguide/procedures/nodes/picknode.md rename to web/docs/userguide/generators/nodes/picknode.md diff --git a/web/docs/userguide/procedures/nodes/pickproximity.md b/web/docs/userguide/generators/nodes/pickproximity.md similarity index 100% rename from web/docs/userguide/procedures/nodes/pickproximity.md rename to web/docs/userguide/generators/nodes/pickproximity.md diff --git a/web/docs/userguide/procedures/nodes/pickregion.md b/web/docs/userguide/generators/nodes/pickregion.md similarity index 100% rename from web/docs/userguide/procedures/nodes/pickregion.md rename to web/docs/userguide/generators/nodes/pickregion.md diff --git a/web/docs/userguide/procedures/nodes/regionalglobalpotential.md b/web/docs/userguide/generators/nodes/regionalglobalpotential.md similarity index 100% rename from web/docs/userguide/procedures/nodes/regionalglobalpotential.md rename to web/docs/userguide/generators/nodes/regionalglobalpotential.md diff --git a/web/docs/userguide/procedures/nodes/removenode.md b/web/docs/userguide/generators/nodes/removenode.md similarity index 100% rename from web/docs/userguide/procedures/nodes/removenode.md rename to web/docs/userguide/generators/nodes/removenode.md diff --git a/web/docs/userguide/procedures/nodes/restraintpotential.md b/web/docs/userguide/generators/nodes/restraintpotential.md similarity index 100% rename from web/docs/userguide/procedures/nodes/restraintpotential.md rename to web/docs/userguide/generators/nodes/restraintpotential.md diff --git a/web/docs/userguide/procedures/nodes/rotatefragment.md b/web/docs/userguide/generators/nodes/rotatefragment.md similarity index 100% rename from web/docs/userguide/procedures/nodes/rotatefragment.md rename to web/docs/userguide/generators/nodes/rotatefragment.md diff --git a/web/docs/userguide/procedures/nodes/selectnode.md b/web/docs/userguide/generators/nodes/selectnode.md similarity index 100% rename from web/docs/userguide/procedures/nodes/selectnode.md rename to web/docs/userguide/generators/nodes/selectnode.md diff --git a/web/docs/userguide/procedures/nodes/sizefactornode.md b/web/docs/userguide/generators/nodes/sizefactornode.md similarity index 100% rename from web/docs/userguide/procedures/nodes/sizefactornode.md rename to web/docs/userguide/generators/nodes/sizefactornode.md diff --git a/web/docs/userguide/procedures/nodes/sphericalglobalpotential.md b/web/docs/userguide/generators/nodes/sphericalglobalpotential.md similarity index 100% rename from web/docs/userguide/procedures/nodes/sphericalglobalpotential.md rename to web/docs/userguide/generators/nodes/sphericalglobalpotential.md diff --git a/web/docs/userguide/procedures/nodes/temperaturenode.md b/web/docs/userguide/generators/nodes/temperaturenode.md similarity index 100% rename from web/docs/userguide/procedures/nodes/temperaturenode.md rename to web/docs/userguide/generators/nodes/temperaturenode.md diff --git a/web/docs/userguide/procedures/nodes/transmutenode.md b/web/docs/userguide/generators/nodes/transmutenode.md similarity index 100% rename from web/docs/userguide/procedures/nodes/transmutenode.md rename to web/docs/userguide/generators/nodes/transmutenode.md diff --git a/web/docs/userguide/gui/configurationtab.md b/web/docs/userguide/gui/configurationtab.md index d8281cb37b..7d0aacb8d3 100644 --- a/web/docs/userguide/gui/configurationtab.md +++ b/web/docs/userguide/gui/configurationtab.md @@ -20,4 +20,4 @@ This option can be used to scale the positions of molecules within the box, incr #### Generator -A configuration is created from a generator [procedure]({{< ref "procedures" >}}) allowing it to be reconstructed automatically on demand. The defined procedure can be viewed and edited directly here. \ No newline at end of file +A configuration is created from a [generatore]({{< ref "generators" >}}) allowing it to be reconstructed automatically on demand. The defined procedure can be viewed and edited directly here. \ No newline at end of file diff --git a/web/docs/userguide/guide/workflow.md b/web/docs/userguide/guide/workflow.md index d6a0496c53..ebd7d21ff9 100644 --- a/web/docs/userguide/guide/workflow.md +++ b/web/docs/userguide/guide/workflow.md @@ -21,7 +21,7 @@ With all of this ready to go, the first step is equilibrating the system. ## Equilibration -Typically, Dissolve will construct your initial configuration box from a defined generator [procedure]({{< ref "procedures" >}}) and which will most likely involve adding molecules at random positions and rotations. The first step is to equilibrate this high-energy system to a state where the energy is stable and there are no bad overlaps between atoms left in the system. The energy is of course completely defined by the forcefield you've used on your species, so we need to make a further assumption here that it is a reasonable forcefield! +Typically, Dissolve will construct your initial configuration box from a defined [generator]({{< ref "generators" >}}) and which will most likely involve adding molecules at random positions and rotations. The first step is to equilibrate this high-energy system to a state where the energy is stable and there are no bad overlaps between atoms left in the system. The energy is of course completely defined by the forcefield you've used on your species, so we need to make a further assumption here that it is a reasonable forcefield! For bulk liquid systems it is generally a good idea to apply a size factor to the box during these initial stages - this scales the box volume and the positions of the molecules, and greatly helps in the removal of overlapping molecules. You can find this option on the [configuration tab]({{< ref "configurationtab" >}}), and a reasonable value to use is `10`. diff --git a/web/docs/userguide/inputfile/configurationblock.md b/web/docs/userguide/inputfile/configurationblock.md index b06774ce5d..6873d2f208 100644 --- a/web/docs/userguide/inputfile/configurationblock.md +++ b/web/docs/userguide/inputfile/configurationblock.md @@ -11,14 +11,14 @@ The block keyword itself takes a single (required) argument - the name of the co ## Keywords -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`CellDivisionLength`|`double`|`7.0`|Set the side length, in Angstroms, of sub-cell regions into which the configuration's unit cell will be partitioned for the purposes of near-neighbour calculation. The actual side length used to partition the cell will likely differ from the supplied value, in order to ensure full coverage of the whole unit cell volume.| -|`EndConfiguration`|--|--|Indicates the end of the current `Configuration` block.| -|`Generator`|[`Procedure`]({{< ref "procedures" >}})|--|Specifies a complete [`Procedure`]({{< ref "procedures" >}}) able to generate the unit cell and contents of the configuration. The 'generator' procedure is called before the main simulation loop begins, unless an existing snapshot of the configuration has been loaded in from a restart file| -|`InputCoordinates`|[`CoordinatesFileAndFormat`]({{< ref "coordinatesformat" >}})|--|Load atomic coordinates from the specified file and format. The `Generator` procedure is still used to construct the initial contents in terms of species etc., but the coordinates of the atoms are subsequently overwritten by those from the file.| -|`SizeFactor`|`double`|`1.0`|Factor by which to temporarily scale the unit cell and molecule centres of geometry. This option is typically used to remove overlaps between molecules containing ring structures, which would otherwise become interlocked for the duration of the simulation. If greater than 1.0, the intermolecular energy is assessed at the beginning of each main loop iteration. If this energy is negative, the size factor is reduced by a predefined factor.| -|`Temperature`|`double`|`300`|Temperature of the configuration in Kelvin.| +|Keyword| Arguments |Default| Description | +|:------|:-------------------------------------------------------------:|:-----:|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +|`CellDivisionLength`| `double` |`7.0`| Set the side length, in Angstroms, of sub-cell regions into which the configuration's unit cell will be partitioned for the purposes of near-neighbour calculation. The actual side length used to partition the cell will likely differ from the supplied value, in order to ensure full coverage of the whole unit cell volume. | +|`EndConfiguration`| -- |--| Indicates the end of the current `Configuration` block. | +|`Generator`| [`Generator`]({{< ref "generators" >}}) |--| Specifies a stepwise [`Generator`]({{< ref "generators" >}}) able to generate the unit cell and contents of the configuration. The generator is called before the main simulation loop begins, unless an existing snapshot of the configuration has been loaded in from a restart file | +|`InputCoordinates`| [`CoordinatesFileAndFormat`]({{< ref "coordinatesformat" >}}) |--| Load atomic coordinates from the specified file and format. The `Generator` procedure is still used to construct the initial contents in terms of species etc., but the coordinates of the atoms are subsequently overwritten by those from the file. | +|`SizeFactor`| `double` |`1.0`| Factor by which to temporarily scale the unit cell and molecule centres of geometry. This option is typically used to remove overlaps between molecules containing ring structures, which would otherwise become interlocked for the duration of the simulation. If greater than 1.0, the intermolecular energy is assessed at the beginning of each main loop iteration. If this energy is negative, the size factor is reduced by a predefined factor. | +|`Temperature`| `double` |`300`| Temperature of the configuration in Kelvin. | ## Example diff --git a/web/docs/userguide/modules/analysis/analyse/_index.md b/web/docs/userguide/modules/analysis/analyse/_index.md deleted file mode 100644 index 7fc7176d61..0000000000 --- a/web/docs/userguide/modules/analysis/analyse/_index.md +++ /dev/null @@ -1,17 +0,0 @@ ---- -title: Analyse (Module) -linkTitle: Analyse -description: Define and perform a custom analysis routine ---- - -## Overview - -The `Analyse` module allows a custom analysis [procedure]({{< ref "procedures" >}}) to be defined, allowing almost any quantity to be calculated from a given configuration. - -## Options - -### Targets - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`Configuration`|`Configuration`|--|{{< required-label >}}Specifies the configuration on which to operate.| diff --git a/web/docs/userguide/procedures/nodes/calculateanglenode.md b/web/docs/userguide/procedures/nodes/calculateanglenode.md deleted file mode 100644 index 8ef7429c59..0000000000 --- a/web/docs/userguide/procedures/nodes/calculateanglenode.md +++ /dev/null @@ -1,39 +0,0 @@ ---- -title: Angle (Node) -linkTitle: Angle -description: Calculate angle between three sites ---- - -{{< htable >}} -| | | -|-|-| -|Context|Analysis| -|Name Required?|Yes| -|Branches|--| -{{< /htable >}} - -## Overview - -The `Angle` node calculates the angle, in degrees, between three provided sites $i$, $j$, and $k$, which are referenced from {{< node "Select" >}} nodes. - -## Description - -`Angle` is one of several calculation nodes that determine and store a numerical result, ready for retrieval and use by other nodes in a procedure. - -`Angle` determines the angle $i$-$j$-$k$ between the selected sites $i$, $j$, and $k$, obeying minimum image distances if the encompassing box is periodic. The resulting value is measured in degrees. - -## Options - -### Sites - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`I`|{{< node "Select" >}}|--|Site that represents $i$ in the angle $i$-$j$-$k$, taken from the named {{< node "Select" >}} node.| -|`J`|{{< node "Select" >}}|--|Site that represents $j$ in the angle $i$-$j$-$k$, taken from the named {{< node "Select" >}} node.| -|`K`|{{< node "Select" >}}|--|Site that represents $k$ in the angle $i$-$j$-$k$, taken from the named {{< node "Select" >}} node.| - -### Control - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`Symmetric`|`bool`|`false`|Whether to consider angles as symmetric about 90, mapping all angles to the range 0 - 90.| diff --git a/web/docs/userguide/procedures/nodes/calculateaxisanglenode.md b/web/docs/userguide/procedures/nodes/calculateaxisanglenode.md deleted file mode 100644 index 5aa821b441..0000000000 --- a/web/docs/userguide/procedures/nodes/calculateaxisanglenode.md +++ /dev/null @@ -1,40 +0,0 @@ ---- -title: AxisAngle (Node) -linkTitle: AxisAngle -description: Calculate angle between axes on two oriented sites ---- - -{{< htable >}} -| | | -|-|-| -|Context|Analysis| -|Name Required?|Yes| -|Branches|--| -{{< /htable >}} - -## Overview - -The `AxisAngle` node calculates the angle, in degrees, between specific axes on two sites $i$ and $j$, which are referenced from {{< node "Select" >}} nodes. - -## Description - -`AxisAngle` is one of several calculation nodes that determine and store a numerical result, ready for retrieval and use by other nodes in a procedure. - -`AxisAngle` determines the angle formed between specific axes on two oriented sites $i$ and $j$, mapping the origins of both axes to {0,0,0}. The resulting value is measured in degrees. - -## Options - -### Sites - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`I`|{{< node "Select" >}}|--|Site that represents $i$ in the angle $i$-$j$-$k$, taken from the named {{< node "Select" >}} node.| -|`J`|{{< node "Select" >}}|--|Site that represents $j$ in the angle $i$-$j$-$k$, taken from the named {{< node "Select" >}} node.| -|`AxisI`|`X|Y|Z`|`X`|Axis to use from site I| -|`AxisJ`|`X|Y|Z`|`X`|Axis to use from site J| - -### Control - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`Symmetric`|`bool`|`false`|Whether to consider angles as symmetric about 90, mapping all angles to the range 0 - 90.| diff --git a/web/docs/userguide/procedures/nodes/calculatedistancenode.md b/web/docs/userguide/procedures/nodes/calculatedistancenode.md deleted file mode 100644 index db4a2c8be4..0000000000 --- a/web/docs/userguide/procedures/nodes/calculatedistancenode.md +++ /dev/null @@ -1,32 +0,0 @@ ---- -title: CalculateDistance (Node) -linkTitle: CalculateDistance -description: Calculate distance between two sites ---- - -{{< htable >}} -| | | -|-|-| -|Context|Analysis| -|Name Required?|Yes| -|Branches|--| -{{< /htable >}} - -## Overview - -The `CalculateDistance` node calculates the distance, in Angstroms, between two provided sites $i$ and $j$, which are referenced from {{< node "Select" >}} nodes. - -## Description - -`CalculateDistance` is one of several calculation nodes that determine and store a numerical result, ready for retrieval and use by other nodes in a procedure. - -`CalculateDistance` determines the distance $i$-$j$ between the selected sites $i$ and $j$, obeying the minimum image convention if the encompassing box is periodic. The resulting value is measured in Angstroms. - -## Options - -### Sites - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`I`|{{< node "Select" >}}|--|Site that represents $i$ in the distance $i$-$j$, taken from the named {{< node "Select" >}} node.| -|`J`|{{< node "Select" >}}|--|Site that represents $j$ in the distance $i$-$j$, taken from the named {{< node "Select" >}} node.| diff --git a/web/docs/userguide/procedures/nodes/calculateexpression.md b/web/docs/userguide/procedures/nodes/calculateexpression.md deleted file mode 100644 index 2c4d9fdf35..0000000000 --- a/web/docs/userguide/procedures/nodes/calculateexpression.md +++ /dev/null @@ -1,29 +0,0 @@ ---- -title: CalculateExpression (Node) -linkTitle: CalculateExpression -description: Calculate distance between two sites ---- - -{{< htable >}} -| | | -|-|-| -|Context|Analysis| -|Name Required?|Yes| -|Branches|--| -{{< /htable >}} - -## Overview - -The `CalculateExpression` node calculates the result of an arbitrary mathematical [expression]({{< ref expressions >}}). - -## Description - -`CalculateExpression` is one of several calculation nodes that determine and store a numerical result, ready for retrieval and use by other nodes in a procedure. - -`CalculateExpression` returns the result of evaluating its defined expression. - -## Options - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`Expression`|``|--|The expression to evaluate.| diff --git a/web/docs/userguide/procedures/nodes/calculatevectornode.md b/web/docs/userguide/procedures/nodes/calculatevectornode.md deleted file mode 100644 index 525e051199..0000000000 --- a/web/docs/userguide/procedures/nodes/calculatevectornode.md +++ /dev/null @@ -1,38 +0,0 @@ ---- -title: CalculateVector (Node) -linkTitle: CalculateVector -description: Calculate a vector between two sites ---- - -{{< htable >}} -| | | -|-|-| -|Context|Analysis| -|Name Required?|Yes| -|Branches|--| -{{< /htable >}} - -## Overview - -The `CalculateVector` node calculates the vector between two provided sites $i$ and $j$, which are referenced from {{< node "Select" >}} nodes. - -## Description - -`CalculateVector` is one of several calculation nodes that determine and store a numerical result, ready for retrieval and use by other nodes in a procedure. - -`CalculateVector` determines the vector $v_{ij}$ in 3D space between the selected sites $i$ and $j$, obeying the minimum image convention if the encompassing box is periodic. The resulting value is measured in Angstroms. - -## Options - -### Sites - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`I`|{{< node "Select" >}}|--|Site that represents $i$ in the distance $i$-$j$, taken from the named {{< node "Select" >}} node.| -|`J`|{{< node "Select" >}}|--|Site that represents $j$ in the distance $i$-$j$, taken from the named {{< node "Select" >}} node.| - -### Control - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`RotateIntoFrame`|`bool`|`false`|Whether to rotate the calculated vector into the local frame defined on $i$. If `true`, and the site $i$ has a set of axes defined, the vector is rotated into the frame of those axes.| diff --git a/web/docs/userguide/procedures/nodes/collect1dnode.md b/web/docs/userguide/procedures/nodes/collect1dnode.md deleted file mode 100644 index ad71d294f5..0000000000 --- a/web/docs/userguide/procedures/nodes/collect1dnode.md +++ /dev/null @@ -1,36 +0,0 @@ ---- -title: Collect1D (Node) -linkTitle: Collect1D -description: Accumulate a 1D histogram ---- - -{{< htable >}} -| | | -|-|-| -|Context|Analysis| -|Name Required?|Yes| -|Branches|`SubCollect`| -{{< /htable >}} - -## Overview - -The `Collect1D` node is used to accumulate a histogram of a one-dimensional quantity, extracted from a `Calculate`-style nodes. - -## Description - -Where the `Calculate*` nodes are responsible for calculating quantities, the `Collect*` nodes are responsible for accumulating averages, typically in histogram format. - -`Collect1D` accumulates a histogram of a target value taken from a `Calculate*` node, over a specified range and binwidth. No post-processing (e.g. normalisation) is performed by `Collect1D` - see the {{< node "Process1D" >}}for processing options. - -## Branching - -The `Collect*` nodes all have a branch (accessed through the hidden `SubCollect` keyword) which is executed if the value is successfully binned (i.e. is within all ranges specified). - -## Options - -### Quantities / Ranges - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`QuantityX`|`name`
`[index]`|--|{{< required-label >}} The calculated observable to collect. The named node must be one of the `Calculate*` nodes. The `index` specifies which value to take from multi-dimensional observables, starting from zero for the first. If not specified, index` defaults to zero.| -|`RangeX `|`min`
`max`
`delta`|--|Defines the range and binwidth of the histogram over which `QuantityX` will be accumulated.| diff --git a/web/docs/userguide/procedures/nodes/collect2dnode.md b/web/docs/userguide/procedures/nodes/collect2dnode.md deleted file mode 100644 index d7640eeb9c..0000000000 --- a/web/docs/userguide/procedures/nodes/collect2dnode.md +++ /dev/null @@ -1,38 +0,0 @@ ---- -title: Collect2D (Node) -linkTitle: Collect2D -description: Accumulate a 2D histogram ---- - -{{< htable >}} -| | | -|-|-| -|Context|Analysis| -|Name Required?|Yes| -|Branches|`SubCollect`| -{{< /htable >}} - -## Overview - -The `Collect2D` node is used to accumulate a histogram over two dimensions, using values extracted from two `Calculate`-style nodes. - -## Description - -Where the `Calculate*` nodes are responsible for calculating quantities, the `Collect*` nodes are responsible for accumulating averages, typically in histogram format. - -`Collect2D` accumulates a histogram over two dimensions using target values taken from two `Calculate*` nodes, over a specified range and binwidth for each dimension. The values are treated as a pair giving the {x,y} coordinate to bin in the histogram. No post-processing (e.g. normalisation) is performed by `Collect2D` - see the {{< node "Process2D" >}}for processing options. - -## Branching - -The `Collect*` nodes all have a branch (accessed through the hidden `SubCollect` keyword) which is executed if the value is successfully binned (i.e. is within all ranges specified). - -## Options - -### Quantities / Ranges - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`QuantityX`|`name`
`[index]`|--|{{< required-label >}} The calculated observable to use for the x axis. The named node must be one of the `Calculate*` nodes. The `index` specifies which value to take from multi-dimensional observables, starting from zero for the first. If not specified, index` defaults to zero.| -|`QuantityY`|`name`
`[index]`|--|{{< required-label >}} The calculated observable to use for the y axis. The named node must be one of the `Calculate*` nodes. The `index` specifies which value to take from multi-dimensional observables, starting from zero for the first. If not specified, index` defaults to zero.| -|`RangeX `|`min`
`max`
`delta`|--|Defines the range and binwidth of the x-axis of the histogram.| -|`RangeY `|`min`
`max`
`delta`|--|Defines the range and binwidth of the y-axis of the histogram.| diff --git a/web/docs/userguide/procedures/nodes/collect3dnode.md b/web/docs/userguide/procedures/nodes/collect3dnode.md deleted file mode 100644 index 26ecc804e6..0000000000 --- a/web/docs/userguide/procedures/nodes/collect3dnode.md +++ /dev/null @@ -1,40 +0,0 @@ ---- -title: Collect3D (Node) -linkTitle: Collect3D -description: Accumulate a 3D histogram ---- - -{{< htable >}} -| | | -|-|-| -|Context|Analysis| -|Name Required?|Yes| -|Branches|`SubCollect`| -{{< /htable >}} - -## Overview - -The `Collect3D` node is used to accumulate a histogram over three dimensions, using values extracted from three `Calculate`-style nodes. - -## Description - -Where the `Calculate*` nodes are responsible for calculating quantities, the `Collect*` nodes are responsible for accumulating averages, typically in histogram format. - -`Collect3D` accumulates a histogram over three dimensions using target values taken from two `Calculate*` nodes, over a specified range and binwidth for each dimension. The values are treated as a triplet giving the {x,y,z} coordinate to bin in the histogram. No post-processing (e.g. normalisation) is performed by `Collect3D` - see the {{< node "Process3D" >}}for processing options. - -## Branching - -The `Collect*` nodes all have a branch (accessed through the hidden `SubCollect` keyword) which is executed if the value is successfully binned (i.e. is within all ranges specified). - -## Options - -### Quantities / Ranges - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`QuantityX`|`name`
`[index]`|--|{{< required-label >}} The calculated observable to use for the x axis. The named node must be one of the `Calculate*` nodes. The `index` specifies which value to take from multi-dimensional observables, starting from zero for the first. If not specified, `index` defaults to zero.| -|`QuantityY`|`name`
`[index]`|--|{{< required-label >}} The calculated observable to use for the y axis. The named node must be one of the `Calculate*` nodes. The `index` specifies which value to take from multi-dimensional observables, starting from zero for the first. If not specified, `index` defaults to zero.| -|`QuantityZ`|`name`
`[index]`|--|{{< required-label >}} The calculated observable to use for the z axis. The named node must be one of the `Calculate*` nodes. The `index` specifies which value to take from multi-dimensional observables, starting from zero for the first. If not specified, `index` defaults to zero.| -|`RangeX `|`min`
`max`
`delta`|--|Defines the range and binwidth of the x-axis of the histogram.| -|`RangeY `|`min`
`max`
`delta`|--|Defines the range and binwidth of the y-axis of the histogram.| -|`RangeZ `|`min`
`max`
`delta`|--|Defines the range and binwidth of the z-axis of the histogram.| diff --git a/web/docs/userguide/procedures/nodes/integercollect1d.md b/web/docs/userguide/procedures/nodes/integercollect1d.md deleted file mode 100644 index 6c38a6417b..0000000000 --- a/web/docs/userguide/procedures/nodes/integercollect1d.md +++ /dev/null @@ -1,37 +0,0 @@ ---- -title: IntegerCollect1D (Node) -linkTitle: IntegerCollect1D -description: Accumulate a 1D histogram of explicit integer values ---- - -{{< htable >}} -| | | -|-|-| -|Context|Analysis| -|Name Required?|Yes| -|Branches|`SubCollect`| -{{< /htable >}} - -## Overview - -The `IntegerCollect1D` node is used to accumulate a histogram of a one-dimensional quantity, extracted from a `Calculate`-style nodes, with strictly integer binning. Unlike its `Collect1D` counterpart it is not necessary to specify the limits for the collection - in such a case all integer values will be binned. - -## Description - -Where the `Calculate*` nodes are responsible for calculating quantities, the `Collect*` nodes are responsible for accumulating averages, typically in histogram format. - -`IntegerCollect1D` accumulates a histogram of a target value taken from a `Calculate*` node and binning into integer-sized bins. No post-processing (e.g. normalisation) is performed by `IntegerCollect1D` - see the {{< node "Process1D" >}}for processing options. - -## Branching - -The `IntegerCollect1D` node has a branch (accessed through the hidden `SubCollect` keyword) which is executed if the value is successfully binned (i.e. is within all ranges specified). - -## Options - -### Quantities / Ranges - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`Maximum `|`int`|--|Defines the optional maximum limit for binning| -|`Minimum `|`int`|--|Defines the optional minimum limit for binning| -|`QuantityX`|`name`
`[index]`|--|{{< required-label >}} The calculated observable to collect. The named node must be one of the `Calculate*` nodes. The `index` specifies which value to take from multi-dimensional observables, starting from zero for the first. If not specified, index` defaults to zero.| diff --git a/web/docs/userguide/procedures/nodes/integrate1d.md b/web/docs/userguide/procedures/nodes/integrate1d.md deleted file mode 100644 index 9dae418c7b..0000000000 --- a/web/docs/userguide/procedures/nodes/integrate1d.md +++ /dev/null @@ -1,33 +0,0 @@ ---- -title: Integrate1D (Node) -linkTitle: Integrate1D -description: Perform integration on 1D data ---- - -{{< htable >}} -| | | -|-|-| -|Context|Operate| -|Name Required?|No| -|Branches|--| -{{< /htable >}} - -## Overview - -The `Integrate1D` node integrates up to three regions of a supplied {{< node "Process1D" >}} node. - -## Options - -### Target - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`SourceData`|{{< node "Process1D" >}}|--|Process1D node containing the data to integrate.| - -### Ranges - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`RangeA`|`double double`|--|X range for first integration region.| -|`RangeB`|`double double`|--|X range for second integration region.| -|`RangeC`|`double double`|--|X range for third integration region.| diff --git a/web/docs/userguide/procedures/nodes/operatedividenode.md b/web/docs/userguide/procedures/nodes/operatedividenode.md deleted file mode 100644 index 9c9f362f14..0000000000 --- a/web/docs/userguide/procedures/nodes/operatedividenode.md +++ /dev/null @@ -1,31 +0,0 @@ ---- -title: OperateDivide (Node) -linkTitle: OperateDivide -description: Perform division on numerical data ---- - -{{< htable >}} -| | | -|-|-| -|Context|Operate| -|Name Required?|No| -|Branches|--| -{{< /htable >}} - -## Overview - -The `OperateDivide` node performs a division operation on data supplied to it. - -## Description - -In the "Operate" context all `Operate*` nodes are passed data of some dimensionality (e.g. from one of the `Process*` nodes) which is then subjected to some kind of mathematical operation. - -The `OperateDivide` node simply divides the values (not the axes) of the supplied data by a specified constant. The target data may be of any dimensionality. - -## Options - -### Inputs - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`Value`|`double`|`1.0`|Constant value to use as the divisor.| diff --git a/web/docs/userguide/procedures/nodes/operateexpressionnode.md b/web/docs/userguide/procedures/nodes/operateexpressionnode.md deleted file mode 100644 index d20b243112..0000000000 --- a/web/docs/userguide/procedures/nodes/operateexpressionnode.md +++ /dev/null @@ -1,31 +0,0 @@ ---- -title: OperateExpression (Node) -linkTitle: OperateExpression -description: Apply an expression to numerical data ---- - -{{< htable >}} -| | | -|-|-| -|Context|Operate| -|Name Required?|No| -|Branches|--| -{{< /htable >}} - -## Overview - -The `OperateExpression` node performs a multiplication operation on data supplied to it, using the result of a numerical expression as the multiplier on a per-bin basis. - -## Description - -In the "Operate" context all `Operate*` nodes are passed data of some dimensionality (e.g. from one of the `Process*` nodes) which is then subjected to some kind of mathematical operation. - -The `OperateExpression` node multiplies the values (not the axes) of the supplied data by the result of the supplied expression. The expression has access to the x, y, and z values of the current bin when performing the multiplication, and so the multiplier can vary according to zero or more of those quantities. The target data may be of any dimensionality. - -## Options - -### Inputs - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`Value`|[`Expression`]({{< ref "expressions" >}})|`1.0`|Value expression to use as the multiplier.| diff --git a/web/docs/userguide/procedures/nodes/operatemultiplynode.md b/web/docs/userguide/procedures/nodes/operatemultiplynode.md deleted file mode 100644 index d3b78a091e..0000000000 --- a/web/docs/userguide/procedures/nodes/operatemultiplynode.md +++ /dev/null @@ -1,31 +0,0 @@ ---- -title: OperateMultiply (Node) -linkTitle: OperateMultiply -description: Perform multiplication of numerical data ---- - -{{< htable >}} -| | | -|-|-| -|Context|Operate| -|Name Required?|No| -|Branches|--| -{{< /htable >}} - -## Overview - -The `OperateMultiply` node performs a multiplication operation on data supplied to it. - -## Description - -In the "Operate" context all `Operate*` nodes are passed data of some dimensionality (e.g. from one of the `Process*` nodes) which is then subjected to some kind of mathematical operation. - -The `OperateMultiply` node simply multiplies the values (not the axes) of the supplied data by a specified constant. The target data may be of any dimensionality. - -## Options - -### Inputs - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`Value`|`double`|`1.0`|Constant value to use as the multiplier.| diff --git a/web/docs/userguide/procedures/nodes/operatenormalisenode.md b/web/docs/userguide/procedures/nodes/operatenormalisenode.md deleted file mode 100644 index 593c113277..0000000000 --- a/web/docs/userguide/procedures/nodes/operatenormalisenode.md +++ /dev/null @@ -1,32 +0,0 @@ ---- -title: OperateNormalise (Node) -linkTitle: OperateNormalise -description: Perform normalisation of numerical data ---- - -{{< htable >}} -| | | -|-|-| -|Context|Operate| -|Name Required?|No| -|Branches|--| -{{< /htable >}} - -## Overview - -The `OperateNormalise` node normalises a data-space sum to a specific value. - -## Description - -In the "Operate" context all `Operate*` nodes are passed data of some dimensionality (e.g. from one of the `Process*` nodes) which is then subjected to some kind of mathematical operation. - -The `OperateNormalise` node calculates the sum (or absolute sum) of the supplied data, and divides all values by the sum in order to give the normalised data whose sum equals 1.0. The data is then multiplied by the supplied value (which also defaults to 1.0) to give a sum other than 1.0. The target data may be of any dimensionality. - -## Options - -### Inputs - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`Value`|`double`|`1.0`|Constant value to normalise to.| -|`Absolute`|`bool`|`false`|Whether to use the absolute sum of values rather than the direct sum.| diff --git a/web/docs/userguide/procedures/nodes/operatenumberdensitynormalisenode.md b/web/docs/userguide/procedures/nodes/operatenumberdensitynormalisenode.md deleted file mode 100644 index 92f0f850f0..0000000000 --- a/web/docs/userguide/procedures/nodes/operatenumberdensitynormalisenode.md +++ /dev/null @@ -1,32 +0,0 @@ ---- -title: OperateNumberDensityNormalise (Node) -linkTitle: OperateNumberDensityNormalise -description: Normalise data to the number density of target site(s) ---- - -{{< htable >}} -| | | -|-|-| -|Context|Operate| -|Name Required?|No| -|Branches|--| -{{< /htable >}} - -## Overview - -The `OperateNumberDensityNormalise` node performs a division operation on data supplied to it, using the number densities of target sites as sequential divisors. - -## Description - -In the "Operate" context all `Operate*` nodes are passed data of some dimensionality (e.g. from one of the `Process*` nodes) which is then subjected to some kind of mathematical operation. - -The `OperateNumberDensityNormalise` node simply divides the values (not the axes) of the supplied data by the number density of one or more target sites. The target data may be of any dimensionality. - -## Options - -### Inputs - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`Population`|{{< ref "selectionpopulation" >}}|`Available`|Aspect of the population defined by the specified {{< node "Select" >}} nodes to use in the normalisation| -|`Site`|{{< node "Select" >}} ...|--|{{< required-label >}} One or more named {{< node "Select" >}} nodes from which the site populations, along with the configuration box volume, are used to calculate number densities in atoms/A3, and which are then used as divisors on the data. If more than one {{< node "Select" >}} nodes is given, the divisions are made sequentially.| diff --git a/web/docs/userguide/procedures/nodes/operatesitepopulationnormalisenode.md b/web/docs/userguide/procedures/nodes/operatesitepopulationnormalisenode.md deleted file mode 100644 index 8767fe7044..0000000000 --- a/web/docs/userguide/procedures/nodes/operatesitepopulationnormalisenode.md +++ /dev/null @@ -1,31 +0,0 @@ ---- -title: OperateSitePopulationNormalise (Node) -linkTitle: OperateSitePopulationNormalise -description: Normalise data to the populations of target site(s) ---- - -{{< htable >}} -| | | -|-|-| -|Context|Operate| -|Name Required?|No| -|Branches|--| -{{< /htable >}} - -## Overview - -The `OperateSitePopulationNormalise` node performs a division operation on data supplied to it, using the populations of target sites as sequential divisors. - -## Description - -In the "Operate" context all `Operate*` nodes are passed data of some dimensionality (e.g. from one of the `Process*` nodes) which is then subjected to some kind of mathematical operation. - -The `OperateSitePopulationNormalise` node simply divides the values (not the axes) of the supplied data by the populations of one or more target sites. The target data may be of any dimensionality. - -## Options - -### Inputs - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`Site`|{{< node "Select" >}} ...|--|{{< required-label >}} One or more named {{< node "Select" >}} nodes from which the site populations are used as divisors on the data. If more than one {{< node "Select" >}} nodes is given, the divisions are made sequentially.| diff --git a/web/docs/userguide/procedures/nodes/operatesphericalshellnormalisenode.md b/web/docs/userguide/procedures/nodes/operatesphericalshellnormalisenode.md deleted file mode 100644 index 76b2f2907a..0000000000 --- a/web/docs/userguide/procedures/nodes/operatesphericalshellnormalisenode.md +++ /dev/null @@ -1,23 +0,0 @@ ---- -title: OperateSphericalShellNormalise (Node) -linkTitle: OperateSphericalShellNormalise -description: Normalise 1D data to spherical shell volumes ---- - -{{< htable >}} -| | | -|-|-| -|Context|Operate| -|Name Required?|No| -|Branches|--| -{{< /htable >}} - -## Overview - -The `OperateSphericalShellNormalise` node is a specialised node which normalises values against spherical shell volumes. As such it is primarily used when normalising histograms in order to achieve a radial distribution function. - -## Description - -In the "Operate" context all `Operate*` nodes are passed data of some dimensionality (e.g. from one of the `Process*` nodes) which is then subjected to some kind of mathematical operation. - -The `OperateSphericalShellNormalise` node can only operate on one-dimensional data (e.g. from a {{< node "Process1D" >}} and assumes that the x axis of the data represents distance, as in a radial distribution function. From the x axis values, the volumes of spherical shells centred at those distances are calculated and used as divisors on the values. diff --git a/web/docs/userguide/procedures/nodes/process1dnode.md b/web/docs/userguide/procedures/nodes/process1dnode.md deleted file mode 100644 index 3153f0088c..0000000000 --- a/web/docs/userguide/procedures/nodes/process1dnode.md +++ /dev/null @@ -1,51 +0,0 @@ ---- -title: Process1D (Node) -linkTitle: Process1D -description: Process a 1D histogram ---- - -{{< htable >}} -| | | -|-|-| -|Context|Analysis| -|Name Required?|Yes| -|Branches|`Normalisation`| -{{< /htable >}} - -## Overview - -The `Process1D` node is used to process histogram data generated by the {{< node "Collect1D" >}}and expose it for visualisation and export. - -## Description - -Once a {{< node "Collect1D" >}} node has accumulated a histogram, the `Process1D` node can process it into something meaningful to the user, adjusting, scaling, and normalising as appropriate. It also lets axis names be assigned to the data, and converts the original histogram data into a form suitable for plotting and/or export. - -Scaling, normalisation, and other operations on the data can be performed through the the node's local branch (see below). - -The `Process1D` node is intended to appear at the very end of a procedure, preparing the collected data for consumption. - -## Branching - -The `Process*` nodes all have a branch with the "Operate" context (accessed through the hidden `Normalisation` keyword) which is always executed, and can be used to perform mathematical operations via a sequence of `Operate*` nodes. - -## Options - -### Source - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`Instantaneous`|`bool`|`false`|Whether the processed data should reflect the accumulated histogram data (`false`) or the "instantaneous" data from the last iteration only (`true`).| -|`SourceData`|`name`|--|{{< required-label >}} The `name` of a {{< node "Collect1D" >}} node containing the histogram data to process.| - -### Labels - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`LabelValue`|`label`|`"Y"`|Label for the value axis| -|`LabelX`|`label`|`"X"`|Label for the x axis| - -### Export - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`Export`|[`Data1DFileAndFormat`]({{< ref "data1dformat" >}})|--|File format and file name under which to save processed data.| diff --git a/web/docs/userguide/procedures/nodes/process2dnode.md b/web/docs/userguide/procedures/nodes/process2dnode.md deleted file mode 100644 index f7ec4d599e..0000000000 --- a/web/docs/userguide/procedures/nodes/process2dnode.md +++ /dev/null @@ -1,51 +0,0 @@ ---- -title: Process2D (Node) -linkTitle: Process2D -description: Process a 2D histogram ---- - -{{< htable >}} -| | | -|-|-| -|Context|Analysis| -|Name Required?|Yes| -|Branches|`Normalisation`| -{{< /htable >}} - -## Overview - -The `Process2D` node is used to process histogram data generated by the {{< node "Collect2D" >}}and expose it for visualisation and export. - -## Description - -Once a {{< node "Collect2D" >}} node has accumulated a histogram, the `Process2D` node can process it into something meaningful to the user, adjusting, scaling, and normalising as appropriate. It also lets axis names be assigned to the data, and converts the original histogram data into a form suitable for plotting and/or export. - -Scaling, normalisation, and other operations on the data can be performed through the the node's local branch (see below). - -The `Process2D` node is intended to appear at the very end of a procedure, preparing the collected data for consumption. - -## Branching - -The `Process*` nodes all have a branch with the "Operate" context (accessed through the hidden `Normalisation` keyword) which is always executed, and can be used to perform mathematical operations via a sequence of `Operate*` nodes. - -## Options - -### Source - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`SourceData`|`name`|--|{{< required-label >}} The `name` of a {{< node "Collect2D" >}} node containing the histogram data to process.| - -### Labels - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`LabelValue`|`label`|`"Counts"`|Label for the value axis| -|`LabelX`|`label`|`"X"`|Label for the x axis| -|`LabelY`|`label`|`"Y"`|Label for the y axis| - -### Export - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`Export`|[`Data2DFileAndFormat`]({{< ref "data2dformat" >}})|--|File format and file name under which to save processed data.| diff --git a/web/docs/userguide/procedures/nodes/process3dnode.md b/web/docs/userguide/procedures/nodes/process3dnode.md deleted file mode 100644 index 8bb57976db..0000000000 --- a/web/docs/userguide/procedures/nodes/process3dnode.md +++ /dev/null @@ -1,52 +0,0 @@ ---- -title: Process3D (Node) -linkTitle: Process3D -description: Process a 3D histogram ---- - -{{< htable >}} -| | | -|-|-| -|Context|Analysis| -|Name Required?|Yes| -|Branches|`Normalisation`| -{{< /htable >}} - -## Overview - -The `Process3D` node is used to process histogram data generated by the {{< node "Collect3D" >}}and expose it for visualisation and export. - -## Description - -Once a {{< node "Collect3D" >}} node has accumulated a histogram, the `Process3D` node can process it into something meaningful to the user, adjusting, scaling, and normalising as appropriate. It also lets axis names be assigned to the data, and converts the original histogram data into a form suitable for plotting and/or export. - -Scaling, normalisation, and other operations on the data can be performed through the the node's local branch (see below). - -The `Process3D` node is intended to appear at the very end of a procedure, preparing the collected data for consumption. - -## Branching - -The `Process*` nodes all have a branch with the "Operate" context (accessed through the hidden `Normalisation` keyword) which is always executed, and can be used to perform mathematical operations via a sequence of `Operate*` nodes. - -## Options - -### Source - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`SourceData`|`name`|--|{{< required-label >}} The `name` of a {{< node "Collect3D" >}} node containing the histogram data to process.| - -### Labels - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`LabelValue`|`label`|`"Counts"`|Label for the value axis| -|`LabelX`|`label`|`"X"`|Label for the x axis| -|`LabelY`|`label`|`"Y"`|Label for the y axis| -|`LabelZ`|`label`|`"Z"`|Label for the z axis| - -### Export - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`Export`|[`Data3DFileAndFormat`]({{< ref "data3dformat" >}})|--|File format and file name under which to save processed data.| diff --git a/web/docs/userguide/procedures/nodes/sum1dnode.md b/web/docs/userguide/procedures/nodes/sum1dnode.md deleted file mode 100644 index f461f61591..0000000000 --- a/web/docs/userguide/procedures/nodes/sum1dnode.md +++ /dev/null @@ -1,42 +0,0 @@ ---- -title: Sum1D (Node) -linkTitle: Sum1D -description: Sum 1D data over ranges ---- - -{{< htable >}} -| | | -|-|-| -|Context|Analysis| -|Name Required?|No| -|Branches|--| -{{< /htable >}} - -## Overview - -The `Sum1D` node is used to form summations over up to three defined regions of data produced by a {{< node "Process1D" >}} node. - -## Description - -Once a {{< node "Process1D" >}} node has processed data into something meaningful the `Sum1D` node can perform a summation of that data over defined ranges, providing an averaged value of the quantity. - -Note that, of the three ranges, the first ("A") is always calculated. - -## Options - -### Source - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`Instantaneous`|`bool`|`false`|Whether the processed data should reflect the accumulated average over the defined ranges (`false`) or the "instantaneous" value (`true`).| -|`SourceData`|`name`|--|{{< required-label >}} The `name` of a {{< node "Process1D" >}} node containing the target data.| - -### Ranges - -|Keyword|Arguments|Default|Description| -|:------|:--:|:-----:|-----------| -|`RangeA`|`min`
`max`|`0.0`
`3.0`|First range to target.| -|`RangeB`|`min`
`max`|`3.0`
`6.0`|Second range to target.| -|`RangeC`|`min`
`max`|`6.0`
`9.0`|Third range to target.| -|`RangeBEnabled`|`bool`|`false`|Whether the second range is enabled for calculation.| -|`RangeCEnabled`|`bool`|`false`|Whether the third range is enabled for calculation.|