Documentation - Revision history

Miguel Caro at 06:54, 16 April 2021

2021-04-16T06:54:08Z

Miguel Caro at 06:51, 16 April 2021

2021-04-16T06:51:23Z

Miguel Caro at 06:51, 16 April 2021

2021-04-16T06:51:10Z

Miguel Caro at 21:20, 19 July 2017

2017-07-19T21:20:46Z

Miguel Caro at 17:59, 17 July 2017

2017-07-17T17:59:10Z

Miguel Caro at 17:55, 17 July 2017

2017-07-17T17:55:29Z

Miguel Caro at 12:13, 17 July 2017

2017-07-17T12:13:00Z

Miguel Caro at 11:01, 24 October 2016

2016-10-24T11:01:19Z

Miguel Caro at 10:59, 24 October 2016

2016-10-24T10:59:51Z

Miguel Caro: Created page with "The DoSPT documentation will be added soon."

2016-09-12T09:07:47Z

Created page with "The DoSPT documentation will be added soon."

New page

The DoSPT documentation will be added soon.

@@ Line 13: / Line 13: @@
 These input files should all be present within the directory where DoSPT is to be executed. Read through the description of each input file to familiarize yourself with the expected format and the scope/effect of the different input parameters accepted by DoSPT.
-An optional input file is the <code>[[topology file|topology]]</code> file. The <code>[[topology file]]</code> file contains bond and molecule information that allows DoSPT to handle bond breaking and bond formation dynamically (that is, as it happens during the MD run).
+An optional input file is the <code>[[topology file|topology]]</code> file. The <code>[[topology file|topology]]</code> file contains bond and molecule information that allows DoSPT to handle bond breaking and bond formation dynamically (that is, as it happens during the MD run).
 {| class="wikitable"
@@ Line 21: / Line 21: @@
 |-
 | <code>[[input]]</code>, <code>[[groups]]</code>, <code>[[supergroups]]</code>, <code>[[masses]]</code>, <code>[[traj.***]]</code>
-| <code>[[topology file]]</code>
+| <code>[[topology file|topology]]</code>
 |}
 You can also check out the [[wishlist]], which summarizes wanted and planned functionality to be (hopefully) incorporated to DoSPT.

@@ Line 21: / Line 21: @@
 |-
 | <code>[[input]]</code>, <code>[[groups]]</code>, <code>[[supergroups]]</code>, <code>[[masses]]</code>, <code>[[traj.***]]</code>
-| <code>[[topology]]</code>
+| <code>[[topology file]]</code>
 |}
 You can also check out the [[wishlist]], which summarizes wanted and planned functionality to be (hopefully) incorporated to DoSPT.

@@ Line 13: / Line 13: @@
 These input files should all be present within the directory where DoSPT is to be executed. Read through the description of each input file to familiarize yourself with the expected format and the scope/effect of the different input parameters accepted by DoSPT.
-An optional input file is the <code>[[topology file|topology]]</code> file. The <code>[[topology]]</code> file contains bond and molecule information that allows DoSPT to handle bond breaking and bond formation dynamically (that is, as it happens during the MD run).
+An optional input file is the <code>[[topology file|topology]]</code> file. The <code>[[topology file]]</code> file contains bond and molecule information that allows DoSPT to handle bond breaking and bond formation dynamically (that is, as it happens during the MD run).
 {| class="wikitable"

← Older revision		Revision as of 21:20, 19 July 2017
Line 24:		Line 24:
	\|}		\|}

−	You can also check out the [[~~whishlist~~]], which summarizes wanted and planned functionality to be (hopefully) incorporated to DoSPT.	+	You can also check out the [[wishlist]], which summarizes wanted and planned functionality to be (hopefully) incorporated to DoSPT.

@@ Line 7: / Line 7: @@
 * Defining atomic <code>[[supergroups file|supergroups]]</code>.
-* Providing <code>[[masses file|mass]]</code> information for the atoms involved in the MD.
+* Providing <code>[[masses file|masses]]</code> information for the atoms involved in the MD.
 * Containing all the <code>[[input file|input]]</code> options and other miscellaneous information pertaining your simulation, such as time step, etc. The <code>[[input]]</code> file can contain minimal input parameters or it can contain special keywords that allow you to fine tune the simulation parameters, e.g., allow you to switch on pre- and post-processing of trajectory data or to choose between different available implementations of the hard-sphere formalism.

@@ Line 1: / Line 1: @@
 The DoSPT code is structured around several input files that serve the purpose of:
-* Providing the MD trajectory information, that is atomic positions (and possibly velocities). This info is contained in a [[trajectory file]], that can be supplied in a variety of popular formats (e.g., traj.gro or traj.xyz).
+* Providing the MD trajectory information, that is atomic positions (and possibly velocities). This info is contained in a [[trajectory file]], that can be supplied in a variety of popular formats (e.g., <code>[[traj.gro]]</code> or <code>[[traj.xyz]]</code>).
-* Defining atomic [[groups file|groups]].
+* Defining atomic <code>[[groups file|groups]]</code>.
-* Defining atomic [[supergroups file|supergroups]].
+* Defining atomic <code>[[supergroups file|supergroups]]</code>.
-* Providing [[masses file|mass]] information for the atoms involved in the MD.
+* Providing <code>[[masses file|mass]]</code> information for the atoms involved in the MD.
-* Containing all the [[input file|input]] options and other miscellaneous information pertaining your simulation, such as time step, etc. The "input" file can contain minimal input parameters or it can contain special keywords that allow you to fine tune the simulation parameters, e.g., allow you to switch on pre- and post-processing of trajectory data or to choose between different available implementations of the hard-sphere formalism.
+* Containing all the <code>[[input file|input]]</code> options and other miscellaneous information pertaining your simulation, such as time step, etc. The <code>[[input]]</code> file can contain minimal input parameters or it can contain special keywords that allow you to fine tune the simulation parameters, e.g., allow you to switch on pre- and post-processing of trajectory data or to choose between different available implementations of the hard-sphere formalism.
 These input files should all be present within the directory where DoSPT is to be executed. Read through the description of each input file to familiarize yourself with the expected format and the scope/effect of the different input parameters accepted by DoSPT.
 You can also check out the [[whishlist]], which summarizes wanted and planned functionality to be (hopefully) incorporated to DoSPT.

← Older revision		Revision as of 12:13, 17 July 2017
Line 12:		Line 12:

	These input files should all be present within the directory where DoSPT is to be executed. Read through the description of each input file to familiarize yourself with the expected format and the scope/effect of the different input parameters accepted by DoSPT.		These input files should all be present within the directory where DoSPT is to be executed. Read through the description of each input file to familiarize yourself with the expected format and the scope/effect of the different input parameters accepted by DoSPT.
		+
		+	You can also check out the [[whishlist]], which summarizes wanted and planned functionality to be (hopefully) incorporated to DoSPT.

← Older revision		Revision as of 10:59, 24 October 2016
Line 1:		Line 1:
−	The DoSPT ~~documentation will~~ be ~~added soon~~.	+	The DoSPT code is structured around several input files that serve the purpose of:
		+
		+	* Providing the MD trajectory information, that is atomic positions (and possibly velocities). This info is contained in a [[trajectory file]], that can be supplied in a variety of popular formats (e.g., traj.gro or traj.xyz).
		+
		+	* Defining atomic [[groups\|groups file]].
		+
		+	* Defining atomic [supergroups\|supergroups file]].
		+
		+	* Providing [[mass\|masses file]] information for the atoms involved in the MD.
		+
		+	* Containing all the [[input\|input file]] options and other miscellaneous information pertaining your simulation, such as time step, etc. The "input" file can contain minimal input parameters or it can contain special keywords that allow you to fine tune the simulation parameters, e.g., allow you to switch on pre- and post-processing of trajectory data or to choose between different available implementations of the hard-sphere formalism.
		+
		+	These input files should all be present within the directory where DoSPT is to be executed. Read through the description of each input file to familiarize yourself with the expected format and the scope/effect of the different input parameters accepted by DoSPT.