Recent changes to Users.Programs.mol_ScanPot_1D

Users.Programs.mol_ScanPot_1D modified by Burkhard Schmidt

Burkhard Schmidt — Wed, 12 Jun 2013 12:32:15 -0000

--- v10
+++ v11
@@ -1,7 +1,13 @@
 mol_scan_1D: Scan force field along specified direction
 ======================================================

-The MATLAB function mol_ScanPot_1D generates a one-dimensional scan of the potential energy hypersurface (force field) of a system of two molecules (equal or different species). Scans are along the distance between the two centers of mass, where rotations of the two molecules can be specified by the user.
+The MATLAB function mol_ScanPot_1D generates a one-dimensional scan of the potential energy hypersurface (force field) of a system of two molecules (equal or different species). Scans are along the distance between the two centers of mass, where rotations and/or shifts of the two molecules can be specified by the user.
+
+In case of molecules of a single species, you will have to prepare special input where this species is duplicated
+    molecule{1}.n_mol = 1;
+    molecule{1}.n_froz = 0;
+    molecule{2} = molecule{1};
+    inter{1,2} = inter{1,1}

 Source code
 -----------

WikiPage Users.Programs.mol_ScanPot_1D modified by Burkhard Schmidt

Burkhard Schmidt — Fri, 23 Nov 2012 13:50:44 -0000

--- v9
+++ v10
@@ -16,7 +16,7 @@
 Variables
 ---------
 
-Note that function  [mol_init.m](Users.Programs.mol_init) has to be run previously in order to initialize all variables in use. Of particular interest are the following structures:
+Note that function  [mol_Initialize.m](Users.Programs.mol_Initialize) has to be run previously in order to initialize all variables in use. Of particular interest are the following structures:
 
 * [molecule](Developers.Variables.molecule)
 * [simulation](Developers.Variables.simulation)

WikiPage Users.Programs.mol_ScanPot_1D modified by Burkhard Schmidt

Burkhard Schmidt — Fri, 23 Nov 2012 13:50:13 -0000

--- v8
+++ v9
@@ -1,12 +1,12 @@
 mol_scan_1D: Scan force field along specified direction
 ======================================================
 
-The MATLAB function mol_scan_1D.m generates a one-dimensional scan of the potential energy hypersurface (force field) of a system of two molecules (equal or different species). Scans are along the distance between the two centers of mass, where rotations of the two molecules can be specified by the user.
+The MATLAB function mol_ScanPot_1D generates a one-dimensional scan of the potential energy hypersurface (force field) of a system of two molecules (equal or different species). Scans are along the distance between the two centers of mass, where rotations of the two molecules can be specified by the user.
 
 Source code
 -----------
 
-The MATLAB function mol_scan_1D.m can be found [here](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/mol_scan_1D.m)
+The MATLAB function mol_ScanPot_1D.m can be found [here](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/mol_ScanPot_1D.m)
 
 File I/O
 --------

WikiPage Users.Programs.mol_scan_1D modified by Burkhard Schmidt

Burkhard Schmidt — Fri, 16 Nov 2012 13:37:14 -0000

--- v7
+++ v8
@@ -6,7 +6,7 @@
 Source code
 -----------
 
-The MATLAB script mol_scan_1D.m can be found [here](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/mol_scan_1D.m)
+The MATLAB function mol_scan_1D.m can be found [here](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/mol_scan_1D.m)
 
 File I/O
 --------

WikiPage Users.Programs.mol_scan_1D modified by Burkhard Schmidt

Burkhard Schmidt — Fri, 16 Nov 2012 13:35:11 -0000

--- v6
+++ v7
@@ -1,7 +1,7 @@
 mol_scan_1D: Scan force field along specified direction
 ======================================================
 
-The MATLAB script mol_scan_1D.m generates a one-dimensional scan of the potential energy hypersurface (force field) of a system of two molecules (equal or different species). Scans are along the distance between the two centers of mass, where rotations of the two molecules can be specified by the user.
+The MATLAB function mol_scan_1D.m generates a one-dimensional scan of the potential energy hypersurface (force field) of a system of two molecules (equal or different species). Scans are along the distance between the two centers of mass, where rotations of the two molecules can be specified by the user.
 
 Source code
 -----------
@@ -11,12 +11,12 @@
 File I/O
 --------
 
-The resulting geometries (steps of the scan) are written to an [xyz-file](Developers.Files.xyz) named scan_1D...xyz. This can be visualized, e.g., using VMD software.
+The resulting geometries (steps of the scan) are written to an [xyz-file](Developers.Files.xyz) named scan_1D...xyz. This can be visualized, e.g., using JMOL or VMD software.
 
 Variables
 ---------
 
-Note that [mol_init.m](Users.Programs.mol_init) has to be run previously in order to initialize all variables in use. Of particular interest are the following structures:
+Note that function  [mol_init.m](Users.Programs.mol_init) has to be run previously in order to initialize all variables in use. Of particular interest are the following structures:
 
 * [molecule](Developers.Variables.molecule)
 * [simulation](Developers.Variables.simulation)

WikiPage Users.Programs.mol_scan_1D modified by Burkhard Schmidt

Burkhard Schmidt — Wed, 14 Nov 2012 12:48:52 -0000

--- v5
+++ v6
@@ -1,7 +1,7 @@
 mol_scan_1D: Scan force field along specified direction
 ======================================================
 
-The MATLAB script mol_scan1D.m generates a one-dimensional scan of the potential energy hypersurface (force field) of a system of two molecules (equal or different species). Scans are along the distance between the two centers of mass, where rotations of the two molecules can be specified by the user.
+The MATLAB script mol_scan_1D.m generates a one-dimensional scan of the potential energy hypersurface (force field) of a system of two molecules (equal or different species). Scans are along the distance between the two centers of mass, where rotations of the two molecules can be specified by the user.
 
 Source code
 -----------
@@ -11,7 +11,7 @@
 File I/O
 --------
 
-The resulting geometries (steps of the scan) are written to an [xyz-file](Developers.Files.xyz) named scan1D...xyz. This can be visualized, e.g., using VMD software.
+The resulting geometries (steps of the scan) are written to an [xyz-file](Developers.Files.xyz) named scan_1D...xyz. This can be visualized, e.g., using VMD software.
 
 Variables
 ---------

WikiPage Users.Programs.mol_scan_1D modified by Burkhard Schmidt

Burkhard Schmidt — Tue, 13 Nov 2012 18:29:30 -0000

--- v4
+++ v5
@@ -22,4 +22,4 @@
 * [simulation](Developers.Variables.simulation)
 * [intra](Developers.Variables.intra)
 * [inter](Developers.Variables.inter)
-* [scan1D](Developers.Variables.optimize)
+* [scan_1D](Developers.Variables.scan_1D)

WikiPage Users.Programs.mol_scan_1D modified by Burkhard Schmidt

Burkhard Schmidt — Tue, 13 Nov 2012 18:28:04 -0000

--- v3
+++ v4
@@ -1,4 +1,4 @@
-mol_scan1D: Scan force field along specified direction
+mol_scan_1D: Scan force field along specified direction
 ======================================================
 
 The MATLAB script mol_scan1D.m generates a one-dimensional scan of the potential energy hypersurface (force field) of a system of two molecules (equal or different species). Scans are along the distance between the two centers of mass, where rotations of the two molecules can be specified by the user.

WikiPage Users.Programs.mol_scan_1D modified by Burkhard Schmidt

Burkhard Schmidt — Tue, 13 Nov 2012 17:10:43 -0000

--- v2
+++ v3
@@ -6,7 +6,7 @@
 Source code
 -----------
 
-The MATLAB script mol_scan1D.m can be found [here](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/mol_scan1D.m)
+The MATLAB script mol_scan_1D.m can be found [here](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/mol_scan_1D.m)
 
 File I/O
 --------

WikiPage Users.Programs.mol_scan1D modified by Burkhard Schmidt

Burkhard Schmidt — Tue, 13 Nov 2012 17:09:48 -0000

--- v1
+++ v2
@@ -1,2 +1,25 @@
 mol_scan1D: Scan force field along specified direction
 ======================================================
+
+The MATLAB script mol_scan1D.m generates a one-dimensional scan of the potential energy hypersurface (force field) of a system of two molecules (equal or different species). Scans are along the distance between the two centers of mass, where rotations of the two molecules can be specified by the user.
+
+Source code
+-----------
+
+The MATLAB script mol_scan1D.m can be found [here](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/mol_scan1D.m)
+
+File I/O
+--------
+
+The resulting geometries (steps of the scan) are written to an [xyz-file](Developers.Files.xyz) named scan1D...xyz. This can be visualized, e.g., using VMD software.
+
+Variables
+---------
+
+Note that [mol_init.m](Users.Programs.mol_init) has to be run previously in order to initialize all variables in use. Of particular interest are the following structures:
+
+* [molecule](Developers.Variables.molecule)
+* [simulation](Developers.Variables.simulation)
+* [intra](Developers.Variables.intra)
+* [inter](Developers.Variables.inter)
+* [scan1D](Developers.Variables.optimize)