Recent changes to Users.Programs.mol_Vibrations

Users.Programs.mol_Vibrations modified by Burkhard Schmidt

Burkhard Schmidt — Fri, 31 May 2013 10:35:44 -0000

--- v11
+++ v12
@@ -20,6 +20,7 @@

 * [molecule](Developers.Variables.molecule)
 * [simulation](Developers.Variables.simulation)
+* [initial](Developers.Variables.initial)
 * [intra](Developers.Variables.intra)
 * [inter](Developers.Variables.inter)
 * [vibrations](Developers.Variables.vibrations)

Users.Programs.mol_Vibrations modified by Burkhard Schmidt

Burkhard Schmidt — Thu, 30 May 2013 18:04:19 -0000

--- v10
+++ v11
@@ -1,7 +1,7 @@
 mol_Vibrations: Normal mode analysis of molecular vibrations
 =======================================================

-Starting from the lowest minimum energy configuration (hopefully the global minimum), the MATLAB function mol_Vibrations.m numerically calculates the Hessian (matrix of 2nd derivatives) of the potential energy hypersurface (force field) of a molecular system and diagonalizes it. The vibrational normal mode frequencies are obtained as square roots of the eigenvalues. The displacements defining the normal mode coordinates are contained in the corresponding eigenvectors. 
+Starting from a given (typically a minimum energy) configuration, the MATLAB function mol_Vibrations.m numerically calculates the Hessian (matrix of 2nd derivatives) of the potential energy hypersurface (force field) of a molecular system and diagonalizes it. The vibrational normal mode frequencies are obtained as square roots of the eigenvalues. The displacements defining the normal mode coordinates are contained in the corresponding eigenvectors. 

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

WikiPage Users.Programs.mol_Vibrations modified by Burkhard Schmidt

Burkhard Schmidt — Tue, 27 Nov 2012 19:27:46 -0000

--- v9
+++ v10
@@ -22,4 +22,4 @@
 * [simulation](Developers.Variables.simulation)
 * [intra](Developers.Variables.intra)
 * [inter](Developers.Variables.inter)
-* [vibration](Developers.Variables.vibration)
+* [vibrations](Developers.Variables.vibrations)

WikiPage Users.Programs.mol_Vibrations modified by Burkhard Schmidt

Burkhard Schmidt — Fri, 23 Nov 2012 13:46:03 -0000

--- v8
+++ v9
@@ -1,12 +1,12 @@
-mol_vib.m: Normal mode analysis of molecular vibrations
+mol_Vibrations: Normal mode analysis of molecular vibrations
 =======================================================
 
-Starting from the lowest minimum energy configuration (hopefully the global minimum), the MATLAB function mol_vib.m numerically calculates the Hessian (matrix of 2nd derivatives) of the potential energy hypersurface (force field) of a molecular system and diagonalizes it. The vibrational normal mode frequencies are obtained as square roots of the eigenvalues. The displacements defining the normal mode coordinates are contained in the corresponding eigenvectors. 
+Starting from the lowest minimum energy configuration (hopefully the global minimum), the MATLAB function mol_Vibrations.m numerically calculates the Hessian (matrix of 2nd derivatives) of the potential energy hypersurface (force field) of a molecular system and diagonalizes it. The vibrational normal mode frequencies are obtained as square roots of the eigenvalues. The displacements defining the normal mode coordinates are contained in the corresponding eigenvectors. 
 
 Source code
 -----------
 
-The MATLAB function mol_vib.m can be found [here](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/mol_vib.m)
+The MATLAB function mol_Vibrations.m can be found [here](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/mol_Vibrations.m)
 
 File I/O
 --------
@@ -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_vib modified by Burkhard Schmidt

Burkhard Schmidt — Fri, 16 Nov 2012 13:40:24 -0000

--- v7
+++ v8
@@ -1,22 +1,22 @@
 mol_vib.m: Normal mode analysis of molecular vibrations
 =======================================================
 
-Starting from the lowest minimum energy configuration (hopefully the global minimum), the MATLAB script mol_vib.m numerically calculates the Hessian (matrix of 2nd derivatives) of the potential energy hypersurface (force field) of a molecular system and diagonalizes it. The vibrational normal mode frequencies are obtained as square roots of the eigenvalues. The displacements defining the normal mode coordinates are contained in the corresponding eigenvectors. 
+Starting from the lowest minimum energy configuration (hopefully the global minimum), the MATLAB function mol_vib.m numerically calculates the Hessian (matrix of 2nd derivatives) of the potential energy hypersurface (force field) of a molecular system and diagonalizes it. The vibrational normal mode frequencies are obtained as square roots of the eigenvalues. The displacements defining the normal mode coordinates are contained in the corresponding eigenvectors. 
 
 Source code
 -----------
 
-The MATLAB script mol_vib.m can be found [here](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/mol_vib.m)
+The MATLAB function mol_vib.m can be found [here](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/mol_vib.m)
 
 File I/O
 --------
 
-The initial optimized geometries is read from the head of an [xyz-file](Developers.Files.xyz) named sorted...xyz. If desired, displacements of the atomic positions can be written to files vib_movie...xyz (one file for each normal mode). These results can be visualized (e.g. using VMD software) If desired, scans of the force field energy along these coordinates can be written to files vib_scan...xyz.
+The initial optimized geometries is read from the head of an [xyz-file](Developers.Files.xyz) named sorted...xyz. If desired, displacements of the atomic positions can be written to files vib_movie...xyz (one file for each normal mode). These results can be visualized (e.g. using JMOL or VMD software). If desired, also scans of the force field energy along these coordinates can be generated and written to files vib_scan...xyz.
 
 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_vib modified by Burkhard Schmidt

Burkhard Schmidt — Wed, 14 Nov 2012 13:53:07 -0000

--- v6
+++ v7
@@ -11,7 +11,7 @@
 File I/O
 --------
 
-The initial optimized geometries is written from the head of an [xyz-file](Developers.Files.xyz) named sorted...xyz. If desired, displacements of the atomic positions are written in files vib_movie...xyz (one file for each normal mode). These results can be visualized (e.g. using VMD software) If desired, scans of the force field energy along these coordinates can be written to files vib_scan...xyz.
+The initial optimized geometries is read from the head of an [xyz-file](Developers.Files.xyz) named sorted...xyz. If desired, displacements of the atomic positions can be written to files vib_movie...xyz (one file for each normal mode). These results can be visualized (e.g. using VMD software) If desired, scans of the force field energy along these coordinates can be written to files vib_scan...xyz.
 
 Variables
 ---------

WikiPage Users.Programs.mol_vib modified by Burkhard Schmidt

Burkhard Schmidt — Wed, 14 Nov 2012 13:01:33 -0000

--- v5
+++ v6
@@ -1,7 +1,7 @@
 mol_vib.m: Normal mode analysis of molecular vibrations
 =======================================================
 
-Starting from the energetically lowest configuration, the MATLAB script mol_vib.m calculates the Hessian (2nd derivatives) of the potential energy hypersurface (force field) of a molecular system numerically and diagonalizes it. The vibrational normal mode frequencies are obtained as square roots of the eigenvalues. The displacements defining the normal mode coordinates are contained in the corresponding eigenvectors. 
+Starting from the lowest minimum energy configuration (hopefully the global minimum), the MATLAB script mol_vib.m numerically calculates the Hessian (matrix of 2nd derivatives) of the potential energy hypersurface (force field) of a molecular system and diagonalizes it. The vibrational normal mode frequencies are obtained as square roots of the eigenvalues. The displacements defining the normal mode coordinates are contained in the corresponding eigenvectors. 
 
 Source code
 -----------

WikiPage Users.Programs.mol_vib modified by Burkhard Schmidt

Burkhard Schmidt — Tue, 13 Nov 2012 17:52:10 -0000

WikiPage Users.Programs.mol_vib modified by Burkhard Schmidt

Burkhard Schmidt — Tue, 13 Nov 2012 17:51:41 -0000

--- v3
+++ v4
@@ -11,7 +11,7 @@
 File I/O
 --------
 
-The resulting optimized geometries are written to an [xyz-file](Developers.Files.xyz) named minima...xyz. Upon repeated runs of mol_opt.m additional data are appended to the end of the file. These results can be visualized (e.g. using VMD software) and/or the geometries can be sorted according to energy by our MATLAB script [mol_sort.m](Users.Programs.mol_sort)
+The initial optimized geometries is written from the head of an [xyz-file](Developers.Files.xyz) named sorted...xyz. If desired, displacements of the atomic positions are written in files vib_movie...xyz (one file for each normal mode). These results can be visualized (e.g. using VMD software) If desired, scans of the force field energy along these coordinates can be written to files vib_scan...xyz.
 
 Variables
 ---------

WikiPage Users.Programs.mol_vib modified by Burkhard Schmidt

Burkhard Schmidt — Tue, 13 Nov 2012 17:47:51 -0000