Recent changes to Users.Programs.mol_Optimize

Users.Programs.mol_Optimize modified by Burkhard Schmidt

Burkhard Schmidt — Fri, 31 May 2013 08:21:14 -0000

--- v38
+++ v39
@@ -2,6 +2,8 @@
 ============================================

 Starting from (more or less) randomly chosen initial configuration, the MATLAB function mol_Optimize finds minima of the potential energy hypersurface of a molecular system by means of multivariate optimization (typically unconstrained). Most often local minima are found. Hence it is recommended to run **many** minimizations to increase the chance of finding the global minimum energy structure.
+
+As an alternative, in particular for very high-dimensional problems, we recommend to use the simulated annealing technique, which is built in as a variant in our [mol_MonteCarlo](Users.Programs.mol_MonteCarlo) code

 Source codes
 ------------

WikiPage Users.Programs.mol_Optimize modified by Burkhard Schmidt

Burkhard Schmidt — Thu, 29 Nov 2012 14:57:50 -0000

--- v37
+++ v38
@@ -6,7 +6,7 @@
 Source codes
 ------------
 
-The MATLAB function mol_opt.m can be found [here](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/mol_Optimize.m)
+The MATLAB function mol_Optimize.m can be found [here](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/mol_Optimize.m)
 
 Initial conformations are generated by one of the following functions

WikiPage Users.Programs.mol_Optimize modified by Burkhard Schmidt

Burkhard Schmidt — Tue, 27 Nov 2012 14:21:38 -0000

--- v36
+++ v37
@@ -33,8 +33,9 @@
 
 Note that function [mol_Initialize](Users.Programs.mol_Initialize) has to be run previously in order to initialize all variables in use. Of particular interest are the following structures:
 
+* [simulation](Developers.Variables.simulation)
+* [initial](Developers.Variables.initial)
 * [molecule](Developers.Variables.molecule)
-* [simulation](Developers.Variables.simulation)
 * [intra](Developers.Variables.intra)
 * [inter](Developers.Variables.inter)
 * [optimize](Developers.Variables.optimize)

WikiPage Users.Programs.mol_Optimize modified by Burkhard Schmidt

Burkhard Schmidt — Fri, 23 Nov 2012 13:59:35 -0000

--- v35
+++ v36
@@ -1,12 +1,12 @@
 mol_Optimize: Find minimum energy conformations 
 ============================================
 
-Starting from (more or less) randomly chosen initial configuration, the MATLAB function mol_Optimize.m finds minima of the potential energy hypersurface of a molecular system by means of multivariate optimization (typically unconstrained). Most often local minima are found. Hence it is recommended to run **many** minimizations to increase the chance of finding the global minimum energy structure.
+Starting from (more or less) randomly chosen initial configuration, the MATLAB function mol_Optimize finds minima of the potential energy hypersurface of a molecular system by means of multivariate optimization (typically unconstrained). Most often local minima are found. Hence it is recommended to run **many** minimizations to increase the chance of finding the global minimum energy structure.
 
 Source codes
 ------------
 
-The MATLAB function mol_opt.m can be found [here](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/mol_opt.m)
+The MATLAB function mol_opt.m can be found [here](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/mol_Optimize.m)
 
 Initial conformations are generated by one of the following functions
 
@@ -31,7 +31,7 @@
 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](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_Optimize modified by Burkhard Schmidt

Burkhard Schmidt — Fri, 23 Nov 2012 13:44:27 -0000

--- v34
+++ v35
@@ -1,7 +1,7 @@
 mol_Optimize: Find minimum energy conformations 
 ============================================
 
-Starting from (more or less) randomly chosen initial configuration, the MATLAB function mol_opt.m finds minima of the potential energy hypersurface of a molecular system by means of multivariate optimization (typically unconstrained). Most often local minima are found. Hence it is recommended to run **many** minimizations to increase the chance of finding the global minimum energy structure.
+Starting from (more or less) randomly chosen initial configuration, the MATLAB function mol_Optimize.m finds minima of the potential energy hypersurface of a molecular system by means of multivariate optimization (typically unconstrained). Most often local minima are found. Hence it is recommended to run **many** minimizations to increase the chance of finding the global minimum energy structure.
 
 Source codes
 ------------
@@ -26,7 +26,7 @@
 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 that file. These results can be visualized (e.g. using JMOL or VMD software) and/or the geometries can be sorted according to energy by our MATLAB function [mol_sort.m](Users.Programs.mol_sort)
+The resulting optimized geometries are written to an [xyz-file](Developers.Files.xyz) named minima...xyz. Upon repeated runs of mol_Optimize.m additional data are appended to the end of that file. These results can be visualized (e.g. using JMOL or VMD software) and/or the geometries can be sorted according to energy by our MATLAB function [mol_SortMimima.m](Users.Programs.mol_SortMinima)
 
 Variables
 ---------

WikiPage Users.Programs.mol_Optimize modified by Burkhard Schmidt

Burkhard Schmidt — Fri, 23 Nov 2012 13:43:26 -0000

--- v33
+++ v34
@@ -1,4 +1,4 @@
-mol_opt.m: Find minimum energy conformations 
+mol_Optimize: Find minimum energy conformations 
 ============================================
 
 Starting from (more or less) randomly chosen initial configuration, the MATLAB function mol_opt.m finds minima of the potential energy hypersurface of a molecular system by means of multivariate optimization (typically unconstrained). Most often local minima are found. Hence it is recommended to run **many** minimizations to increase the chance of finding the global minimum energy structure.

WikiPage Users.Programs.mol_opt modified by Burkhard Schmidt

Burkhard Schmidt — Fri, 16 Nov 2012 13:36:38 -0000

--- v32
+++ v33
@@ -1,12 +1,12 @@
 mol_opt.m: Find minimum energy conformations 
 ============================================
 
-Starting from (more or less) randomly chosen initial configuration, the MATLAB script mol_opt.m finds minima of the potential energy hypersurface of a molecular system by means of multivariate optimization (typically unconstrained). Most often local minima are found. Hence it is recommended to run **many** minimizations to increase the chance of finding the global minimum energy structure.
+Starting from (more or less) randomly chosen initial configuration, the MATLAB function mol_opt.m finds minima of the potential energy hypersurface of a molecular system by means of multivariate optimization (typically unconstrained). Most often local minima are found. Hence it is recommended to run **many** minimizations to increase the chance of finding the global minimum energy structure.
 
 Source codes
 ------------
 
-The MATLAB script mol_opt.m can be found [here](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/mol_opt.m)
+The MATLAB function mol_opt.m can be found [here](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/mol_opt.m)
 
 Initial conformations are generated by one of the following functions
 
@@ -26,12 +26,12 @@
 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 that 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 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 that file. These results can be visualized (e.g. using JMOL or VMD software) and/or the geometries can be sorted according to energy by our MATLAB function [mol_sort.m](Users.Programs.mol_sort)
 
 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_opt modified by Burkhard Schmidt

Burkhard Schmidt — Thu, 15 Nov 2012 13:46:29 -0000

--- v31
+++ v32
@@ -16,9 +16,9 @@
 
 * [ini_icosahedral.m](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/ini_icosahedral.m): Putting all molecules to center and 12 vertices of an icosahedron of given size
 
-* [ini_fcc.m](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/ini_fcc.m): Set up a face-centered cubic (fcc) lattice
+* [ini_fcc.m](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/ini_fcc.m): Set up a face-centered cubic (fcc) lattice with given lattice constant (scalar)  and given numbers of unit cells
 
-* [ini_hcp.m](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/ini_hcp.m): Set up a hexagonal close packed (hcp) lattice
+* [ini_hcp.m](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/ini_hcp.m): Set up a hexagonal close packed (hcp) lattice  with given lattice constants (vector) and given numbers of unit cells
 
 
 Note that conformations are discarded where molecules come too close to one another.

WikiPage Users.Programs.mol_opt modified by Burkhard Schmidt

Burkhard Schmidt — Thu, 15 Nov 2012 13:43:47 -0000

--- v30
+++ v31
@@ -10,9 +10,16 @@
 
 Initial conformations are generated by one of the following functions
 
-* [ini_spheroid.m](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/ini_spheroid.m): Randomly putting all molecules inside a spheroid of given radius
+* [ini_spheroid.m](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/ini_spheroid.m): Randomly putting all molecules on the surface of a spheroid of given radius
 
-* other choices: to be written ...
+* [ini_cuboid.m](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/ini_cuboid.m): Randomly putting all molecules inside a cuboid of given size
+
+* [ini_icosahedral.m](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/ini_icosahedral.m): Putting all molecules to center and 12 vertices of an icosahedron of given size
+
+* [ini_fcc.m](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/ini_fcc.m): Set up a face-centered cubic (fcc) lattice
+
+* [ini_hcp.m](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/ini_hcp.m): Set up a hexagonal close packed (hcp) lattice
+
 
 Note that conformations are discarded where molecules come too close to one another.

WikiPage Users.Programs.mol_opt modified by Burkhard Schmidt

Burkhard Schmidt — Thu, 15 Nov 2012 08:54:49 -0000

--- v29
+++ v30
@@ -40,5 +40,8 @@
 
 * fminsearch (part of MATLAB standard distribution)
   Nelder-Mead Simplex method
+  Lagarias, J.C., J. A. Reeds, M. H. Wright, and P. E. Wright,
+  Convergence Properties of the Nelder-Mead Simplex Method in Low Dimensions
+  SIAM  Journal of Optimization, Vol. 9 Number 1, pp. 112-147, 1998.
 * fminunc (from MATLAB optimization toolbox, if available)
   BFGS Quasi-Newton method