Recent changes to Developers.Variables.molecule

Developers.Variables.molecule modified by Burkhard Schmidt

Burkhard Schmidt — Tue, 18 Jun 2013 06:45:02 -0000

--- v20
+++ v21
@@ -8,9 +8,9 @@

 field | description
 ---|---
-type| type of molecule, used for labeling, e.g., 'water' (character string) 
+type| type of molecular species, used for labeling, e.g., 'water' (character string) 
 n_mol | number of molecules of this species (integer)
-n_froz | Optional: The last n_froz molecules of this species can be frozen. (integer, between 0 and n_mol)
+n_froz | Optional: The last n_froz molecules of this species can be frozen. (integer, between 0 and n_mol, default=0)
 n_atom | number of atoms in each molecules of this species (integer)
 atomtype | atom types, e.g., {'O' 'H' 'H'} (row cell(!) vector of strings indicating chemical elements)
 mass| atomic masses (row vector of real numbers, length n_atom)
@@ -21,5 +21,5 @@

 field | description
 ---|---
-n_thaw | The first n_thaw molecules of this species are not frozen: n_mol-n_froz (integer, between 0 and n_mol)
+n_thaw | The first n_thaw molecules of this species are not frozen: n_mol-n_froz (integer, between 0 and n_mol, default=n_mol)
 frozen | coordinates of all frozen atoms (3-dim arrays). Only if n_froz>0

Developers.Variables.molecule modified by Burkhard Schmidt

Burkhard Schmidt — Wed, 12 Jun 2013 12:08:38 -0000

--- v19
+++ v20
@@ -21,5 +21,5 @@

 field | description
 ---|---
-n_thaw | number of thawed molecules: n_mol-n_froz (integer, between 0 and n_mol)
+n_thaw | The first n_thaw molecules of this species are not frozen: n_mol-n_froz (integer, between 0 and n_mol)
 frozen | coordinates of all frozen atoms (3-dim arrays). Only if n_froz>0

Developers.Variables.molecule modified by Burkhard Schmidt

Burkhard Schmidt — Mon, 10 Jun 2013 07:11:06 -0000

--- v18
+++ v19
@@ -1,7 +1,7 @@
-Variable "molecule{i}" in MolDynSim
+Variable "molecule{.}" in MolDynSim
 ====================================

-This variable characterizes the *i*-th molecular species to be used in all of the MolDynSim programs. Every entry *{i}* of the cell vector is a structured variable that should initially contain the following fields :
+This variable characterizes each molecular species to be used in all of the MolDynSim programs. Every entry of the cell vector is a structured variable that should initially contain the following fields :

 Settable parameters
 ------------------

Developers.Variables.molecule modified by Burkhard Schmidt

Burkhard Schmidt — Mon, 10 Jun 2013 07:08:22 -0000

--- v17
+++ v18
@@ -22,3 +22,4 @@
 field | description
 ---|---
 n_thaw | number of thawed molecules: n_mol-n_froz (integer, between 0 and n_mol)
+frozen | coordinates of all frozen atoms (3-dim arrays). Only if n_froz>0

Developers.Variables.molecule modified by Burkhard Schmidt

Burkhard Schmidt — Sat, 08 Jun 2013 17:55:07 -0000

--- v16
+++ v17
@@ -2,6 +2,9 @@
 ====================================

 This variable characterizes the *i*-th molecular species to be used in all of the MolDynSim programs. Every entry *{i}* of the cell vector is a structured variable that should initially contain the following fields :
+
+Settable parameters
+------------------

 field | description
 ---|---
@@ -12,3 +15,10 @@
 atomtype | atom types, e.g., {'O' 'H' 'H'} (row cell(!) vector of strings indicating chemical elements)
 mass| atomic masses (row vector of real numbers, length n_atom)
 geometry | positions of all atoms inside a molecule (n_dim * n_atom matrix). Not required for monatomic species. 
+
+Internal variables
+------------------
+
+field | description
+---|---
+n_thaw | number of thawed molecules: n_mol-n_froz (integer, between 0 and n_mol)

Developers.Variables.molecule modified by Burkhard Schmidt

Burkhard Schmidt — Sat, 08 Jun 2013 10:30:02 -0000

--- v15
+++ v16
@@ -10,5 +10,5 @@
 n_froz | Optional: The last n_froz molecules of this species can be frozen. (integer, between 0 and n_mol)
 n_atom | number of atoms in each molecules of this species (integer)
 atomtype | atom types, e.g., {'O' 'H' 'H'} (row cell(!) vector of strings indicating chemical elements)
-mass| atomic masses (row vector of real numbers)
-geometry | positions of all atoms inside a molecule (n_dim * n_atom matrix)
+mass| atomic masses (row vector of real numbers, length n_atom)
+geometry | positions of all atoms inside a molecule (n_dim * n_atom matrix). Not required for monatomic species.

Developers.Variables.molecule modified by Burkhard Schmidt

Burkhard Schmidt — Sat, 08 Jun 2013 10:27:59 -0000

--- v14
+++ v15
@@ -7,6 +7,7 @@
 ---|---
 type| type of molecule, used for labeling, e.g., 'water' (character string) 
 n_mol | number of molecules of this species (integer)
+n_froz | Optional: The last n_froz molecules of this species can be frozen. (integer, between 0 and n_mol)
 n_atom | number of atoms in each molecules of this species (integer)
 atomtype | atom types, e.g., {'O' 'H' 'H'} (row cell(!) vector of strings indicating chemical elements)
 mass| atomic masses (row vector of real numbers)

Developers.Variables.molecule modified by Burkhard Schmidt

Burkhard Schmidt — Fri, 31 May 2013 11:56:31 -0000

--- v13
+++ v14
@@ -8,6 +8,6 @@
 type| type of molecule, used for labeling, e.g., 'water' (character string) 
 n_mol | number of molecules of this species (integer)
 n_atom | number of atoms in each molecules of this species (integer)
-atomtype | atom types, e.g., {'O' 'H' 'H'} (cell(!) vector of strings indicating chemical elements)
-mass| atomic masses (vector of real numbers)
+atomtype | atom types, e.g., {'O' 'H' 'H'} (row cell(!) vector of strings indicating chemical elements)
+mass| atomic masses (row vector of real numbers)
 geometry | positions of all atoms inside a molecule (n_dim * n_atom matrix)

Developers.Variables.molecule modified by Burkhard Schmidt

Burkhard Schmidt — Fri, 31 May 2013 11:46:21 -0000

--- v12
+++ v13
@@ -1,7 +1,7 @@
 Variable "molecule{i}" in MolDynSim
 ====================================

-This variable characterizes the *i*-th molecular species to be used in all of the MolDynSim programs. Every field *{i}* of the cell vector is a structured variable that should initially contain the following fields :
+This variable characterizes the *i*-th molecular species to be used in all of the MolDynSim programs. Every entry *{i}* of the cell vector is a structured variable that should initially contain the following fields :

 field | description
 ---|---

Developers.Variables.molecule modified by Burkhard Schmidt

Burkhard Schmidt — Fri, 31 May 2013 11:45:40 -0000

--- v11
+++ v12
@@ -5,21 +5,9 @@

 field | description
 ---|---
-name | type of molecule, used for labeling, e.g., 'water' (character string) 
+type| type of molecule, used for labeling, e.g., 'water' (character string) 
 n_mol | number of molecules of this species (integer)
 n_atom | number of atoms in each molecules of this species (integer)
-
-atomtype
---------
-* atom types 
-* example: {'O' 'H' 'H'} (row (cell!) vector of strings indicating chemical elements)
-
-mass
-----
-* atomic masses
-* example: [16 1 1]  (row vector of real numbers)
-
-geometry
---------
-* positions of all atoms inside a molecule 
-* example: (n_dim * n_atom matrix)
+atomtype | atom types, e.g., {'O' 'H' 'H'} (cell(!) vector of strings indicating chemical elements)
+mass| atomic masses (vector of real numbers)
+geometry | positions of all atoms inside a molecule (n_dim * n_atom matrix)