Recent changes to Developers.Variables.simulation

Developers.Variables.simulation modified by Burkhard Schmidt

Burkhard Schmidt — Thu, 13 Jun 2013 15:45:05 -0000

--- v33
+++ v34
@@ -20,9 +20,8 @@
 ---|---
 title | cell vector of character strings
 n_spec | number of molecular species, simply deduced from length(molecule). 
-n_atom | total number of atoms in all molecules of all species (integer)
-n_thaw | How many of them are thawed
-n_froz | How many of them are frozen
+n_thaw | total number of thawed atoms in all molecules/species
+n_froz | total number of frozen atoms in all molecules/species
 mass | mass of all atoms in our system (real matrix of size n_dim x n_thaw)
 density | mass per volume in units of g / (mol*nm3). Available  only if periodic=true

Developers.Variables.simulation modified by Burkhard Schmidt

Burkhard Schmidt — Wed, 12 Jun 2013 09:25:12 -0000

--- v32
+++ v33
@@ -8,10 +8,10 @@

 field | description
 ---|---
-n_dim | number of dimensions (integer). Note that most often you choose 3. However, MolDynSim should also work in reduced (1 or 2) dimensionality (although that hasn't been tested yet)
-periodic | whether to use periodic boundary conditions (logical)
+n_dim | number of dimensions (integer, default:3). However, MolDynSim should also work in reduced (1 or 2) dimensionality (although that hasn't been tested yet)
+periodic | whether to use periodic boundary conditions (logical, default:false)
 box |  size of (periodic) simulation box (column vector of real numbers, length n_dim). Needed only if periodic=true
-verbose | whether to produce (tons of) extra output (logical)
+verbose | whether to produce (tons of) extra output (logical, default: false)

 Internal variables
 ------------------

Developers.Variables.simulation modified by Burkhard Schmidt

Burkhard Schmidt — Wed, 12 Jun 2013 08:54:34 -0000

--- v31
+++ v32
@@ -23,7 +23,7 @@
 n_atom | total number of atoms in all molecules of all species (integer)
 n_thaw | How many of them are thawed
 n_froz | How many of them are frozen
-mass | mass of all atoms in our system (real vector of length n_thaw)
+mass | mass of all atoms in our system (real matrix of size n_dim x n_thaw)
 density | mass per volume in units of g / (mol*nm3). Available  only if periodic=true

 Internal constants

Developers.Variables.simulation modified by Burkhard Schmidt

Burkhard Schmidt — Wed, 12 Jun 2013 08:53:40 -0000

--- v30
+++ v31
@@ -23,7 +23,6 @@
 n_atom | total number of atoms in all molecules of all species (integer)
 n_thaw | How many of them are thawed
 n_froz | How many of them are frozen
-atomtype | types of all atoms in our system (character cell vector of length n_thaw)
 mass | mass of all atoms in our system (real vector of length n_thaw)
 density | mass per volume in units of g / (mol*nm3). Available  only if periodic=true

Developers.Variables.simulation modified by Burkhard Schmidt

Burkhard Schmidt — Tue, 11 Jun 2013 18:05:28 -0000

--- v29
+++ v30
@@ -23,8 +23,8 @@
 n_atom | total number of atoms in all molecules of all species (integer)
 n_thaw | How many of them are thawed
 n_froz | How many of them are frozen
-atomtype | types of all atoms in our system (character cell vector of length n_atom)
-mass | mass of all atoms in our system (real vector of length n_atom)
+atomtype | types of all atoms in our system (character cell vector of length n_thaw)
+mass | mass of all atoms in our system (real vector of length n_thaw)
 density | mass per volume in units of g / (mol*nm3). Available  only if periodic=true

 Internal constants

Developers.Variables.simulation modified by Burkhard Schmidt

Burkhard Schmidt — Tue, 11 Jun 2013 18:04:46 -0000

--- v28
+++ v29
@@ -21,6 +21,8 @@
 title | cell vector of character strings
 n_spec | number of molecular species, simply deduced from length(molecule). 
 n_atom | total number of atoms in all molecules of all species (integer)
+n_thaw | How many of them are thawed
+n_froz | How many of them are frozen
 atomtype | types of all atoms in our system (character cell vector of length n_atom)
 mass | mass of all atoms in our system (real vector of length n_atom)
 density | mass per volume in units of g / (mol*nm3). Available  only if periodic=true

Developers.Variables.simulation modified by Burkhard Schmidt

Burkhard Schmidt — Mon, 10 Jun 2013 07:07:15 -0000

--- v27
+++ v28
@@ -24,7 +24,6 @@
 atomtype | types of all atoms in our system (character cell vector of length n_atom)
 mass | mass of all atoms in our system (real vector of length n_atom)
 density | mass per volume in units of g / (mol*nm3). Available  only if periodic=true
-frozen | coordinates of all frozen atoms (cell vector of 3-dim arrays)

 Internal constants
 ------------------

Developers.Variables.simulation modified by Burkhard Schmidt

Burkhard Schmidt — Sat, 08 Jun 2013 17:57:10 -0000

--- v26
+++ v27
@@ -24,6 +24,7 @@
 atomtype | types of all atoms in our system (character cell vector of length n_atom)
 mass | mass of all atoms in our system (real vector of length n_atom)
 density | mass per volume in units of g / (mol*nm3). Available  only if periodic=true
+frozen | coordinates of all frozen atoms (cell vector of 3-dim arrays)

 Internal constants
 ------------------

Developers.Variables.simulation modified by Burkhard Schmidt

Burkhard Schmidt — Sat, 08 Jun 2013 10:25:19 -0000

--- v25
+++ v26
@@ -12,7 +12,6 @@
 periodic | whether to use periodic boundary conditions (logical)
 box |  size of (periodic) simulation box (column vector of real numbers, length n_dim). Needed only if periodic=true
 verbose | whether to produce (tons of) extra output (logical)
-n_froz | Optional: Treat the last n_froz species as frozen

 Internal variables
 ------------------
@@ -20,9 +19,9 @@
 field | description
 ---|---
 title | cell vector of character strings
-n_spec | number of molecular species, simply deduced from length(molecule). In case of some species being frozen (n_froz>0), only n_spec-n_froz species are dynamically evolving.
-n_atom | total number of atoms (in all molecules of all non-frozen species)
-atomtype | types of all atoms in our system (character cell vector of length n_atom
+n_spec | number of molecular species, simply deduced from length(molecule). 
+n_atom | total number of atoms in all molecules of all species (integer)
+atomtype | types of all atoms in our system (character cell vector of length n_atom)
 mass | mass of all atoms in our system (real vector of length n_atom)
 density | mass per volume in units of g / (mol*nm3). Available  only if periodic=true

Developers.Variables.simulation modified by Burkhard Schmidt

Burkhard Schmidt — Fri, 07 Jun 2013 16:26:31 -0000

--- v24
+++ v25
@@ -31,9 +31,7 @@

 field | description
 ---|---
-k_boltz | 0.0083145 kJ/(mol*K)
-coulomb | 138.935 kJ*nm/(mol e^2)
-planck  | 0.0635 kJ/(mol*ps)
-avogadro | 6.02214129e23
-
-Note the use of [molecular units](Users.Molecular Units) throughout
+k_boltz | see the definition of [molecular units](Users.Molecular Units)
+coulomb | see the definition of [molecular units](Users.Molecular Units)
+planck  | see the definition of [molecular units](Users.Molecular Units)
+avogadro | see the definition of [molecular units](Users.Molecular Units)