Recent changes to Users.Programs.mol_Dynamics

Users.Programs.mol_Dynamics modified by Burkhard Schmidt

Burkhard Schmidt — Fri, 15 Nov 2013 07:21:34 -0000

--- v47
+++ v48
@@ -1,7 +1,7 @@
 mol_Dynamics.m: Molecular dynamics simulations
 ==============================================

-Starting from a given configuration (in many but not in all cases a minimum energy configuration), the MATLAB function mol_Dynamics.m propagates the molecular system according to Newton's equations of motion (Langevin and/or Smoluchowski should follow soon), thereby generating a trajectory with (hopefully!) constant energy (sampling an NVE ensemble). Alternatively, a simulation for constant temperature (sampling an NVT ensemble) can be run by using a numerical "thermostat".
+Starting from a given configuration (in many but not in all cases a minimum energy configuration), the MATLAB function mol_Dynamics.m propagates the molecular system according to Newton's equations of motion (Langevin and/or Smoluchowski should follow soon), thereby generating a trajectory with (hopefully!) constant energy (sampling an NVE ensemble). Alternatively, a simulation for constant temperature (sampling an NVT ensemble) can be run by using a numerical "thermostat". Implementation of a "barostat" (sampling an NPT ensemble) for simulations at constant pressure coming soon ... 

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

Users.Programs.mol_Dynamics modified by Burkhard Schmidt

Burkhard Schmidt — Fri, 07 Jun 2013 11:56:58 -0000

--- v46
+++ v47
@@ -44,16 +44,9 @@

 Propagators

-* Velocity Verlet algorithm: [Reference](http://dx.doi.org/10.1063/1.442716) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/vel_verlet.m)
-* Original Verlet algorithm: [Reference](http://dx.doi.org/10.1103/PhysRev.159.98) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/old_verlet.m)
-* Leap frog algorithm: [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/leap_frog.m)
-* Beeman algorithm:  [Reference](http://dx.doi.org/10.1016/0021-9991(76)90059-0), [other reference](http://dx.doi.org/10.1016/0010-4655(73)90004-0) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/beeman.m)
-* Gear algorithm:  [Reference](http://dx.doi.org/10.1080/00268977700102571) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/gear_45678.m)
-* Euler 1st/2nd order algorithm: [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/euler_12.m)
+* For a list of implemented algorithms, see [here](Developers.Variables.dynamics.md)

 Thermostats

-* Andersen's method: [Reference](http://dx.doi.org/10.1063/1.439486 ) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+thermo/andersen.m)
-* Berendsen's method: [Reference](http://dx.doi.org/10.1063/1.448118) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+thermo/berendsen.m)
-* Naive rescaling:  [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+thermo/rescaling.m)
+* For a list of implemented algorithms, see [here](Developers.Variables.dynamics.tmp)

Users.Programs.mol_Dynamics modified by Burkhard Schmidt

Burkhard Schmidt — Thu, 06 Jun 2013 06:56:37 -0000

--- v45
+++ v46
@@ -48,7 +48,7 @@
 * Original Verlet algorithm: [Reference](http://dx.doi.org/10.1103/PhysRev.159.98) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/old_verlet.m)
 * Leap frog algorithm: [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/leap_frog.m)
 * Beeman algorithm:  [Reference](http://dx.doi.org/10.1016/0021-9991(76)90059-0), [other reference](http://dx.doi.org/10.1016/0010-4655(73)90004-0) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/beeman.m)
-* Gear algorithm:  [Reference](http://dx.doi.org/10.1080/00268977700102571) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/gear_456.m)
+* Gear algorithm:  [Reference](http://dx.doi.org/10.1080/00268977700102571) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/gear_45678.m)
 * Euler 1st/2nd order algorithm: [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/euler_12.m)

Users.Programs.mol_Dynamics modified by Burkhard Schmidt

Burkhard Schmidt — Thu, 06 Jun 2013 06:55:48 -0000

--- v44
+++ v45
@@ -48,7 +48,7 @@
 * Original Verlet algorithm: [Reference](http://dx.doi.org/10.1103/PhysRev.159.98) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/old_verlet.m)
 * Leap frog algorithm: [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/leap_frog.m)
 * Beeman algorithm:  [Reference](http://dx.doi.org/10.1016/0021-9991(76)90059-0), [other reference](http://dx.doi.org/10.1016/0010-4655(73)90004-0) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/beeman.m)
-* Gear algorithm:  [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/gear_456.m)
+* Gear algorithm:  [Reference](http://dx.doi.org/10.1080/00268977700102571) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/gear_456.m)
 * Euler 1st/2nd order algorithm: [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/euler_12.m)

Users.Programs.mol_Dynamics modified by Burkhard Schmidt

Burkhard Schmidt — Wed, 05 Jun 2013 16:59:49 -0000

--- v43
+++ v44
@@ -47,8 +47,7 @@
 * Velocity Verlet algorithm: [Reference](http://dx.doi.org/10.1063/1.442716) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/vel_verlet.m)
 * Original Verlet algorithm: [Reference](http://dx.doi.org/10.1103/PhysRev.159.98) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/old_verlet.m)
 * Leap frog algorithm: [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/leap_frog.m)
-* Beeman algorithm:  [Reference](http://dx.doi.org/10.1016/0021-9991(76)90059-0), [other reference](http://dx.doi.org/10.1016/0010-4655(73)90004-0) and [source code]
-(https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/beeman.m)
+* Beeman algorithm:  [Reference](http://dx.doi.org/10.1016/0021-9991(76)90059-0), [other reference](http://dx.doi.org/10.1016/0010-4655(73)90004-0) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/beeman.m)
 * Gear algorithm:  [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/gear_456.m)
 * Euler 1st/2nd order algorithm: [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/euler_12.m)

Users.Programs.mol_Dynamics modified by Burkhard Schmidt

Burkhard Schmidt — Wed, 05 Jun 2013 16:59:08 -0000

--- v42
+++ v43
@@ -48,6 +48,7 @@
 * Original Verlet algorithm: [Reference](http://dx.doi.org/10.1103/PhysRev.159.98) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/old_verlet.m)
 * Leap frog algorithm: [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/leap_frog.m)
 * Beeman algorithm:  [Reference](http://dx.doi.org/10.1016/0021-9991(76)90059-0), [other reference](http://dx.doi.org/10.1016/0010-4655(73)90004-0) and [source code]
+(https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/beeman.m)
 * Gear algorithm:  [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/gear_456.m)
 * Euler 1st/2nd order algorithm: [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/euler_12.m)

Users.Programs.mol_Dynamics modified by Burkhard Schmidt

Burkhard Schmidt — Wed, 05 Jun 2013 16:57:40 -0000

--- v41
+++ v42
@@ -47,7 +47,8 @@
 * Velocity Verlet algorithm: [Reference](http://dx.doi.org/10.1063/1.442716) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/vel_verlet.m)
 * Original Verlet algorithm: [Reference](http://dx.doi.org/10.1103/PhysRev.159.98) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/old_verlet.m)
 * Leap frog algorithm: [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/leap_frog.m)
-* Beeman algorithm:  [Reference](http://dx.doi.org/10.1016/0021-9991(76)90059-0), [other reference](http://dx.doi.org/10.1016/0010-4655(73)90004-0) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/beeman.m)
+* Beeman algorithm:  [Reference](http://dx.doi.org/10.1016/0021-9991(76)90059-0), [other reference](http://dx.doi.org/10.1016/0010-4655(73)90004-0) and [source code]
+* Gear algorithm:  [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/gear_456.m)
 * Euler 1st/2nd order algorithm: [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/euler_12.m)

Users.Programs.mol_Dynamics modified by Burkhard Schmidt

Burkhard Schmidt — Wed, 05 Jun 2013 16:53:06 -0000

--- v40
+++ v41
@@ -6,11 +6,13 @@
 Source code
 -----------

-The MATLAB function mol_Dynamics.m can be found [here](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/mol_Dynamics.m)
+* [The MATLAB function mol_Dynamics.m](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/mol_Dynamics.m)

-* [Generate initial velocity distribution for constant E](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+dyn/init_E.m) 
+* [Analysis of MD data](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+dyn/analyze.m) 

-* [Generate initial velocity distribution for constant T](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+dyn/init_T.m) 
+* [Graphs of MD data](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+dyn/plot.m) 
+ 
+* [Saving MD data](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+dyn/save.m) 

 File I/O
@@ -34,6 +36,12 @@
 Algorithms
 ----------

+Generation of initial conditions
+
+* [Velocity distribution for constant E](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+dyn/init_E.m) 
+
+* [Velocity distribution for constant T](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+dyn/init_T.m) 
+
 Propagators

 * Velocity Verlet algorithm: [Reference](http://dx.doi.org/10.1063/1.442716) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/vel_verlet.m)

Users.Programs.mol_Dynamics modified by Burkhard Schmidt

Burkhard Schmidt — Wed, 05 Jun 2013 16:47:39 -0000

--- v39
+++ v40
@@ -36,15 +36,15 @@

 Propagators

-* Velocity Verlet algorithm: [Reference](http://dx.doi.org/10.1063/1.442716) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+dyn/vel_verlet.m)
-* Original Verlet algorithm: [Reference](http://dx.doi.org/10.1103/PhysRev.159.98) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+dyn/old_verlet.m)
-* Leap frog algorithm: [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+dyn/leap_frog.m)
-* Beeman algorithm:  [Reference](http://dx.doi.org/10.1016/0021-9991(76)90059-0), [other reference](http://dx.doi.org/10.1016/0010-4655(73)90004-0) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+dyn/beeman.m)
-* Euler 1st/2nd order algorithm: [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+dyn/euler_12.m)
+* Velocity Verlet algorithm: [Reference](http://dx.doi.org/10.1063/1.442716) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/vel_verlet.m)
+* Original Verlet algorithm: [Reference](http://dx.doi.org/10.1103/PhysRev.159.98) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/old_verlet.m)
+* Leap frog algorithm: [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/leap_frog.m)
+* Beeman algorithm:  [Reference](http://dx.doi.org/10.1016/0021-9991(76)90059-0), [other reference](http://dx.doi.org/10.1016/0010-4655(73)90004-0) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/beeman.m)
+* Euler 1st/2nd order algorithm: [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+propa/euler_12.m)

 Thermostats

-* Andersen's method: [Reference](http://dx.doi.org/10.1063/1.439486 ) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+dyn/andersen.m)
-* Berendsen's method: [Reference](http://dx.doi.org/10.1063/1.448118) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+dyn/berendsen.m)
-* Naive rescaling:  [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+dyn/rescaling.m)
+* Andersen's method: [Reference](http://dx.doi.org/10.1063/1.439486 ) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+thermo/andersen.m)
+* Berendsen's method: [Reference](http://dx.doi.org/10.1063/1.448118) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+thermo/berendsen.m)
+* Naive rescaling:  [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+thermo/rescaling.m)

Users.Programs.mol_Dynamics modified by Burkhard Schmidt

Burkhard Schmidt — Wed, 05 Jun 2013 13:54:16 -0000

--- v38
+++ v39
@@ -45,6 +45,6 @@

 Thermostats

-* Andersen's method: [Reference](http://dx.doi.org/) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+dyn/andersen.m)
+* Andersen's method: [Reference](http://dx.doi.org/10.1063/1.439486 ) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+dyn/andersen.m)
 * Berendsen's method: [Reference](http://dx.doi.org/10.1063/1.448118) and [source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+dyn/berendsen.m)
 * Naive rescaling:  [Source code](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+dyn/rescaling.m)