DL POLY: Difference between revisions

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[http://www.cse.clrc.ac.uk/ccg/software/DL_POLY/index.shtml DL_POLY] is a general purpose serial and parallel [[molecular dynamics]] simulation package developed at Daresbury Laboratory by W. Smith, T.R. Forester and I.T. Todorov.
DL_POLY
<ref>[http://dx.doi.org/10.1016/S0263-7855(96)00043-4  W. Smith and T. R. Forester "DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package", Journal of Molecular Graphics  '''14''' pp. 136-141 (1996)]</ref>
<ref>[http://dx.doi.org/10.1080/08927020290018769 W. Smith,  C. W. Yong and P. M. Rodger "DL_POLY: application to molecular simulation", Molecular Simulation '''28''' pp. 385-471 (2002)]</ref>
is a general purpose serial and parallel [[molecular dynamics]] simulation package developed at Daresbury Laboratory by W. Smith, T.R. Forester and I.T. Todorov  
==Units==
==Units==
DL_POLY employs an interesting set of units which have molecular relevance:
DL_POLY employs an interesting set of units which have molecular relevance <ref> source: DL_POLY User Manual (v. 2.20) &sect; 1.3.10</ref>.:
{| border="1"
{| border="1"
|-  
|-  
Line 22: Line 25:
| [[Boltzmann constant]] || <math>k_B</math>|| <math>0.83145 E_0/K </math>
| [[Boltzmann constant]] || <math>k_B</math>|| <math>0.83145 E_0/K </math>
|}
|}
==DL_POLY_2==
==Force field==
The [[force fields | force field]] used in DL_POLY consists (or can consist) of the following components <ref> source: DL_POLY User Manual (v. 2.20) &sect; 4.1.3</ref>:
*Chemical bond potentials:
**[[Harmonic bond potential]]
**[[Morse potential]]
**[[Lennard-Jones model | Lennard-Jones 12-6]]
**[[Restraint bond potential]]
**[[Quartic bond potential]]
**[[Buckingham potential]]
**[[FENE potential]]
*Angle potentials:
**[[Harmonic angle potential]]
**[[Quartic angle potential]]
**[[Truncated harmonic angle potential]]
**[[Screened harmonic angle potential]]
**[[Screened Vessal angle potential]]
**[[Truncated Vessal angle potential]]
**[[Harmonic cosine angle potential]]
**[[Cosine angle potential]]
**[[MM stretch-bend angle potential]]
**[[COMPASS stretch-stretch]]
**[[COMPASS stretch-bend]]
**[[COMPASS all terms]]
*Dihedral angle potentials:
**[[Cosine dihedral angle potential]]
**[[Harmonic dihedral angle potential]]
**[[Harmonic cosine dihedral angle potential]]
**[[Triple cosine dihedral angle potential]]
**[[Ryckaert-Bellemans dihedral angle potential]]
***[[Flourinated Ryckaert-Bellemans dihedral angle potential]]
**[[OPLS | OPLS dihedral angle potential]]
*Inversion angle potentials:
**[[Harmonic inversion angle potential]]
**[[Harmonic inversion angle potential]]
**[[Planar inversion angle potential]]
*Tethering potentials:
*Non-bonded potentials
*Three-body potentials
*Four-body potentials
*Metal potentials
**[[Embedded atom model]]
**[[Finnis-Sinclair]]
**[[Sutton-Chen]]
**[[Gupta potential]]
*External fields
==Constraint algorithms==
DL POLY can use either the [[SHAKE]] or the [[RATTLE]] algorithms as well as [[Q-SHAKE]] <ref> source: DL_POLY User Manual (v. 2.20) &sect; 2.5.2</ref>.
==Versions of DL_POLY==
The current version of DL_POLY is DL_POLY_4.07
====Previous versions====
;DL_POLY_2
DL_POLY_2 was designed for simulations of up to 30,000 atoms and on parallel computers using up to 100 processors.
DL_POLY_2 was designed for simulations of up to 30,000 atoms and on parallel computers using up to 100 processors.
==DL_POLY_3==
;DL_POLY_3
DL_POLY_3 was designed for simulations of order 100,000 to 1,000,000 atoms running on up to 1000 processors.  
DL_POLY_3 was designed for simulations of order 100,000 to 1,000,000 atoms running on up to 1000 processors.  
*DL_POLY_3 does not handle rigid body molecules.
*DL_POLY_3 does not handle rigid body molecules.
==DL_POLY_4==
====Other versions====
The first DL_POLY_4 release is expected early in 2010.
;DL_MULTI
==DL_MULTI==
A DL_POLY package to simulate rigid molecules with multipoles <ref>[http://dx.doi.org/10.1080/00268970802175308 M. Leslie "DL_MULTI—A molecular dynamics program to use distributed multipole electrostatic models to simulate the dynamics of organic crystals", Molecular Physics '''106''' pp. 1567-1578 (2008)]</ref>.
A DL_POLY package to simulate rigid molecules with multipoles.
 
*[http://dx.doi.org/10.1080/00268970802175308 M. Leslie "DL_MULTI—A molecular dynamics program to use distributed multipole electrostatic models to simulate the dynamics of organic crystals", Molecular Physics '''106''' pp. 1567-1578 (2008)]  
==Visualising DL_POLY output==
==Visualising DL_POLY output==
The visualisation program [[VMD]] is capable of displaying the HISTORY trajectory file.  
The visualisation program [[VMD]] is capable of displaying the HISTORY trajectory file.  
==References==
==References==
#[http://dx.doi.org/10.1016/S0263-7855(96)00043-4  W. Smith and T. R. Forester "DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package", Journal of Molecular Graphics  '''14''' pp. 136-141 (1996)]
<references/>
#[http://dx.doi.org/10.1080/08927020290018769 W. Smith,  C. W. Yong and P. M. Rodger "DL_POLY: application to molecular simulation", Molecular Simulation '''28''' pp. 385-471 (2002)]
==External links==
==External links==
*[http://www.stfc.ac.uk/SCD/research/app/ccg/software/DL_POLY/44516.aspx DL_POLY Home page]
*[http://community.hartree.stfc.ac.uk/portal/site/DL_SOFTWARE DL_Software Portal]
*[http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/MANUALS/USRMAN2.20.pdf DL_POLY_2.20 User Manual (PDF)]
*[http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/MANUALS/USRMAN2.20.pdf DL_POLY_2.20 User Manual (PDF)]
*[http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/MANUALS/USRMAN3.10.pdf DL_POLY_3.10 User Manual (PDF)]
*[http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/MANUALS/USRMAN3.10.pdf DL_POLY_3.10 User Manual (PDF)]


[[Category: Materials modelling and computer simulation codes]]
[[Category: Materials modelling and computer simulation codes]]

Latest revision as of 11:49, 2 February 2015

DL_POLY [1] [2] is a general purpose serial and parallel molecular dynamics simulation package developed at Daresbury Laboratory by W. Smith, T.R. Forester and I.T. Todorov

Units[edit]

DL_POLY employs an interesting set of units which have molecular relevance [3].:

physical quantity symbol unit value
time seconds (picoseconds)
length metres (Angstroms)
mass kilograms (amu)
charge Coulombs (electron charge)
energy Joules = 10 J mol
pressure Pascal = 166.054 bar
Planck constant
Boltzmann constant

Force field[edit]

The force field used in DL_POLY consists (or can consist) of the following components [4]:

Constraint algorithms[edit]

DL POLY can use either the SHAKE or the RATTLE algorithms as well as Q-SHAKE [5].

Versions of DL_POLY[edit]

The current version of DL_POLY is DL_POLY_4.07

Previous versions[edit]

DL_POLY_2

DL_POLY_2 was designed for simulations of up to 30,000 atoms and on parallel computers using up to 100 processors.

DL_POLY_3

DL_POLY_3 was designed for simulations of order 100,000 to 1,000,000 atoms running on up to 1000 processors.

  • DL_POLY_3 does not handle rigid body molecules.

Other versions[edit]

DL_MULTI

A DL_POLY package to simulate rigid molecules with multipoles [6].

Visualising DL_POLY output[edit]

The visualisation program VMD is capable of displaying the HISTORY trajectory file.

References[edit]

External links[edit]