Examples¶

Example Simulations¶

Because of the size of the data files for the DL_POLY_5 standard test cases, they are not shipped in the standard download of the DL_POLY_5 source. Test files are downloaded automatically when building/ running CMake with the CMake variable BUILD_TESTING=ON. This can be done as follows:

folder="build-mpi-testing"
rm -rf $folder && mkdir $folder && pushd $folder
cmake ../ -DCMAKE_BUILD_TYPE=Debug -DBUILD_TESTING=ON

Unpack the files in the ‘data’ subdirectory using ‘gunzip’ and ‘tar -xf’ to create the ‘TEST_X’ directory.

These are provided to give examples of DL_POLY_5 simulations and demonstrate a limited set of relevant functionality over a limited extent of molecular systems’ complexity only. Without modification, they are not necessarily appropriate for serious simulation of the given systems. In other words, the examples are not warranted to have well-defined force fields in terms of applicability, transferability and fullness, nor are they likely to have a well-defined state point (i.e. initial configurations may be away from equilibrium, if physical at all).

The README.txt file supplied both in the data directory and in the directory on the CCP5 FTP server provides a list of all example simulations used as test cases to check that DL_POLY_5 is working correctly, including those described in more detail below. All the jobs are of a size suitable to test the code in parallel execution. They may not be suitable for a single processor computer. The files are stored in compressed format. The examples can be run by typing

select n

from the execute directory, where n is the number of the test case. The select macro will copy the appropriate input files (at least CONTROL, CONFIG, and FIELD in all cases) to the execute directory ready for execution. The output file OUTPUT may be compared with the file supplied in the data directory.

Example 1: Sodium Chloride¶

This is a 27,000 ion system with unit electric charges on sodium and chlorine. Simulation at 500 K with a NVT Berendsen ensemble. The SPME method is used to calculate the Coulombic interactions.

Example 2: DPMC in Water¶

The system consists of 200 DMPC molecules in 9379 and water molecules. Simulation at 300 K using NVE ensemble with SPME and RATTLE algorithm for the constrained motion. The total system size is 51,737 atoms.

Example 3: KNaSi\(_{2}\)O\(_{5}\) - Potassium/Sodium Disilicate Glass¶

Potassium Sodium disilicate glass (NaKSi:math:_{2}O\(_{5}\)) using two and three-body potentials. Some of the two-body potentials are read from the TABVDW file. Simulation at 1000 K using NVT Nosé-Hoover ensemble with SPME. Cubic periodic boundaries are in use. The total system size is 69,120 ions.

Example 4: Gramicidin A Molecules in Water¶

The system consists of 8 gramicidin A molecules in aqueous solution (32,096 water molecules) with total of 99,120 of atoms. Simulation at 300 K using NPT Berendsen ensemble with SPME and SHAKE/RATTLE algorithm for the constrained motion.

Example 5: SiC with Tersoff Potentials¶

The system consists of 74,088 atoms. Simulation at 300 K using NPT Nosé-Hoover ensemble with Tersoff forces and no electrostatics.

Example 6: Cu\(_{3}\)Au alloy with Sutton-Chen (metal) Potentials¶

The systems consists of 32,000 atoms. Simulation at 300 K using NVT Nosé-Hoover ensemble with Sutton-Chen forces and no electrostatics.

Example 7: Lipid Bilayer in Water¶

The systems consists of 12,428 atoms. Simulation at 300 K using NVT Berendsen ensemble with SPME and SHAKE/RATTLE algorithm for the constrained motion.

Examples 8 and 9: MgO with Adiabatic and with Relaxed Shell Models¶

These system consist of 8,000 (4,000 shells) charged points. Simulation at 3000 K using NPT Berendsen ensemble with SPME.

Example 10: Potential of Mean Force on K+ in Water¶

The system consists of 13,500 (500 PMFs) atoms. Simulation at 300 K using NPT Berendsen ensemble with SPME and SHAKE/RATTLE algorithm for the constrained motion.

Example 11: Cu\(_{3}\)Au Alloy with Gupta (metal) Potentials¶

The system consists of 32,000 atoms. Simulation at 300 K using NVT Nosé-Hoover ensemble with Gupta forces and no electrostatics.

Example 12: Cu with EAM (metal) Potential¶

The system consists of 32,000 atoms. Simulation at 300 K using NPT Berendsen ensemble with EAM tabulated forces and no electrostatics.

Examples 13 and 14: Al with Analytic and with EAM Tabulated Sutton-Chen (metal) Potentials¶

The system consists of 32,000 atoms. Simulation at 300 K using NVT Evans ensemble with Sutton-Chen forces and no electrostatics.

Examples 15: NiAl Alloy with EAM (metal) Potentials¶

The system consists of 27,648 atoms. Simulation at 300 K using NVT Evans ensemble with EAM tabulated forces and no electrostatics.

Examples 16: Fe with Finnis-Sincair (metal) Potential¶

The system consists of 31,250 atoms. Simulation at 300 K using NPT Berendsen ensemble with Finnis-Sinclair forces and no electrostatics.

Examples 17: Ni with EAM (metal) Potential¶

The system consists of 32,000 atoms. Simulation at 300 K using NPT Berendsen ensemble with EAM tabulated forces and no electrostatics.

Examples 18 and 19: SPC IceVII Water with CBs and with RBs¶

The system consists of 11,664 (34,992 atoms) water molecules. Simulation at 25 K using NVE ensemble with CGM force minimisation and SPME electrostatics.

Example 20: NaCl Molecules in SPC Water Represented as CBs+RBs¶

The system consists of 64 NaCl ion pairs with 4,480 water molecules represented by constraint bonds and 4,416 water molecules represented by ridig bodies. Totalling 26,816 atoms. Simulation at 295 K using NPT Berendsen ensemble with CGM energy minimisation and SPME electrostatics.

Example 21: TIP4P Water: RBs with a Massless Charged Site¶

The system consists of 7,263 TIP4P rigid body water molecules totaling 29,052 particles. Simulation at 295 K using NPT Berendsen ensemble with CGM energy minimisation and SPME electrostatics.

Example 22: Ionic Liquid Dimethylimidazolium Chloride as RBs¶

The system consists of 44,352 ions. Simulation at 400 K using NPT Berendsen ensemble, using both particle and rigid body dynamics with SPME electrostatics.

Example 23: Calcite Nano-Particles in TIP3P Water¶

In this case 600 molecules of calcium carbonate in the calcite structure form 8 nano-particles which are suspended in 6,904 water molecules, represented by a flexible 3-centre TIP3P model. Simulation with SPME electrostatics at 310 K and 1 atmosphere maintained in a Hoover NPT ensemble. The system consists of 23,712 ions.

Example 24: Iron/Carbon Alloy with 2BEAM (metal) Potentials¶

In this case a steel alloy of iron and carbon in ratio 35132 to 1651 is modelled using an EEAM potential forcefield. Simulation at 1000 K and 0 atmosphere is maintained in a Berendsen NPT ensemble. The system consists of 36,803 particles.

Example 25: Iron/Chromium Alloy with 2BEAM (metal) Potentials¶

In this case a steel alloy of iron and chromium in ratio 27635 to 4365 is modelled using an 2BEAM potential forcefield. Simulation at 300 K and 0 atmosphere is maintained in an Evans NVT isokinetic ensemble. The system consists of 32,000 particles.

Examples 26 and 27: Hexane and Methanol Melts, with Full Atomistic and Coarse-Grained Force-Fields¶

These two examples contain a Hexane and a Methanol melt respectively, (1000 molecules each) modelled by the OPLSAA force-field (FF). Each system is also supplied in a CG-mapped representation as converted by VOTCA, http://www.votca.org/, or DL_CGMAP http://www.ccp5.ac.uk/projects/ccp5_cg.shtml.

These test cases are to exemplify the Coarse-Graining (CG) procedure (see Chapter Coarse Graining), including FA-to-CG mapping and obtaining the PMF data by means of Boltzmann Inversion ⁹⁸. As a result, DL_POLY_5 could be used for simulating a CG system with numerically defined, tabulated FFs, see TABBND, TABANG, TABDIH and TABINV files for intra-molecular potentials, and TABVDW for inter-molecular (short-range, VDW) potentials.

Both tests are also available as parts of the tutorial cases from the VOTCA package ⁹². Therefore, the CONFIG, CONTROL and FIELD input files are fully consistent with the corresponding setup files found in the VOTCA tutorial directories “csg-tutorials/hexane” and “csg-tutorials/methanol’.

Example 28: Butane in CCl\(_{4}\) Solution with Umbrella Sampling via PLUMED¶

Free Energy calculation for Buthane with respect to the dihedral angle as collective variable. We use umbrella sampling as implemented in PLUMED.

PLUMED enabling in CONTROL:

plumed input umbrella.dat

Contents of umbrella.dat:

phi: TORSION ATOMS=1,2,3,4
restraint-phi: RESTRAINT ARG=phi KAPPA=500 AT=1.20
PRINT STRIDE=10 ARG=phi,restraint-phi.bias FILE=COLVAR

Two extra output files are generated in this case: OUTPUT.PLUMED and COLVAR.

Note

a DL_POLY_5 version with PLUMED enabled is used for this.

Example 29: Iron with tabulated EAM (metal) Potential, TTM and Cascade¶

In this example 54,000 atoms of iron are modelled with a tabulated embedded-atom potential optimised to produce correct energetics of point defects and clusters (M07 in ⁷⁰). An energy impact of 10 keV is applied to an atom and the resulting radiation damage is evolved using the Two-Temperature Model (TTM) to represent energy transfers due to electron-phonon coupling and electronic stopping between atoms and a continuum electronic gas ¹⁵⁰.

This test case produces additional output files: DUMP_E, LATS_E, LATS_I, PEAK_E and PEAK_I. It also requires an additional input file (Ce.dat) to supply tabulated heat capacity data required for evolving the electronic system.

Example 30: Silicon with original Tersoff Potential, TTM and Swift heavy ion irradiation¶

This system consists of 200,000 atoms of silicon modelled using an original Tersoff (T3) potential. The Two-Temperature Model (TTM) is in use and an energy deposition is applied to the electronic system using a Gaussian spatial function, an exponentially decaying temporal function and an electronic stopping power of 50,000 eV/nm. This simulation represents Swift heavy ion irradiation in silicon, including the resulting creation of ion tracks ⁵⁹.

Example 31: Tungsten with extended Finnis-Sinclair Potential, TTM and laser irradiation¶

This system consists of 722,672 atoms of tungsten modelled using an extended Finnis-Sinclair potential. The Two-Temperature Model (TTM) is in use and an energy deposition is applied to the electronic system using a spatial function that is homogeneous in x and y directions and exponentially decaying in the z direction, as well as a Gaussian temporal function. This energy deposition represents a laser applied to the surface of a thin film of tungsten ⁸¹ with a surface fluence of 36 mJ/cm\(^2\) and penetration depth of 12.5 nm, causing the film to expand outwards in the z direction.

Additional input files (Ce.dat and g.dat) are required to supply tabulated heat capacity and electron-phonon coupling values.