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This is a list of Python versions of the code examples appearing in the text, in order, indicating the corresponding online program files. The online GUIDE provides more information about running these programs, but there they are grouped together by system studied, for easier comparison of the typical test results. Although links are provided here to the individual files, it is expected that you will have downloaded them all together.

Not all the examples have online files: in some cases the code was provided in the text. We have only provided a selection of examples in Python, whereas the full set is provided in Fortran.

The utility module files averages_module.py, config_io_module.py, and maths_module.py, and a small module containing long-range-correction formulae lrc_lj_module.py are widely used by the simulation programs. They are not explicitly listed in most cases below.

Several other small programs are not described in the text, but are mentioned in the online GUIDE:

An additional molecular dynamics program using quaternions md_nvt_poly_lj.py and md_poly_lj_module.py is described in the online GUIDE, but does not appear in the text.

1.1 Calculation of T tensors

t_tensor.py.

1.2 Double loop for Lennard-Jones potential

A Fortran version of this code snippet appears in the text, not online. However working Python examples of a similar kind may be found in mc_lj_module.py and md_lj_module.py.

1.3 Site–site potential energy calculation

A Fortran version of this code snippet appears in the text, not online.

1.4 Periodic boundaries for truncated octahedron

A Fortran version of this code snippet appears in the text, not online.

1.5 Periodic boundaries for rhombic dodecahedron

A Fortran version of this code snippet appears in the text, not online.

1.6 Periodic boundaries for rhombus

A Fortran version of this code snippet appears in the text, not online.

3.1 Velocity Verlet algorithm

A Fortran version of this code snippet appears in the text, not online. However a working Python example of a similar kind may be found in md_nve_lj.py.

3.2 Velocity Verlet algorithm (original)

A Fortran version of this code snippet appears in the text, not online.

3.3 Classic Verlet algorithm

A Fortran version of this code snippet appears in the text, not online.

3.4 Molecular dynamics, NVE-ensemble, Lennard-Jones

md_nve_lj.py and md_lj_module.py.

3.5 Constraint algorithms for a chain molecule

md_chain_nve_lj.py and md_chain_lj_module.py.

3.6 Multiple-timestep algorithm

md_chain_mts_lj.py and md_chain_lj_module.py.

3.7 Molecular dynamics of hard spheres

md_nve_hs.py and md_nve_hs_module.py.

3.8 Measure-preserving constant-NVT MD algorithm

md_nvt_lj.py and md_lj_module.py.

3.9 Measure-preserving constant-NPT MD algorithm

md_npt_lj.py and md_lj_module.py.

4.1 Hit-and-miss integration

hit_and_miss.py (a Fortran version also appears in full in the text).

4.2 Sample mean integration

sample_mean.py (a Fortran version also appears in full in the text).

4.3 Monte Carlo NVT-ensemble for Lennard-Jones atoms

mc_nvt_lj.py and mc_lj_module.py.

4.4 Monte Carlo of hard spheres

mc_nvt_hs.py and mc_hs_module.py. We also supply a constant-pressure version mc_npt_hs.py.

4.5 Monte Carlo NPT-ensemble for Lennard-Jones atoms

mc_npt_lj.py and mc_lj_module.py.

4.6 Monte Carlo μVT-ensemble for Lennard-Jones atoms

mc_zvt_lj.py and mc_lj_module.py.

4.7 Monte Carlo program using quaternions

mc_nvt_poly_lj.py and mc_poly_lj_module.py. We also supply a molecular dynamics program md_nvt_poly_lj.py and md_poly_lj_module.py to simulate the same model.

4.8 Monte Carlo of hard spherocylinders

mc_nvt_sc.py and mc_sc_module.py. We also supply a constant-pressure version mc_npt_sc.py.

5.1 Force routine using Verlet neighbour list

We do not provide a Python version of this example. A Fortran version is available.

5.2 Building a cell structure with linked lists

A Fortran version of this code snippet appears in the text, not online.

5.3 Force routine using linked lists

md_lj_ll_module.py. This may be used in combination with md_nve_lj.py, md_nvt_lj.py, or md_npt_lj.py. In each case, the program needs to be edited so as to import routines from this module instead of md_lj_module.py. Despite the name, linked lists are not used, as there is no advantage in Python. However, the module illustrates the cell structure, and the calculation of forces between neighbouring cells, analogous to the Fortran example.

5.4 Monte Carlo routines using linked lists

We do not provide a Python version of this example. A Fortran version is available.

5.5 Multiple-timestep algorithm, Lennard-Jones atoms

We do not provide a Python version of this example. A Fortran version is available.

5.6 Initialization of a crystal lattice

initialize.py. This program also has options to initialize a random configuration, and a chain of atoms.

6.1 Force routine using the Ewald sum

ewald.py with ewald_module.py and mesh_module.py. As well as the real-space and reciprocal-space routines mentioned in the text, we also illustrate the particle-mesh-Ewald method.

6.2 Assignment of charge to a uniform mesh

mesh.py and mesh_module.py.

7.1 Parallelized double-loop, shared memory

A Fortran version of this code snippet appears in the text, not online.

7.2 Parallelized force routine, shared memory

We do not provide a Python version of this example. A Fortran version is available.

7.3 Replica exchange, by message-passing

mc_nvt_lj_re.py and mc_lj_module.py.

8.1 Calculating the pair distribution function

pair_distribution.py. A Fortran version of part of the code also appears in the text.

8.2 Calculating a time correlation function

A Fortran version of this code snippet appears in the text, not online. However working Python examples of a similar kind may be found in diffusion.py of Code 8.3 and corfun.py of Code 8.4.

8.3 Program to compute diffusion coefficients

diffusion.py. Also supplied is a program diffusion_test.py to generate test data.

8.4 Calculating time correlation functions

corfun.py.

8.5 Calculating statistical inefficiency and errors

error_calc.py.

9.1 Wang–Landau simulation of chain molecule

mc_chain_wl_sw.py and mc_chain_sw_module.py. Also provided is a small program wl_hist.py to do post-processing of the histograms produced by the Wang-Landau simulation and, for comparison, a constant-temperature MC program mc_chain_nvt_sw.py.

9.2 Configuration-biased simulation of chain molecule

mc_chain_nvt_cbmc_lj.py and mc_chain_lj_module.py.

9.3 Gibbs ensemble simulation

mc_gibbs_lj.py.

11.1 Molecular dynamics using Lees–Edwards boundaries

md_nvt_lj_le.py and md_lj_le_module.py.

11.2 Cell structure and linked lists in sheared boundaries

md_lj_llle_module.py. This may be used in combination with md_nvt_lj_le.py, edited so as to import routines from this module instead of md_lj_le_module.py. Despite the name, linked lists are not used, as there is no advantage in Python. However, the module illustrates the cell structure, and the calculation of forces between neighbouring cells, analogous to the Fortran example.

12.1 Brownian dynamics program

bd_nvt_lj.py and md_lj_module.py.

12.2 Smart Monte Carlo simulation

smc_nvt_lj.py and smc_lj_module.py.

12.3 Dissipative particle dynamics

dpd.py and dpd_module.py.

13.1 Path-integral Monte Carlo

qmc_pi_sho.py for the simple harmonic oscillator. qmc_pi_lj.py and qmc_pi_lj_module.py for Lennard-Jones.

13.2 Quantum Monte Carlo using a diffusion equation

qmc_walk_sho.py.

14.1 Calculating the temperature and density profiles

A Fortran version of this code snippet appears in the text, not online.

14.2 Radial distribution function in a planar interface

grint.py. We also provide a (comparatively large) file grint_data.zip containing test data in the Data repository.

14.3 Cluster analysis

cluster.py. We also provide a test configuration file cluster.inp.

A.1 Utility modules

averages_module.py, config_io_module.py, and maths_module.py, used by many of the programs listed above.

C.1 Programs to test forces and torques

test_pot_atom.py together with any one of test_pot_at.py, test_pot_bend.py, or test_pot_twist.py.

test_pot_linear.py together with any one of test_pot_dd.py, test_pot_dq.py, test_pot_qq.py, or test_pot_gb.py.

D.1 3D Fourier transform example

fft3dwrap.py.

F.1 Calculating the configurational temperature

A Fortran version of this code snippet appears in the text, not online. However, a working Python example may be found in mc_nvt_lj.py and its module mc_lj_module.py.

F.2 Correction to configurational temperature

A Fortran version of this code snippet appears in the text, not online. However, a working Python example may be found in md_nve_lj.py and its module md_lj_module.py.