Contents

This is a list of the Fortran 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.

The utility module files averages_module.f90, config_io_module.f90, and maths_module.f90, and a small module containing long-range-correction formulae lrc_lj_module.f90 are widely used by the simulation programs. They are not explicitly listed in most cases below: the SConstruct file gives a full list of the build dependencies in each case.

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.f90 and md_poly_lj_module.f90 is described in the online GUIDE, but does not appear in the text.

1.1 Calculation of T tensors

1.2 Double loop for Lennard-Jones potential

This code snippet appears in the text, not online. However working examples of a similar kind may be found in mc_lj_module.f90 and md_lj_module.f90.

1.3 Site–site potential energy calculation

This code snippet appears in the text, not online. However a working example of a similar kind may be found in mc_poly_lj_module.f90.

1.4 Periodic boundaries for truncated octahedron

This code snippet appears in the text, not online.

1.5 Periodic boundaries for rhombic dodecahedron

This code snippet appears in the text, not online.

1.6 Periodic boundaries for rhombus

This code snippet appears in the text, not online.

3.1 Velocity Verlet algorithm

This code snippet appears in the text, not online. However a working example of a similar kind may be found in md_nve_lj.f90, and in several other MD program files.

3.2 Velocity Verlet algorithm (original)

This code snippet appears in the text, not online.

3.3 Classic Verlet algorithm

This code snippet appears in the text, not online.

3.4 Molecular dynamics, NVE-ensemble, Lennard-Jones

md_nve_lj.f90 and md_lj_module.f90.

3.5 Constraint algorithms for a chain molecule

md_chain_nve_lj.f90 and md_chain_lj_module.f90.

3.6 Multiple-timestep algorithm

md_chain_mts_lj.f90 and md_chain_lj_module.f90.

3.7 Molecular dynamics of hard spheres

md_nve_hs.f90 and md_nve_hs_module.f90.

3.8 Measure-preserving constant-NVT MD algorithm

md_nvt_lj.f90 and md_lj_module.f90.

3.9 Measure-preserving constant-NPT MD algorithm

md_npt_lj.f90 and md_lj_module.f90.

4.1 Hit-and-miss integration

hit_and_miss.f90 (also appears in full in the text).

4.2 Sample mean integration

sample_mean.f90 (also appears in full in the text).

4.3 Monte Carlo NVT-ensemble for Lennard-Jones atoms

mc_nvt_lj.f90 and mc_lj_module.f90.

4.4 Monte Carlo of hard spheres

mc_nvt_hs.f90 and mc_hs_module.f90. We also supply a constant-pressure version mc_npt_hs.f90.

4.5 Monte Carlo NPT-ensemble for Lennard-Jones atoms

mc_npt_lj.f90 and mc_lj_module.f90.

4.6 Monte Carlo μVT-ensemble for Lennard-Jones atoms

mc_zvt_lj.f90 and mc_lj_module.f90.

4.7 Monte Carlo program using quaternions

mc_nvt_poly_lj.f90 and mc_poly_lj_module.f90. We also supply a molecular dynamics program md_nvt_poly_lj.f90 and md_poly_lj_module.f90 to simulate the same model.

4.8 Monte Carlo of hard spherocylinders

mc_nvt_sc.f90 and mc_sc_module.f90. We also supply a constant-pressure version mc_npt_sc.f90.

5.1 Force routine using Verlet neighbour list

md_lj_vl_module.f90 and verlet_list_module.f90. These may be used instead of md_lj_module.f90 in combination with md_nve_lj.f90.

5.2 Building a cell structure with linked lists

This code snippet appears in the text, not online. However a working version of a similar kind may be found in link_list_module.f90 of Code 5.3.

5.3 Force routine using linked lists

md_lj_ll_module.f90 and link_list_module.f90. These may be used instead of md_lj_module.f90 in combination with md_nve_lj.f90 or md_nvt_lj.f90.

5.4 Monte Carlo routines using linked lists

mc_lj_ll_module.f90 and link_list_module.f90. These may be used instead of mc_lj_module.f90 in combination with mc_nvt_lj.f90, mc_npt_lj.f90, or mc_zvt_lj.f90. However, for simplicity the routines have not been designed to be especially robust against large changes in system dimensions or number of particles: this could be fixed by including some memory reallocation statements in the Fortran.

5.5 Multiple-timestep algorithm, Lennard-Jones atoms

md_lj_mts.f90 and md_lj_mts_module.f90.

5.6 Initialization of a crystal lattice

initialize.f90 and initialize_module.f90. This program also has options to initialize a random configuration, and a chain of atoms.

6.1 Force routine using the Ewald sum

ewald.f90 with ewald_module.f90 and mesh_module.f90. 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.f90 and mesh_module.f90.

7.1 Parallelized double-loop, shared memory

This code snippet appears in the text, not online. However a working example of a similar kind may be found in md_lj_omp_module.f90 of Code 7.2.

7.2 Parallelized force routine, shared memory

md_lj_omp_module.f90. This may be used instead of md_lj_module.f90 in combination with md_nve_lj.f90.

7.3 Replica exchange, by message-passing

mc_nvt_lj_re.f90 and mc_lj_module.f90.

8.1 Calculating the pair distribution function

pair_distribution.f90. Part of the code also appears in the text.

8.2 Calculating a time correlation function

This code snippet appears in the text, not online. However working examples of a similar kind may be found in diffusion.f90 of Code 8.3 and corfun.f90 of Code 8.4.

8.3 Program to compute diffusion coefficients

diffusion.f90. Also supplied is a program diffusion_test.f90 to generate test data.

8.4 Calculating time correlation functions

8.5 Calculating statistical inefficiency and errors

error_calc.f90.

9.1 Wang–Landau simulation of chain molecule

mc_chain_wl_sw.f90 and mc_chain_sw_module.f90. Also provided is a small program wl_hist.f90 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.f90.

9.2 Configuration-biased simulation of chain molecule

mc_chain_nvt_cbmc_lj.f90 and mc_chain_lj_module.f90.

9.3 Gibbs ensemble simulation

mc_gibbs_lj.f90 and mc_gibbs_lj_module.f90.

11.1 Molecular dynamics using Lees–Edwards boundaries

md_nvt_lj_le.f90 and md_lj_le_module.f90.

11.2 Cell structure and linked lists in sheared boundaries

md_lj_llle_module.f90 and link_list_module.f90. These may be used instead of md_lj_le_module.f90 in combination with md_nvt_lj_le.f90.

12.1 Brownian dynamics program

bd_nvt_lj.f90 and md_lj_module.f90.

12.2 Smart Monte Carlo simulation

smc_nvt_lj.f90 and smc_lj_module.f90.

12.3 Dissipative particle dynamics

dpd.f90 and dpd_module.f90.

13.1 Path-integral Monte Carlo

qmc_pi_sho.f90 for the simple harmonic oscillator. qmc_pi_lj.f90 and qmc_pi_lj_module.f90 for Lennard-Jones.

13.2 Quantum Monte Carlo using a diffusion equation

qmc_walk_sho.f90.

14.1 Calculating the temperature and density profiles

This code snippet appears in the text, not online. However, a working example of the density profile calculation may be found in grint.f90 of Code 14.2.

14.2 Radial distribution function in a planar interface

grint.f90 and grint_module.f90. We also provide a (comparatively large) file grint_data.zip containing test data in the Data repository.

14.3 Cluster analysis

cluster.f90. We also provide a test configuration file cluster.inp.

A.1 Utility modules

averages_module.f90, config_io_module.f90, and maths_module.f90, used by many of the programs listed above.

C.1 Programs to test forces and torques

test_pot_atom.f90 together with any one of test_pot_at.f90, test_pot_bend.f90, or test_pot_twist.f90.

test_pot_linear.f90 together with any one of test_pot_dd.f90, test_pot_dq.f90, test_pot_qq.f90, or test_pot_gb.f90.

D.1 3D Fourier transform example

F.1 Calculating the configurational temperature

This code snippet appears in the text, not online. However, a working example may be found in mc_nvt_lj.f90 and its module mc_lj_module.f90.

F.2 Correction to configurational temperature

This code snippet appears in the text, not online. However, a working example may be found in md_nve_lj.f90 and its module md_lj_module.f90.