pNMRsim

An NMR simulation tool optimised for dense dipolar coupled networks

For pre-compiled binaries (strongly recommended), do refer to the this webpage. The links in this page are sadly broken, but a zip file containing all the files can be downloaded from this page.

This repository is the bleeding edge source code, currently a maintenance version of V18.05.13.

Introduction

pNMRsim is a SIMPSON-like simulation program which is suited to the simulation of extended systems of spin-1/2 nuclei - the p refers to the use of 'periodic' geometries to introduce additional symmetry and block diagonalisation. pNMRsim tries hard to only recalculate quantities when strictly necessary, and historically at least will generally be faster than the equivalent SIMPSON simulation, but this added complexity does increase the chances of bugs surfacing in odd situations. In short, use at your own risk and always check that initial results make sense before relying on the output.

Requirements

pNMRsim is dependent on the following components:

A moderatately up-to-date C++ compiler (supporting C++11). The code is only tested only GCC compilers under Linux, and some tweaks may be required for other compilers / run-times.

The libcmatrix NMR library. pNMRsim is in effect a "user interface" to these underlying library routines. The library is updated as required by pNMRsim and so it is advisable to compile an up-to-date of the library when compiling pNMRsim.

The Minuit library (in its C++ incarnation) is required for optimisation problems. It is not required, however, for data fitting which uses libcmatrix routines. The "version 2" form of the C++ Minuit library is recommended as more up to date, but it must be a stand-alone version rather than one integrated into ROOT (see the README for libcmatrix).

The "classic" version of the Boost Spirit library is used for parsing. You will need a standalone version, 1.8.5, not the later versions of Spirit that are currently supplied with Boost.

SIMPLOT is useful for visualising pNMRsim output (although a variety of output formats are supported).

Installation

It is most efficient to compile libcmatrix and pNMRsim one after the other since the same configuration options are involved.

The options to configure are:

--with-atlas, --with-acml, --with-mkl, --with-openblas  enable use of one of the ATLAS, ACML, MKL or OpenBLAS libraries 
--with-MPI  enable the use of MPI for parallel computations
--with-minuit  enable the use of Minuit
--with-sse  enable the use of SSE3 instructions for complex arithmetic 

See the installation instructions for libcmatrix for more details.

pNMRsim specific options

--enable-static Use static linkage (default off). This is recommended when compiling for Windows. It will generate stand-alone (but rather large) .exe files.

--disable-CXX11 Disable C++11 features (default enabled). Up-to-date compilers should be happy with the minimal use of C++11 features. Note that the flags used to enable C++11 features may need tweaking depending on compiler (uses -std=c++11)

1. Ensure libcmatrix is compiled and (optionally) installed.

2. Configure pNMRsim as above, making sure that configure can find the libcmatrix header files and library (CPPFLAGS and LDFLAGS respectively - again the libcmatrix INSTALL instructions discuss this). You will need to add the path to the Spirit files by adding -I<Spirit directory (containing boost/spirit)>.

Hence a minimal configure run will typically be CPPFLAGS="-I../spirit-1.8.5-miniboost-patched -I<basedir>/libcmatrix/include" LDFLAGS="-L<basedir>/libcmatrix/lib" ./configure

Note that absolute paths should be used rather than relative ones so that the paths are transferable.

3. make will compile pNMRsim, pNMRproc and extras/magres2pNMRsim.

These is currently an issue with configure failing to find std::isnan on Windows. If compile errors involving isnan are raised, try adding -DISNAN_IN_STD to CPPFLAGS. In general, compilation for Linux is strongly recommended.

Other files

The test directory contains a varied and rather chaotic collection of input files. Many have been hacked around for testing purposes so check that the input file actually does what suggests it does...