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ænet-Tinker Interface

If you make use of the aenet-Tinker interface, please cite the following reference:

M.S. Chen, T. Morawietz, H. Mori, T.E. Markland, N. Artrith, AENET-LAMMPS and AENET-TINKER: Interfaces for Accurate and Efficient Molecular Dynamics Simulations with Machine Learning Potentials, J. Chem. Phys. 155, 074801 (2021). doi: https://doi.org/10.1063/5.0063880

Preprint (Preprint where the data is discussed) arXiv (2021) doi: https://arxiv.org/abs/2107.11311

The database can be obtained from the Materials Cloud repository, DOI: https://doi.org/10.24435/materialscloud:dx-ct

ænet-Tinker

This directory provides all files needed to link the Tinker molecular dynamics code with aenetLib.

The present interface code has been tested with Tinker version 8.2.1 (from June 2017).

Note

The interface supports OpenMP shared memory parallelism, but only using the GNU Fortran compiler. The OpenMP implementation provided by Intel compilers (as of version 15) is not compatible. However, even using the GNU compiler aenetLib a significant speed-up can be achieved by linking with the Intel MKL library when available.

Presently, only energies and forces are provided by the interface. This means Tinker functionality that requires derivatives of higher orders are not supported.

Prerequisites

To be linked with Tinker, ænet has to be compiled as library. Build the library by running

make -f ./makefiles/Makefile.gfortran_serial lib

in the ænet src directory. Alternatively, if the Intel MKL library is available, Makefile.gfortran_mkl_serial can be used.

Building Tinker with ænet support

Copy the following files to the Tinker source directory:

  • aenettinker.f90
  • extra.f
  • extra1.f
  • Makefile.aenetlib_gfortran

and adjust the path to aenet (AENETDIR) in the Makefile. The Makefile contains two alternative blocks for numerical libraries. To use the system LAPACK and BLAS libraries uncomment the line

NUMLIB = -llapack -lblas

for use with the Intel MKL library, use the following instead

NUMLIB = -Wl,--start-group \
         $(MKLROOT)/lib/intel64/libmkl_intel_lp64.a \
         $(MKLROOT)/lib/intel64/libmkl_core.a \
         $(MKLROOT)/lib/intel64/libmkl_sequential.a \
         -Wl,--end-group -lpthread -lm -ldl

Tinker can then be compiled with

make -f Makefile.aenetlib_gfortran

from within the source directory.

Running Tinker simulations using ænet potentials

To run simulations using ænet artificial neural network (ANN) potentials, the parameter file aenet.prm can be used. It only contains the masses of all chemical species, as no further information is required.

All ANN potential files have to follow the naming convention

<species>.ann

where <species> is the chemical symbol (H, He, Li, etc.) and have to be present in the working directory.

In the Tinker key principal input file, ænet potentials are activated with the keyword

EXTRATERM only

The number of threads used in parallel runs can be controlled with the keyword OPENMP-THREADS.

See also the example Tinker input file tinker.key.