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QM/MM support toplevel library
Axel Kohlmeyer, akohlmey@gmail.com
Temple University, Philadelphia and ICTP, Trieste
This library provides the basic glue code to combine LAMMPS with the
Quantum ESPRESSO package plane wave density functional theory code for
performing QM/MM molecular dynamics simulations. More information on
Quantum ESPRESSO can be found at: http://www.quantum-espresso.org
The interface code itself is designed so it can also be combined with
other QM codes, however only support for Quantum ESPRESSO is currently
the only option. Adding support for a different QM code will require
to write a new version of the top-level wrapper code, pwqmmm.c, and
also an interface layer into the QM code similar to the one in QE.
-------------------------------------------------
This directory has the source files to build a library and an
executable for combining the pw.x program from Quantum ESPRESSO and
LAMMPS into a single executable that can be used for QM/MM molecular
dynamics simulations. LAMMPS will act as the MD "driver" and will
delegate computation of forces for the QM subset of the system to
Quantum ESPRESSO.
The toplevel code provided here will split the total number of cpus
into three partitions: the first for running a DFT calculation, the
second for running the "master" classical MD calculation, and the
third for a "slave" classical MD calculation. Each calculation will
have to be run in its own subdirectory with its own specific input
data and will write its output there as well. This and other settings
are provided in the QM/MM input file that is mandatory argument to the
QM/MM executable. The number of MM cpus is provided as the optional
second argument. The MM "slave" partition is always run with only 1
cpu thus the minimum number is 2, which is also the default. Therefore
a QM/MM calculation with this code requires at least 3 processes.
Thus the overall calling sequence is like this:
mpirun -np <total #cpus> ./pwqmmm.x <QM/MM input> [<#cpus for MM>]
A commented example is given below.
-------------------------------------------------
Build the library using one of the provided Makefile.* files or create
your own, specific to your compiler and system. For example:
make -f Makefile.gfortran
When you are done building this library, two new files should
exist in this directory:
libqmmm.a the library LAMMPS will link against
Makefile.lammps settings the LAMMPS Makefile will import
Makefile.lammps is created by the make command by simply copying the
Makefile.lammps.empty file. Currently no additional dependencies for
this library exist.
-------------------------------------------------
To compile and link the final QM/MM executable, you have to build
quantum espresso with the "pw" and "couple" targets. You also have
to to install the USER-QMMM package for LAMMPS. You have to specify
the path to the toplevel Quantum ESPRESSO directory, so that the
compiler and linker settings can be imported.
The makefile variable MPILIBS needs to be set to include all linker
flags that will need to be used in addition to the various libraries
from the two packages. Please see the provided example(s).
"make -f Makefile.gfortran" all by itself will only compile the
library (so that LAMMPS can be compiled into a standalone executable
as well, when the USER-QMMM package is installed).
"make -f Makefile.gfortran pwqmmm.x" will compile and link the QM/MM
executable; "make -f Makefile.gfortran all" will recurse through the
Quantum ESPRESSO and LAMMPS directories to compile all files that
require recompilation and then link the executable.
Please refer to the specific LAMMPS and Quantum ESPRESSO documentation
for details on how to set up compilation for each package and make
sure you have a set of settings and flags that allow you to build
each package successfully, so that it can run on its own.
-------------------------------------------------
# configuration file for QMMM wrapper
mode mech # coupling choices: o(ff), m(echanical), e(lectrostatic)
steps 20 # number of QM/MM (MD) steps
verbose 1 # verbosity level (0=no QM/MM output during run)
restart water.restart # checkpoint/restart file to write out at end
# QM system config
qmdir qm-pw # directory to run QM system in
qminp water.in # input file for QM code
qmout NULL # output file for QM code (or NULL to print to screen)
# MM master config
madir mm-master # directory to run MM master in
mainp water.in # input file for MM master
maout water.out # output file for MM master (or NULL to print to screen)
# MM slave config
sldir mm-slave # directory to run MM slave in
slinp water_single.in # input file for MM slave
slout water_single.out # output file for MM slave (or NULL to print to screen)
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