QM/MM support 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.

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WARNING: This is experimental code under developementand is provided
at this early stage to encourage others to write interfaces to other
QM codes. Please test *very* carefully before using this software for
production calculations.

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Building the QM/MM executable has to be done in multiple stages.

Step 1) 
Build the qmmm coupling library in this directory using one of the
provided Makefile.<compiler> files or create your own, specific to
your compiler and system.  For example with:

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.

Step 2)
Build a standalone LAMMPS executable as described in the LAMMPS 
documentation and include the USER-QMMM package. This executable
is not functional for QM/MM, but it will usually be needed to
run all MM calculations for equilibration and testing and also
to confirm that the classical part of the code is set up correctly.

Step 3)
Build a standalone pw.x executable in the Quantum ESPRESSO directory
and also make the "couple" target. At the time of this writing 
(April 2014) you have to download a QE snapshot from the SVN 
repository, since no official release with the library interface
to couple other codes to QE has been made yet. This is also needed
to confirm that corresponding code is working correctly and to
run test calculations on the cluster of QM atoms.

Step 4)
To compile and link the final QM/MM executable, which combines the
compiled sources from both packages, you have to return to the lib/qmmm
directory and now edit the Makefile.<compiler> for the Makefile 
configuration used to compile LAMMPS and also update the directory
and library settings for the Quantum ESPRESSO installation.

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 _both_ packages. Please see the provided example(s).

"make -f Makefile.<compiler> all" will now recurse through both the
Quantum ESPRESSO and LAMMPS directories to compile all files that 
require recompilation and then link the combined QM/MM executable.

If you want to only update the local objects and the QM/MM executable,
you can use "make -f Makefile.<compiler> pwqmmm.x"

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.

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How it works.

This directory has the source files for an interface layer and a
toplevel code that combines objects/libraries from the QM code and
LAMMPS to build a QM/MM executable. LAMMPS will act as the MD "driver"
and will delegate computation of forces for the QM subset of the QM
code, i.e. Quantum ESPRESSO currently. While the code is combined into
a single executable, this executable can only act as either "QM slave",
"MM slave" or "MM master" and information between those is done solely
via MPI. Thus MPI is required to make it work, and both codes have
to be configured to use the same MPI library.

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 required number of MM CPU 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 QM/MM input file is given below.

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To run a QM/MM calculation, you need to set up 4 inputs, each is
best placed in a separate subdirectory:

1: the total system as classical MD input. this becomes the MM master
and in addition to the regular MD setup it needs to define a group,
e.g. "wat" for the atoms that are treated as QM atoms and then add
the QM/MM fix like this:

fix  1 wat qmmm

2: the QM system as classical MD input
This system must only contain the atom (and bonds, angles, etc) for
the subsystem that is supposed to be treated with the QM code. This
will become the MM slave run and here the QM/MM fix needs to be
applied to all atoms:

fix  1 all qmmm

3: the QM system as QM input
This needs to be a cluster calculation for the QM subset, i.e. the
same atoms as in the MM slave configuration. For Quantum ESPRESSO
this is a regular input which in addition contains the line

tqmmm = .true.

in the &CONTROL namelist. This will make the include QE code 
connect to the LAMMPS code and receive updated positions while
it sends QM forces back to the MM code.

4: the fourth input is the QM/MM configuration file which tells the
QM/MM wrapper code where to find the other 3 inputs, where to place
the corresponding output of the partitions and how many MD steps are
to run with this setup.

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# 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)
