QM/MM support toplevel library Axel Kohlmeyer, akohlmey@gmail.com ICTP, Trieste, Italy 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 ------------------------------------------------- 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)