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lib/qmmm/README
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lib/qmmm/README
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@ -1,11 +1,11 @@
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QM/MM support toplevel library
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QM/MM support library
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Axel Kohlmeyer, akohlmey@gmail.com
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Temple University, Philadelphia and ICTP, Trieste
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This library provides the basic glue code to combine LAMMPS with the
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Quantum ESPRESSO package plane wave density functional theory code for
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performing QM/MM molecular dynamics simulations. More information on
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performing QM/MM molecular dynamics simulations. More information on
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Quantum ESPRESSO can be found at: http://www.quantum-espresso.org
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The interface code itself is designed so it can also be combined with
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@ -16,35 +16,19 @@ also an interface layer into the QM code similar to the one in QE.
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-------------------------------------------------
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This directory has the source files to build a library and an
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executable for combining the pw.x program from Quantum ESPRESSO and
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LAMMPS into a single executable that can be used for QM/MM molecular
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dynamics simulations. LAMMPS will act as the MD "driver" and will
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delegate computation of forces for the QM subset of the system to
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Quantum ESPRESSO.
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The toplevel code provided here will split the total number of cpus
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into three partitions: the first for running a DFT calculation, the
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second for running the "master" classical MD calculation, and the
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third for a "slave" classical MD calculation. Each calculation will
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have to be run in its own subdirectory with its own specific input
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data and will write its output there as well. This and other settings
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are provided in the QM/MM input file that is mandatory argument to the
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QM/MM executable. The number of MM cpus is provided as the optional
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second argument. The MM "slave" partition is always run with only 1
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cpu thus the minimum number is 2, which is also the default. Therefore
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a QM/MM calculation with this code requires at least 3 processes.
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Thus the overall calling sequence is like this:
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mpirun -np <total #cpus> ./pwqmmm.x <QM/MM input> [<#cpus for MM>]
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A commented example is given below.
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WARNING: This is experimental code under developementand is provided
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at this early stage to encourage others to write interfaces to other
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QM codes. Please test *very* carefully before using this software for
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production calculations.
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-------------------------------------------------
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Build the library using one of the provided Makefile.* files or create
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your own, specific to your compiler and system. For example:
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Building the QM/MM executable has to be done in multiple stages.
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Step 1)
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Build the qmmm coupling library in this directory using one of the
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provided Makefile.<compiler> files or create your own, specific to
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your compiler and system. For example with:
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make -f Makefile.gfortran
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@ -58,25 +42,39 @@ Makefile.lammps is created by the make command by simply copying the
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Makefile.lammps.empty file. Currently no additional dependencies for
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this library exist.
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-------------------------------------------------
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Step 2)
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Build a standalone LAMMPS executable as described in the LAMMPS
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documentation and include the USER-QMMM package. This executable
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is not functional for QM/MM, but it will usually be needed to
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run all MM calculations for equilibration and testing and also
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to confirm that the classical part of the code is set up correctly.
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To compile and link the final QM/MM executable, you have to build
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quantum espresso with the "pw" and "couple" targets. You also have
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to to install the USER-QMMM package for LAMMPS. You have to specify
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the path to the toplevel Quantum ESPRESSO directory, so that the
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compiler and linker settings can be imported.
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Step 3)
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Build a standalone pw.x executable in the Quantum ESPRESSO directory
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and also make the "couple" target. At the time of this writing
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(April 2014) you have to download a QE snapshot from the SVN
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repository, since no official release with the library interface
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to couple other codes to QE has been made yet. This is also needed
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to confirm that corresponding code is working correctly and to
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run test calculations on the cluster of QM atoms.
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Step 4)
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To compile and link the final QM/MM executable, which combines the
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compiled sources from both packages, you have to return to the lib/qmmm
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directory and now edit the Makefile.<compiler> for the Makefile
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configuration used to compile LAMMPS and also update the directory
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and library settings for the Quantum ESPRESSO installation.
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The makefile variable MPILIBS needs to be set to include all linker
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flags that will need to be used in addition to the various libraries
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from the two packages. Please see the provided example(s).
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from _both_ packages. Please see the provided example(s).
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"make -f Makefile.gfortran" all by itself will only compile the
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library (so that LAMMPS can be compiled into a standalone executable
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as well, when the USER-QMMM package is installed).
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"make -f Makefile.gfortran pwqmmm.x" will compile and link the QM/MM
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executable; "make -f Makefile.gfortran all" will recurse through the
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"make -f Makefile.<compiler> all" will now recurse through both the
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Quantum ESPRESSO and LAMMPS directories to compile all files that
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require recompilation and then link the executable.
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require recompilation and then link the combined QM/MM executable.
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If you want to only update the local objects and the QM/MM executable,
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you can use "make -f Makefile.<compiler> pwqmmm.x"
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Please refer to the specific LAMMPS and Quantum ESPRESSO documentation
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for details on how to set up compilation for each package and make
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@ -85,6 +83,75 @@ each package successfully, so that it can run on its own.
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-------------------------------------------------
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How it works.
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This directory has the source files for an interface layer and a
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toplevel code that combines objects/libraries from the QM code and
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LAMMPS to build a QM/MM executable. LAMMPS will act as the MD "driver"
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and will delegate computation of forces for the QM subset of the QM
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code, i.e. Quantum ESPRESSO currently. While the code is combined into
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a single executable, this executable can only act as either "QM slave",
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"MM slave" or "MM master" and information between those is done solely
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via MPI. Thus MPI is required to make it work, and both codes have
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to be configured to use the same MPI library.
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The toplevel code provided here will split the total number of cpus
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into three partitions: the first for running a DFT calculation, the
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second for running the "master" classical MD calculation, and the
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third for a "slave" classical MD calculation. Each calculation will
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have to be run in its own subdirectory with its own specific input
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data and will write its output there as well. This and other settings
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are provided in the QM/MM input file that is mandatory argument to the
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QM/MM executable. The number of MM cpus is provided as the optional
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second argument. The MM "slave" partition is always run with only 1
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cpu thus the minimum required number of MM CPU is 2, which is also
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the default. Therefore a QM/MM calculation with this code requires at
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least 3 processes.
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Thus the overall calling sequence is like this:
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mpirun -np <total #cpus> ./pwqmmm.x <QM/MM input> [<#cpus for MM>]
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A commented example QM/MM input file is given below.
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-------------------------------------------------
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To run a QM/MM calculation, you need to set up 4 inputs, each is
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best placed in a separate subdirectory:
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1: the total system as classical MD input. this becomes the MM master
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and in addition to the regular MD setup it needs to define a group,
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e.g. "wat" for the atoms that are treated as QM atoms and then add
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the QM/MM fix like this:
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fix 1 wat qmmm
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2: the QM system as classical MD input
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This system must only contain the atom (and bonds, angles, etc) for
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the subsystem that is supposed to be treated with the QM code. This
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will become the MM slave run and here the QM/MM fix needs to be
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applied to all atoms:
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fix 1 all qmmm
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3: the QM system as QM input
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This needs to be a cluster calculation for the QM subset, i.e. the
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same atoms as in the MM slave configuration. For Quantum ESPRESSO
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this is a regular input which in addition contains the line
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tqmmm = .true.
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in the &CONTROL namelist. This will make the include QE code
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connect to the LAMMPS code and receive updated positions while
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it sends QM forces back to the MM code.
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4: the fourth input is the QM/MM configuration file which tells the
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QM/MM wrapper code where to find the other 3 inputs, where to place
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the corresponding output of the partitions and how many MD steps are
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to run with this setup.
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-------------------------------------------------
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# configuration file for QMMM wrapper
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mode mech # coupling choices: o(ff), m(echanical), e(lectrostatic)
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