forked from lijiext/lammps
update instructions for in qmmm README to cover both build systems and include more details
This commit is contained in:
Axel Kohlmeyer
parent
febb381880
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# -*- Makefile -*- for coupling LAMMPS to PWscf for QM/MM molecular dynamics
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# adapted for the case of compiling LAMMPS with CMake. This assumes that
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# LAMMPS was configured to build a shared library and installed with "make install"
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# as it used the PKG config configuration file. You may need to extend
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# the PKG_CONFIG_PATH environment variable to have pkgconf find the liblammps.pc file.
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# This is set up for using GNU Fortran and OpenMPI to compile both LAMMPS and QE
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# this file will be copied to Makefile.lammps
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EXTRAMAKE = Makefile.lammps.empty
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# top level directory of Quantum ESPRESSO 6.3 or later (tested up to QE 6.5)
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QETOPDIR=$(HOME)/compile/espresso
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# import compiler settings from Quantum ESPRESSO
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sinclude $(QETOPDIR)/make.inc
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# FLAGS for compiling and linking the pwqmmm.x executable
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MPICXX=mpicxx
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MPICXXFLAGS=-DOMPI_SKIP_MPICXX=1 -O2 -Wall -g -fPIC\
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-I../../src -I$(QETOPDIR)/COUPLE/include
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# location of required libraries
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# part 1: hi-level libraries for building pw.x
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PWOBJS = \
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$(QETOPDIR)/COUPLE/src/libqecouple.a \
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$(QETOPDIR)/PW/src/libpw.a \
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$(QETOPDIR)/Modules/libqemod.a
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# part 2: lo-level libraries for all of Q-E
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LIBOBJS = \
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$(QETOPDIR)/FFTXlib/libqefft.a \
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$(QETOPDIR)/dft-d3/libdftd3qe.a \
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$(QETOPDIR)/KS_Solvers/PPCG/libppcg.a \
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$(QETOPDIR)/KS_Solvers/CG/libcg.a \
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$(QETOPDIR)/KS_Solvers/Davidson/libdavid.a \
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$(QETOPDIR)/UtilXlib/libutil.a \
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$(QETOPDIR)/LAXlib/libqela.a \
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$(QETOPDIR)/clib/clib.a \
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$(QETOPDIR)/iotk/src/libiotk.a
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# add support for fortran runtimes for compiler and MPI library
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# those are automatically included when linking QE executables,
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# since they use mpifort/mpif90 to link, but we are using the
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# C++ MPI compiler wrapper instead, so those need to be added
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# as a dependency for QE objects and libraries
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QELIBS += -lgfortran -lmpi_mpifh
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# part 3: add-on libraries and main library for LAMMPS
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sinclude ../../src/Makefile.package
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LAMMPSFLAGS = $(shell pkgconf liblammps --cflags)
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LAMMPSLIB = $(shell pkgconf liblammps --libs)
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# part 4: local QM/MM library and progams
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SRC=pwqmmm.c libqmmm.c
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OBJ=$(SRC:%.c=%.o)
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default: libqmmm.a
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all : tldeps libqmmm.a pwqmmm.x
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pwqmmm.x : pwqmmm.o $(PWOBJS) $(LIBOBJS)
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$(MPICXX) $(LDFLAGS) -o $@ $^ $(LAMMPSLIB) $(QELIBS) $(LIBS)
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libqmmm.a: libqmmm.o
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$(AR) $(ARFLAGS) $@ $^
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@cp $(EXTRAMAKE) Makefile.lammps
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%.o: %.c
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$(MPICXX) -c $(LAMMPSFLAGS) $(MPICXXFLAGS) $< -o $@
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tldeps:
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( cd $(QETOPDIR) ; $(MAKE) $(MFLAGS) couple || exit 1)
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$(MAKE) -C ../../src $(MFLAGS) $(LAMMPSCFG)
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$(MAKE) -C ../../src $(MFLAGS) mode=lib $(LAMMPSCFG)
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clean :
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-rm -f *.x *.o *.a *~ *.F90 *.d *.mod *.i *.L
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# explicit dependencies
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pwqmmm.o: pwqmmm.c libqmmm.h
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libqmmm.o: libqmmm.c libqmmm.h
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148
lib/qmmm/README
148
lib/qmmm/README
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@ -1,4 +1,5 @@
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QM/MM support library
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=====================
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Axel Kohlmeyer, akohlmey@gmail.com
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Temple University, Philadelphia and ICTP, Trieste
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@ -13,25 +14,26 @@ 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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other QM codes, however only support for Quantum ESPRESSO is currently
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the only option. Adding support for a different QM code will require
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to write a new version of the top-level wrapper code, pwqmmm.c, and
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also an interface layer into the QM code similar to the one in QE.
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other QM codes, however coupling to Quantum ESPRESSO is currently the
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only available option. Adding support for a different QM code will
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require to write a new version of the top-level wrapper code, pwqmmm.c,
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and also an interface layer into the QM code similar to the one in QE.
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You can type "make lib-qmmm" from the src directory to see help on how
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to build this library (steps 1 and 2 below) via make commands, or you
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can do the same thing by typing "python Install.py" from within this
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directory, or you can do it manually by following the instructions
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below.
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LAMMPS has support for two build systems, the traditional make based
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one and a newer one based on CMake. You have to build LAMMPS as a
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library with the USER-QMMM package included and for that you need to
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also build the libqmmm.a library in this folder.
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However you perform steps 1 and 2, you will need to perform steps 3
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and 4 manually, as outlined below.
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Below you will find some description of the steps needed in either case.
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However you build LAMMPS and the liblammps and libqmmm libraries, you
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will need to perform the remaining steps manually, as outlined below.
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-------------------------------------------------
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WARNING: This is experimental code under developement and 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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WARNING: This is code depending on two software packages that are
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independently maitained and are under continuous active developement.
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It is thus much easier to break the QM/MM interface without noticing.
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Thus please test *very* carefully before using this software for
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production calculations.
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At this point, both mechanical and multipole based electrostatic
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@ -40,17 +42,92 @@ molecules as included in the two example folders.
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-------------------------------------------------
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Building the QM/MM executable has to be done in multiple stages.
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Building the QM/MM executable has to be done in multiple stages
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Building with CMake for LAMMPS
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==============================
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Step 1)
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Go to the top-level folder of the LAMMPS source code and create
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a custom build folder (e.g. build-qmmm) and create a suitable
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build configuration with CMake:
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mkdir build-qmmm
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cd build-qmmm
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cmake -C ../cmake/presets/minimal.cmake -D PKG_USER-QMMM=yes \
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-D BUILD_LIB=yes -DBUILD_SHARED_LIBS=yes ../cmake
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make
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make install
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This will build a LAMMPS executable "lmp" and a shared library
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"liblammps.so" and install them and additional configuration and
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supporting files into the ${HOME}/.local directory tree (unless
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you set -D CMAKE_INSTALL_PREFIX to a different location). If the
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installation is not into a system folder, you need to update
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the LD_LIBRARY_PATH and PKG_CONFIG_PATH environment variables.
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LD_LIBRARY_PATH=${LD_LIBRARY_PATH-/usr/lib64}:${HOME}/.local/lib64
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PKG_CONFIG_PATH=${PKG_CONFIG_PATH-/usr/lib64/pkgconfig}:${HOME}/.local/lib64/pkgconfig
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export LD_LIBRARY_PATH PKG_CONFIG_PATH
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The standalone LAMMPS executable is not capable of doing QM/MM
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calculations itself, but it will be needed to run all MM calculations
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for equilibration and testing and also to confirm that the classical
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part of the code is set up correctly.
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Step 2)
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Build a standalone pw.x executable from source code in the Quantum
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ESPRESSO directory and also make the "couple" target. This is typically
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done with:
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./configure
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make pw couple
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You may need to review and edit the make.inc file created by configure.
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Make certain, that both LAMMPS and QE use the same MPI library and
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compatible compilers. In the examples here we assume GNU compilers
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(gfortran, gcc, g++) and OpenMPI.
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Building the standalone pw.x binary is needed to confirm that
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corresponding QM input is working correctly and to run test calculations
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on the QM atoms only.
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Step 3)
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Go back to this folder (lib/qmmm) and now review the file
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Makefile.gfortran-cmake and make adjustments to the makefile variables
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according to the comments in the file. You probably need to adjust
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the QETOPDIR variable to point to the location of your QE
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compilation/installation.
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Please also check that the command "pkgconf liblammps --libs" works.
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Then you should be able to compile the QM/MM executable with:
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make -f Makefile.gfortran-cmake pwqmmm.x
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If this is successful, you should be able to run a QM/MM calculation
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and can try the examples in the example-mc and example-ec folders:
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mpirun -np 4 ../pwqmmm.x qmmm.inp 2
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Building with traditional make for LAMMPS
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=========================================
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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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Go to src folder under the top-level folder of the LAMMPS source code
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and build the qmmm coupling library in this directory using one of
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the provided Makefile.<compiler> files. E.g. for use with GNU fortran:
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make lib-qmmm args="-m gfortran"
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This file is specific to your compiler and system. You may need to
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create a specific one for your choice of compilers, MPI, and OS.
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When you are done building this library, two new files should
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exist in this directory:
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exist in this directory (lib/qmmm):
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libqmmm.a the library LAMMPS will link against
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Makefile.lammps settings the LAMMPS Makefile will import
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@ -60,21 +137,42 @@ Makefile.lammps.empty file. Currently no additional dependencies for
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this library exist.
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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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Also build a the LAMMPS library. This can be a static library
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or a shared library. For example for a static library with the
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minimum set of packages required for the examples here:
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make yes-molecule yes-kspace yes-rigid yes-user-qmmm
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make mpi
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make mode=lib mpi
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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. Building the standalone pw.x
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binary is also needed to confirm that corresponding QM input is
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working correctly and to run test calculations on QM atoms only.
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Build a standalone pw.x executable from source code in the Quantum
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ESPRESSO directory and also make the "couple" target. This is typically
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done with:
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./configure
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make pw couple
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You may need to review and edit the make.inc file created by configure.
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Make certain, that both LAMMPS and QE use the same MPI library and
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compatible compilers. In the examples here we assume GNU compilers
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(gfortran, gcc, g++) and OpenMPI.
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Building the standalone pw.x binary is needed to confirm that
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corresponding QM input is working correctly and to run test calculations
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on the QM atoms only.
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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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compiled code 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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