Merge branch 'mliappy_unified' of github.com:Boogie3D/lammps into mliappy_unified
This commit is contained in:
Steven Ray Anaya
@ -1105,7 +1105,7 @@ contains !! Wrapper functions local to this module {{{1
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C_xy = xy
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C_xz = xz
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C_yz = yz
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call lammps_actual_reset_box (ptr, C_boxlo, C_boxhi, C_xy, C_xz, C_yz)
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call lammps_actual_reset_box (ptr, C_boxlo, C_boxhi, C_xy, C_yz, C_xz)
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end subroutine lammps_reset_box
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! lammps_gather_atoms {{{2
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@ -40,7 +40,7 @@ the dynamically-linkable library (liblammps_fortran.so).
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(2) Copy said library to your Fortran program's source directory or replace
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${LAMMPS_LIB} with its full path in the instructions below.
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(3) Compile (but don't link!) LAMMPS.F90. Example:
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mpif90 -c LAMMPS.f90
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mpifort -c LAMMPS.f90
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OR
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gfortran -c LAMMPS.F90
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NOTE: you may get a warning such as,
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@ -72,8 +72,8 @@ the dynamically-linkable library (liblammps_fortran.so).
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were part of the usual LAMMPS library interface (if you have the module
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file visible to the compiler, that is).
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(6) Compile (but don't link) your Fortran program. Example:
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mpif90 -c myfreeformatfile.f90
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mpif90 -c myfixedformatfile.f
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mpifort -c myfreeformatfile.f90
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mpifort -c myfixedformatfile.f
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OR
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gfortran -c myfreeformatfile.f90
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gfortran -c myfixedformatfile.f
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@ -83,12 +83,12 @@ the dynamically-linkable library (liblammps_fortran.so).
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IMPORTANT: If the Fortran module from part (3) is not in the current
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directory or in one searched by the compiler for module files, you will
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need to include that location via the -I flag to the compiler, like so:
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mpif90 -I${LAMMPS_SRC}/examples/COUPLE/fortran2 -c myfreeformatfile.f90
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mpifort -I${LAMMPS_SRC}/examples/COUPLE/fortran2 -c myfreeformatfile.f90
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(7) Link everything together, including any libraries needed by LAMMPS (such
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as the C++ standard library, the C math library, the JPEG library, fftw,
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etc.) For example,
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mpif90 LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
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mpifort LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
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${LAMMPS_LIB} -lmpi_cxx -lstdc++ -lm
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OR
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gfortran LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
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@ -105,17 +105,17 @@ You should now have a working executable.
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(1) Compile LAMMPS as a dynamic library
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(make makeshlib && make -f Makefile.shlib [targetname]).
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(2) Compile, but don't link, LAMMPS.F90 using the -fPIC flag, such as
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mpif90 -fPIC -c LAMMPS.f90
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mpifort -fPIC -c LAMMPS.f90
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(3) Compile, but don't link, LAMMPS-wrapper.cpp in the same manner, e.g.
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mpicxx -fPIC -c LAMMPS-wrapper.cpp
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(4) Make the dynamic library, like so:
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mpif90 -fPIC -shared -o liblammps_fortran.so LAMMPS.o LAMMPS-wrapper.o
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mpifort -fPIC -shared -o liblammps_fortran.so LAMMPS.o LAMMPS-wrapper.o
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(5) Compile your program, such as,
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mpif90 -I${LAMMPS_SRC}/examples/COUPLE/fortran2 -c myfreeformatfile.f90
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mpifort -I${LAMMPS_SRC}/examples/COUPLE/fortran2 -c myfreeformatfile.f90
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where ${LAMMPS_SRC}/examples/COUPLE/fortran2 contains the .mod file from
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step (3)
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(6) Link everything together, such as
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mpif90 ${my_object_files} -L${LAMMPS_SRC} \
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mpifort ${my_object_files} -L${LAMMPS_SRC} \
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-L${LAMMPS_SRC}/examples/COUPLE/fortran2 -llammps_fortran \
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-llammps_openmpi -lmpi_cxx -lstdc++ -lm
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@ -31,7 +31,7 @@ spkpath.h contains path to SPPARKS home directory
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After editing the Makefile, lmppath.h, and spkpath.h to make them
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suitable for your box, type:
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g++ -f Makefile.g++
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make -f Makefile.g++
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and you should get the lmpspk executable.
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@ -1,66 +1,66 @@
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# 2d NEB surface simulation, hop from surface to become adatom
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dimension 2
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boundary p s p
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dimension 2
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boundary p s p
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atom_style atomic
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neighbor 0.3 bin
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neigh_modify delay 5
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atom_modify map array sort 0 0.0
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atom_style atomic
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neighbor 0.3 bin
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neigh_modify delay 5
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atom_modify map array sort 0 0.0
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variable u uloop 20
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variable u uloop 20
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# create geometry with flat surface
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lattice hex 0.9
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region box block 0 20 0 10 -0.25 0.25
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lattice hex 0.9
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region box block 0 20 0 10 -0.25 0.25
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#create_box 3 box
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#create_atoms 1 box
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#mass * 1.0
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#create_box 3 box
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#create_atoms 1 box
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#mass * 1.0
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#write_data initial.hop1
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read_data initial.hop1
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# LJ potentials
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0 2.5
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pair_modify shift yes
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0 2.5
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pair_modify shift yes
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# initial minimization to relax surface
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minimize 1.0e-6 1.0e-4 1000 10000
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reset_timestep 0
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minimize 1.0e-6 1.0e-4 1000 10000
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reset_timestep 0
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# define groups
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region 1 block INF INF INF 1.25 INF INF
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group lower region 1
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group mobile subtract all lower
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set group lower type 2
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region 1 block INF INF INF 1.25 INF INF
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group lower region 1
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group mobile subtract all lower
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set group lower type 2
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timestep 0.05
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timestep 0.05
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# group of NEB atoms - either block or single atom ID 412
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region surround block 10 18 17 20 0 0 units box
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group nebatoms region surround
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#group nebatoms id 412
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set group nebatoms type 3
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group nonneb subtract all nebatoms
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region surround block 10 18 17 20 0 0 units box
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group nebatoms region surround
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#group nebatoms id 412
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set group nebatoms type 3
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group nonneb subtract all nebatoms
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fix 1 lower setforce 0.0 0.0 0.0
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fix 2 nebatoms neb 1.0 parallel ideal
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fix 3 all enforce2d
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fix 1 lower setforce 0.0 0.0 0.0
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fix 2 nebatoms neb 1.0 parallel ideal
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fix 3 all enforce2d
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thermo 100
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thermo 100
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#dump 1 nebatoms atom 10 dump.neb.$u
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#dump 2 nonneb atom 10 dump.nonneb.$u
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#dump 1 nebatoms atom 10 dump.neb.$u
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#dump 2 nonneb atom 10 dump.nonneb.$u
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# run NEB for 2000 steps or to force tolerance
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min_style quickmin
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min_style quickmin
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neb 0.0 0.1 1000 1000 100 final final.hop1
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neb 0.0 0.1 1000 1000 100 final final.hop1
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@ -1,56 +1,56 @@
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# 2d NEB surface simulation, hop from surface to become adatom
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dimension 2
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boundary p s p
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dimension 2
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boundary p s p
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atom_style atomic
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neighbor 0.3 bin
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neigh_modify delay 5
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atom_modify map array sort 0 0.0
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atom_style atomic
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neighbor 0.3 bin
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neigh_modify delay 5
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atom_modify map array sort 0 0.0
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variable u uloop 20
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variable u uloop 20
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# create geometry with flat surface
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lattice hex 0.9
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region box block 0 20 0 10 -0.25 0.25
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lattice hex 0.9
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region box block 0 20 0 10 -0.25 0.25
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read_data initial.hop1.end
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# LJ potentials
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0 2.5
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pair_modify shift yes
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0 2.5
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pair_modify shift yes
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# define groups
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region 1 block INF INF INF 1.25 INF INF
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group lower region 1
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group mobile subtract all lower
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set group lower type 2
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region 1 block INF INF INF 1.25 INF INF
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group lower region 1
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group mobile subtract all lower
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set group lower type 2
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timestep 0.05
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timestep 0.05
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# group of NEB atoms - either block or single atom ID 412
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region surround block 10 18 17 20 0 0 units box
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group nebatoms region surround
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#group nebatoms id 412
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set group nebatoms type 3
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group nonneb subtract all nebatoms
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region surround block 10 18 17 20 0 0 units box
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group nebatoms region surround
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#group nebatoms id 412
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set group nebatoms type 3
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group nonneb subtract all nebatoms
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fix 1 lower setforce 0.0 0.0 0.0
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fix 2 nebatoms neb 1.0 parallel ideal end first 1.0
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fix 3 all enforce2d
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fix 1 lower setforce 0.0 0.0 0.0
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fix 2 nebatoms neb 1.0 parallel ideal end first 1.0
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fix 3 all enforce2d
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thermo 100
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thermo 100
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#dump 1 nebatoms atom 10 dump.neb.$u
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#dump 2 nonneb atom 10 dump.nonneb.$u
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#dump 1 nebatoms atom 10 dump.neb.$u
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#dump 2 nonneb atom 10 dump.nonneb.$u
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# run NEB for 2000 steps or to force tolerance
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min_style quickmin
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min_style quickmin
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neb 0.0 0.1 1000 1000 100 final final.hop1
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neb 0.0 0.1 1000 1000 100 final final.hop1
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@ -1,68 +1,68 @@
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# 2d NEB surface simulation, hop of adatom on surface
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dimension 2
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boundary p s p
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dimension 2
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boundary p s p
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atom_style atomic
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neighbor 0.3 bin
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neigh_modify delay 5
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atom_modify map array sort 0 0.0
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atom_style atomic
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neighbor 0.3 bin
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neigh_modify delay 5
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atom_modify map array sort 0 0.0
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variable u uloop 20
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variable u uloop 20
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# create geometry with adatom
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lattice hex 0.9
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region box block 0 20 0 11 -0.25 0.25
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region box1 block 0 20 0 10 -0.25 0.25
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lattice hex 0.9
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region box block 0 20 0 11 -0.25 0.25
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region box1 block 0 20 0 10 -0.25 0.25
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#create_box 3 box
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#create_atoms 1 region box1
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#create_atoms 1 single 11.5 10.5 0
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#mass * 1.0
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#create_box 3 box
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#create_atoms 1 region box1
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#create_atoms 1 single 11.5 10.5 0
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#mass * 1.0
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#write_data initial.hop2
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read_data initial.hop2
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# LJ potentials
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0 2.5
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pair_modify shift yes
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0 2.5
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pair_modify shift yes
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# initial minimization to relax surface
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minimize 1.0e-6 1.0e-4 1000 10000
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reset_timestep 0
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minimize 1.0e-6 1.0e-4 1000 10000
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reset_timestep 0
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# define groups
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region 1 block INF INF INF 1.25 INF INF
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group lower region 1
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group mobile subtract all lower
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set group lower type 2
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region 1 block INF INF INF 1.25 INF INF
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group lower region 1
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group mobile subtract all lower
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set group lower type 2
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timestep 0.05
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timestep 0.05
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# group of NEB atoms - either block or single atom ID 421
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region surround block 10 18 17 21 0 0 units box
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group nebatoms region surround
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#group nebatoms id 421
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set group nebatoms type 3
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group nonneb subtract all nebatoms
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region surround block 10 18 17 21 0 0 units box
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group nebatoms region surround
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#group nebatoms id 421
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set group nebatoms type 3
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group nonneb subtract all nebatoms
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fix 1 lower setforce 0.0 0.0 0.0
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fix 2 nebatoms neb 1.0
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fix 3 all enforce2d
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fix 1 lower setforce 0.0 0.0 0.0
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fix 2 nebatoms neb 1.0
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fix 3 all enforce2d
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thermo 100
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thermo 100
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#dump 1 nebatoms atom 10 dump.neb.$u
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#dump 2 nonneb atom 10 dump.nonneb.$u
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#dump 1 nebatoms atom 10 dump.neb.$u
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#dump 2 nonneb atom 10 dump.nonneb.$u
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# run NEB for 2000 steps or to force tolerance
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min_style fire
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min_style fire
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neb 0.0 0.05 1000 1000 100 final final.hop2
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neb 0.0 0.05 1000 1000 100 final final.hop2
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@ -5,7 +5,7 @@ units metal
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atom_style atomic
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atom_modify map array
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boundary p p p
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atom_modify sort 0 0.0
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atom_modify sort 0 0.0
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# coordination number cutoff
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@ -45,7 +45,7 @@ group Si type 1
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group del id 300
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delete_atoms group del compress no
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group vacneigh id 174 175 301 304 306 331 337
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# choose potential
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pair_style sw
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@ -53,26 +53,26 @@ pair_coeff * * Si.sw Si
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# set up neb run
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variable u uloop 20
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variable u uloop 20
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# initial minimization to relax vacancy
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displace_atoms all random 0.1 0.1 0.1 123456
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minimize 1.0e-6 1.0e-4 1000 10000
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reset_timestep 0
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# only output atoms near vacancy
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#dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z
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# initial minimization to relax vacancy
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fix 1 all neb 1.0
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displace_atoms all random 0.1 0.1 0.1 123456
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minimize 1.0e-6 1.0e-4 1000 10000
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reset_timestep 0
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fix 1 all neb 1.0
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thermo 100
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thermo 100
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# run NEB for 2000 steps or to force tolerance
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timestep 0.01
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min_style quickmin
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min_style quickmin
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neb 0.0 0.01 100 100 10 final final.sivac
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neb 0.0 0.01 100 100 10 final final.sivac
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Reference in New Issue
Block a user