git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8604 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
78
examples/COUPLE/simple/README
Normal file
78
examples/COUPLE/simple/README
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@ -0,0 +1,78 @@
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This directory has a simple C, C++, and Fortran code that shows how
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LAMMPS can be linked to a driver application as a library. The purpose
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is to illustrate how another code could perform computations while
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||||
using LAMMPS to perform MD on all or a subset of the processors, or
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how an umbrella code or script could call both LAMMPS and some other
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code to perform a coupled calculation.
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simple.cpp is the C++ driver
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simple.c is the C driver
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simple.f90 is the Fortran driver
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libfwrapper.c is the Fortran-to-C wrapper
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The 3 codes do the same thing, so you can compare them to see how to
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drive LAMMPS in this manner. The C driver is similar in spirit to what
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one could use to write a scripting language interface. The Fortran
|
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driver in addition requires a wrapper library that interfaces the C
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interface of the LAMMPS library to Fortran and also translates the MPI
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communicator from Fortran to C.
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You can then build either driver code with a compile line something
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like this, which includes paths to the LAMMPS library interface, MPI,
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and FFTW (assuming you built LAMMPS as a library with its PPPM
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solver).
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This builds the C++ driver with the LAMMPS library using a C++ compiler:
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g++ -I/home/sjplimp/lammps/src -c simple.cpp
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g++ -L/home/sjplimp/lammps/src simple.o \
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-llmp_g++ -lfftw -lmpich -lmpl -lpthread -o simpleCC
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This builds the C driver with the LAMMPS library using a C compiler:
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gcc -I/home/sjplimp/lammps/src -c simple.c
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gcc -L/home/sjplimp/lammps/src simple.o \
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-llmp_g++ -lfftw -lmpich -lmpl -lpthread -lstdc++ -o simpleC
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This builds the Fortran wrapper and driver with the LAMMPS library
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using a Fortran and C compiler:
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cp ../fortran/libfwrapper.c .
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gcc -I/home/sjplimp/lammps/src -c libfwrapper.c
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gfortran -I/home/sjplimp/lammps/src -c simple.f90
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gfortran -L/home/sjplimp/lammps/src simple.o libfwrapper.o \
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-llmp_g++ -lfftw -lfmpich -lmpich -lpthread -lstdc++ -o simpleF
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|
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You then run simpleCC, simpleC, or simpleF on a parallel machine
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on some number of processors Q with 2 arguments:
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mpirun -np Q simpleCC P in.lj
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P is the number of procs you want LAMMPS to run on (must be <= Q) and
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in.lj is a LAMMPS input script.
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|
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The driver will launch LAMMPS on P procs, read the input script a line
|
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at a time, and pass each command line to LAMMPS. The final line of
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the script is a "run" command, so LAMMPS will run the problem.
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The driver then requests all the atom coordinates from LAMMPS, moves
|
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one of the atoms a small amount "epsilon", passes the coordinates back
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to LAMMPS, and runs LAMMPS again. If you look at the output, you
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should see a small energy change between runs, due to the moved atom.
|
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The C driver is calling C-style routines in the src/library.cpp file
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of LAMMPS. You could add any functions you wish to this file to
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manipulate LAMMPS data however you wish.
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The Fortran driver is using the same C-style routines, but requires an
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additional wrapper to make them Fortran callable. Only a subset of the
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library functions are currently wrapped, but it should be clear how to
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extend the wrapper if desired.
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The C++ driver does the same thing, except that it instantiates LAMMPS
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as an object first. Some of the functions in src/library.cpp can be
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invoked directly as methods within appropriate LAMMPS classes, which
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is what the driver does. Any public LAMMPS class method could be
|
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called from the driver this way. However the get/put functions are
|
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only implemented in src/library.cpp, so the C++ driver calls them as
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C-style functions.
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24
examples/COUPLE/simple/in.lj
Normal file
24
examples/COUPLE/simple/in.lj
Normal file
@ -0,0 +1,24 @@
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# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map array
|
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|
||||
lattice fcc 0.8442
|
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region box block 0 4 0 4 0 4
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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|
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velocity all create 1.44 87287 loop geom
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|
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pair_style lj/cut 2.5
|
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pair_coeff 1 1 1.0 1.0 2.5
|
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|
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neighbor 0.3 bin
|
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neigh_modify delay 0 every 20 check no
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|
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fix 1 all nve
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|
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run 10
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150
examples/COUPLE/simple/log.lammps
Normal file
150
examples/COUPLE/simple/log.lammps
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@ -0,0 +1,150 @@
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LAMMPS (14 Aug 2012)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
|
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|
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units lj
|
||||
|
||||
atom_style atomic
|
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|
||||
atom_modify map array
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|
||||
|
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|
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lattice fcc 0.8442
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|
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Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 4 0 4 0 4
|
||||
|
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create_box 1 box
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|
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Created orthogonal box = (0 0 0) to (6.71838 6.71838 6.71838)
|
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 256 atoms
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mass 1 1.0
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|
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|
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|
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velocity all create 1.44 87287 loop geom
|
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|
||||
|
||||
|
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pair_style lj/cut 2.5
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
|
||||
|
||||
neighbor 0.3 bin
|
||||
|
||||
neigh_modify delay 0 every 20 check no
|
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|
||||
|
||||
|
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fix 1 all nve
|
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|
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|
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run 10
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|
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Memory usage per processor = 1.82446 Mbytes
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Step Temp E_pair E_mol TotEng Press
|
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0 1.44 -6.7733681 0 -4.6218056 -5.0244179
|
||||
10 1.1298532 -6.3095502 0 -4.6213906 -2.6058175
|
||||
Loop time of 0.00204515 on 1 procs for 10 steps with 256 atoms
|
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|
||||
Pair time (%) = 0.00186634 (91.2567)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000108242 (5.29261)
|
||||
Outpt time (%) = 7.86781e-06 (0.384705)
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||||
Other time (%) = 6.27041e-05 (3.06598)
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|
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Nlocal: 256 ave 256 max 256 min
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||||
Histogram: 1 0 0 0 0 0 0 0 0 0
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||||
Nghost: 1431 ave 1431 max 1431 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9984 ave 9984 max 9984 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9984
|
||||
Ave neighs/atom = 39
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
run 10
|
||||
Memory usage per processor = 1.82446 Mbytes
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||||
Step Temp E_pair E_mol TotEng Press
|
||||
10 1.1298532 -6.3095502 0 -4.6213906 -2.6058175
|
||||
20 0.6239063 -5.557644 0 -4.6254403 0.97451173
|
||||
Loop time of 0.00205898 on 1 procs for 10 steps with 256 atoms
|
||||
|
||||
Pair time (%) = 0.00188446 (91.5239)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000113249 (5.50023)
|
||||
Outpt time (%) = 7.86781e-06 (0.382121)
|
||||
Other time (%) = 5.34058e-05 (2.59379)
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1431 ave 1431 max 1431 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9952 ave 9952 max 9952 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9952
|
||||
Ave neighs/atom = 38.875
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
print 'Hello'
|
||||
Hello
|
||||
run 100
|
||||
Memory usage per processor = 1.82446 Mbytes
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||||
Step Temp E_pair E_mol TotEng Press
|
||||
20 0.6239063 -5.557644 0 -4.6254403 0.97451173
|
||||
120 0.76618392 -5.7755399 0 -4.6307534 0.043194007
|
||||
Loop time of 0.0224361 on 1 procs for 100 steps with 256 atoms
|
||||
|
||||
Pair time (%) = 0.01788 (79.6927)
|
||||
Neigh time (%) = 0.00273871 (12.2067)
|
||||
Comm time (%) = 0.00126839 (5.65332)
|
||||
Outpt time (%) = 1.00136e-05 (0.0446315)
|
||||
Other time (%) = 0.000539064 (2.40266)
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1403 ave 1403 max 1403 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9634 ave 9634 max 9634 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9634
|
||||
Ave neighs/atom = 37.6328
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
run 1
|
||||
Memory usage per processor = 1.82446 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
120 0.76618392 -5.7490597 0 -4.6042731 0.15552489
|
||||
121 0.7701256 -5.7552684 0 -4.6045924 0.12926088
|
||||
Loop time of 0.000268936 on 1 procs for 1 steps with 256 atoms
|
||||
|
||||
Pair time (%) = 0.000243902 (90.6915)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 1.09673e-05 (4.07801)
|
||||
Outpt time (%) = 7.15256e-06 (2.65957)
|
||||
Other time (%) = 6.91414e-06 (2.57092)
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1403 ave 1403 max 1403 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9635 ave 9635 max 9635 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9635
|
||||
Ave neighs/atom = 37.6367
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
124
examples/COUPLE/simple/log.simple.c++.1
Normal file
124
examples/COUPLE/simple/log.simple.c++.1
Normal file
@ -0,0 +1,124 @@
|
||||
LAMMPS (20 Sep 2010)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
|
||||
|
||||
units lj
|
||||
|
||||
atom_style atomic
|
||||
|
||||
atom_modify map array
|
||||
|
||||
|
||||
|
||||
lattice fcc 0.8442
|
||||
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 4 0 4 0 4
|
||||
|
||||
create_box 1 box
|
||||
|
||||
Created orthogonal box = (0 0 0) to (6.71838 6.71838 6.71838)
|
||||
1 by 1 by 1 processor grid
|
||||
create_atoms 1 box
|
||||
|
||||
Created 256 atoms
|
||||
mass 1 1.0
|
||||
|
||||
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
|
||||
|
||||
neighbor 0.3 bin
|
||||
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
|
||||
|
||||
run 10
|
||||
|
||||
Memory usage per processor = 1.50139 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6218056 -5.0244179
|
||||
10 1.1298532 -6.3095502 0 -4.6213906 -2.6058175
|
||||
Loop time of 0.00370193 on 1 procs for 10 steps with 256 atoms
|
||||
|
||||
Pair time (%) = 0.00340414 (91.9559)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000165701 (4.47607)
|
||||
Outpt time (%) = 2.31266e-05 (0.624718)
|
||||
Other time (%) = 0.000108957 (2.94326)
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1431 ave 1431 max 1431 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9984 ave 9984 max 9984 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9984
|
||||
Ave neighs/atom = 39
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
run 10
|
||||
Memory usage per processor = 1.50139 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
10 1.1298532 -6.3095502 0 -4.6213906 -2.6058175
|
||||
20 0.6239063 -5.557644 0 -4.6254403 0.97451173
|
||||
Loop time of 0.00365806 on 1 procs for 10 steps with 256 atoms
|
||||
|
||||
Pair time (%) = 0.0033741 (92.2375)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000161886 (4.42547)
|
||||
Outpt time (%) = 1.09673e-05 (0.299811)
|
||||
Other time (%) = 0.000111103 (3.03722)
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1431 ave 1431 max 1431 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9952 ave 9952 max 9952 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9952
|
||||
Ave neighs/atom = 38.875
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
run 1
|
||||
Memory usage per processor = 1.50139 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
20 0.6239063 -5.5404291 0 -4.6082254 1.0394285
|
||||
21 0.63845863 -5.5628733 0 -4.6089263 0.99398278
|
||||
Loop time of 0.000490904 on 1 procs for 1 steps with 256 atoms
|
||||
|
||||
Pair time (%) = 0.000452042 (92.0835)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 1.69277e-05 (3.44828)
|
||||
Outpt time (%) = 1.00136e-05 (2.03983)
|
||||
Other time (%) = 1.19209e-05 (2.42836)
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1431 ave 1431 max 1431 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9705 ave 9705 max 9705 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9705
|
||||
Ave neighs/atom = 37.9102
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
124
examples/COUPLE/simple/log.simple.c++.4
Normal file
124
examples/COUPLE/simple/log.simple.c++.4
Normal file
@ -0,0 +1,124 @@
|
||||
LAMMPS (20 Sep 2010)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
|
||||
|
||||
units lj
|
||||
|
||||
atom_style atomic
|
||||
|
||||
atom_modify map array
|
||||
|
||||
|
||||
|
||||
lattice fcc 0.8442
|
||||
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 4 0 4 0 4
|
||||
|
||||
create_box 1 box
|
||||
|
||||
Created orthogonal box = (0 0 0) to (6.71838 6.71838 6.71838)
|
||||
1 by 2 by 2 processor grid
|
||||
create_atoms 1 box
|
||||
|
||||
Created 256 atoms
|
||||
mass 1 1.0
|
||||
|
||||
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
|
||||
|
||||
neighbor 0.3 bin
|
||||
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
|
||||
|
||||
run 10
|
||||
|
||||
Memory usage per processor = 1.48354 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6218056 -5.0244179
|
||||
10 1.1298532 -6.3095502 0 -4.6213906 -2.6058175
|
||||
Loop time of 0.00202775 on 4 procs for 10 steps with 256 atoms
|
||||
|
||||
Pair time (%) = 0.00085938 (42.381)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.00108671 (53.592)
|
||||
Outpt time (%) = 2.79546e-05 (1.3786)
|
||||
Other time (%) = 5.37038e-05 (2.64844)
|
||||
|
||||
Nlocal: 64 ave 64 max 64 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 843 ave 843 max 843 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2496 ave 2496 max 2496 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9984
|
||||
Ave neighs/atom = 39
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
run 10
|
||||
Memory usage per processor = 1.48354 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
10 1.1298532 -6.3095502 0 -4.6213906 -2.6058175
|
||||
20 0.6239063 -5.557644 0 -4.6254403 0.97451173
|
||||
Loop time of 0.00224167 on 4 procs for 10 steps with 256 atoms
|
||||
|
||||
Pair time (%) = 0.000862718 (38.4855)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.00127524 (56.888)
|
||||
Outpt time (%) = 5.19753e-05 (2.31859)
|
||||
Other time (%) = 5.17368e-05 (2.30796)
|
||||
|
||||
Nlocal: 64 ave 69 max 59 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Nghost: 843 ave 848 max 838 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 2488 ave 2745 max 2319 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 9952
|
||||
Ave neighs/atom = 38.875
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
run 1
|
||||
Memory usage per processor = 1.48354 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
20 0.6239063 -5.5404291 0 -4.6082254 1.0394285
|
||||
21 0.63845863 -5.5628733 0 -4.6089263 0.99398278
|
||||
Loop time of 0.000325441 on 4 procs for 1 steps with 256 atoms
|
||||
|
||||
Pair time (%) = 0.000120759 (37.1062)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000165045 (50.7143)
|
||||
Outpt time (%) = 2.86698e-05 (8.80952)
|
||||
Other time (%) = 1.09673e-05 (3.36996)
|
||||
|
||||
Nlocal: 64 ave 70 max 58 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 843 ave 849 max 837 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 2426.25 ave 2704 max 2229 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 9705
|
||||
Ave neighs/atom = 37.9102
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
116
examples/COUPLE/simple/simple.c
Normal file
116
examples/COUPLE/simple/simple.c
Normal file
@ -0,0 +1,116 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
www.cs.sandia.gov/~sjplimp/lammps.html
|
||||
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* c_driver = simple example of how an umbrella program
|
||||
can invoke LAMMPS as a library on some subset of procs
|
||||
Syntax: c_driver P in.lammps
|
||||
P = # of procs to run LAMMPS on
|
||||
must be <= # of procs the driver code itself runs on
|
||||
in.lammps = LAMMPS input script
|
||||
See README for compilation instructions */
|
||||
|
||||
#include "stdio.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "mpi.h"
|
||||
#include "library.h" /* this is a LAMMPS include file */
|
||||
|
||||
int main(int narg, char **arg)
|
||||
{
|
||||
/* setup MPI and various communicators
|
||||
driver runs on all procs in MPI_COMM_WORLD
|
||||
comm_lammps only has 1st P procs (could be all or any subset) */
|
||||
|
||||
MPI_Init(&narg,&arg);
|
||||
|
||||
if (narg != 3) {
|
||||
printf("Syntax: c_driver P in.lammps\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
int me,nprocs;
|
||||
MPI_Comm_rank(MPI_COMM_WORLD,&me);
|
||||
MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
|
||||
|
||||
int nprocs_lammps = atoi(arg[1]);
|
||||
if (nprocs_lammps > nprocs) {
|
||||
if (me == 0)
|
||||
printf("ERROR: LAMMPS cannot use more procs than available\n");
|
||||
MPI_Abort(MPI_COMM_WORLD,1);
|
||||
}
|
||||
|
||||
int lammps;
|
||||
if (me < nprocs_lammps) lammps = 1;
|
||||
else lammps = MPI_UNDEFINED;
|
||||
MPI_Comm comm_lammps;
|
||||
MPI_Comm_split(MPI_COMM_WORLD,lammps,0,&comm_lammps);
|
||||
|
||||
/* open LAMMPS input script */
|
||||
|
||||
FILE *fp;
|
||||
if (me == 0) {
|
||||
fp = fopen(arg[2],"r");
|
||||
if (fp == NULL) {
|
||||
printf("ERROR: Could not open LAMMPS input script\n");
|
||||
MPI_Abort(MPI_COMM_WORLD,1);
|
||||
}
|
||||
}
|
||||
|
||||
/* run the input script thru LAMMPS one line at a time until end-of-file
|
||||
driver proc 0 reads a line, Bcasts it to all procs
|
||||
(could just send it to proc 0 of comm_lammps and let it Bcast)
|
||||
all LAMMPS procs call lammps_command() on the line */
|
||||
|
||||
void *ptr;
|
||||
if (lammps == 1) lammps_open(0,NULL,comm_lammps,&ptr);
|
||||
|
||||
int n;
|
||||
char line[1024];
|
||||
while (1) {
|
||||
if (me == 0) {
|
||||
if (fgets(line,1024,fp) == NULL) n = 0;
|
||||
else n = strlen(line) + 1;
|
||||
if (n == 0) fclose(fp);
|
||||
}
|
||||
MPI_Bcast(&n,1,MPI_INT,0,MPI_COMM_WORLD);
|
||||
if (n == 0) break;
|
||||
MPI_Bcast(line,n,MPI_CHAR,0,MPI_COMM_WORLD);
|
||||
if (lammps == 1) lammps_command(ptr,line);
|
||||
}
|
||||
|
||||
/* run 10 more steps
|
||||
get coords from LAMMPS
|
||||
change coords of 1st atom
|
||||
put coords back into LAMMPS
|
||||
run a single step with changed coords */
|
||||
|
||||
if (lammps == 1) {
|
||||
lammps_command(ptr,"run 10");
|
||||
|
||||
int natoms = lammps_get_natoms(ptr);
|
||||
double *x = (double *) malloc(3*natoms*sizeof(double));
|
||||
lammps_get_coords(ptr,x);
|
||||
double epsilon = 0.1;
|
||||
x[0] += epsilon;
|
||||
lammps_put_coords(ptr,x);
|
||||
free(x);
|
||||
|
||||
lammps_command(ptr,"run 1");
|
||||
}
|
||||
|
||||
if (lammps == 1) lammps_close(ptr);
|
||||
|
||||
/* close down MPI */
|
||||
|
||||
MPI_Finalize();
|
||||
}
|
||||
121
examples/COUPLE/simple/simple.cpp
Normal file
121
examples/COUPLE/simple/simple.cpp
Normal file
@ -0,0 +1,121 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
www.cs.sandia.gov/~sjplimp/lammps.html
|
||||
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
// c++_driver = simple example of how an umbrella program
|
||||
// can invoke LAMMPS as a library on some subset of procs
|
||||
// Syntax: c++_driver P in.lammps
|
||||
// P = # of procs to run LAMMPS on
|
||||
// must be <= # of procs the driver code itself runs on
|
||||
// in.lammps = LAMMPS input script
|
||||
// See README for compilation instructions
|
||||
|
||||
#include "stdio.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "mpi.h"
|
||||
#include "lammps.h" // these are LAMMPS include files
|
||||
#include "input.h"
|
||||
#include "atom.h"
|
||||
#include "library.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
int main(int narg, char **arg)
|
||||
{
|
||||
// setup MPI and various communicators
|
||||
// driver runs on all procs in MPI_COMM_WORLD
|
||||
// comm_lammps only has 1st P procs (could be all or any subset)
|
||||
|
||||
MPI_Init(&narg,&arg);
|
||||
|
||||
if (narg != 3) {
|
||||
printf("Syntax: c++_driver P in.lammps\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
int me,nprocs;
|
||||
MPI_Comm_rank(MPI_COMM_WORLD,&me);
|
||||
MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
|
||||
|
||||
int nprocs_lammps = atoi(arg[1]);
|
||||
if (nprocs_lammps > nprocs) {
|
||||
if (me == 0)
|
||||
printf("ERROR: LAMMPS cannot use more procs than available\n");
|
||||
MPI_Abort(MPI_COMM_WORLD,1);
|
||||
}
|
||||
|
||||
int lammps;
|
||||
if (me < nprocs_lammps) lammps = 1;
|
||||
else lammps = MPI_UNDEFINED;
|
||||
MPI_Comm comm_lammps;
|
||||
MPI_Comm_split(MPI_COMM_WORLD,lammps,0,&comm_lammps);
|
||||
|
||||
// open LAMMPS input script
|
||||
|
||||
FILE *fp;
|
||||
if (me == 0) {
|
||||
fp = fopen(arg[2],"r");
|
||||
if (fp == NULL) {
|
||||
printf("ERROR: Could not open LAMMPS input script\n");
|
||||
MPI_Abort(MPI_COMM_WORLD,1);
|
||||
}
|
||||
}
|
||||
|
||||
// run the input script thru LAMMPS one line at a time until end-of-file
|
||||
// driver proc 0 reads a line, Bcasts it to all procs
|
||||
// (could just send it to proc 0 of comm_lammps and let it Bcast)
|
||||
// all LAMMPS procs call input->one() on the line
|
||||
|
||||
LAMMPS *lmp;
|
||||
if (lammps == 1) lmp = new LAMMPS(0,NULL,comm_lammps);
|
||||
|
||||
int n;
|
||||
char line[1024];
|
||||
while (1) {
|
||||
if (me == 0) {
|
||||
if (fgets(line,1024,fp) == NULL) n = 0;
|
||||
else n = strlen(line) + 1;
|
||||
if (n == 0) fclose(fp);
|
||||
}
|
||||
MPI_Bcast(&n,1,MPI_INT,0,MPI_COMM_WORLD);
|
||||
if (n == 0) break;
|
||||
MPI_Bcast(line,n,MPI_CHAR,0,MPI_COMM_WORLD);
|
||||
if (lammps == 1) lmp->input->one(line);
|
||||
}
|
||||
|
||||
// run 10 more steps
|
||||
// get coords from LAMMPS
|
||||
// change coords of 1st atom
|
||||
// put coords back into LAMMPS
|
||||
// run a single step with changed coords
|
||||
|
||||
if (lammps == 1) {
|
||||
lmp->input->one("run 10");
|
||||
|
||||
int natoms = static_cast<int> (lmp->atom->natoms);
|
||||
double *x = new double[3*natoms];
|
||||
lammps_get_coords(lmp,x); // no LAMMPS class function for this
|
||||
double epsilon = 0.1;
|
||||
x[0] += epsilon;
|
||||
lammps_put_coords(lmp,x); // no LAMMPS class function for this
|
||||
delete [] x;
|
||||
|
||||
lmp->input->one("run 1");
|
||||
}
|
||||
|
||||
if (lammps == 1) delete lmp;
|
||||
|
||||
// close down MPI
|
||||
|
||||
MPI_Finalize();
|
||||
}
|
||||
135
examples/COUPLE/simple/simple.f90
Normal file
135
examples/COUPLE/simple/simple.f90
Normal file
@ -0,0 +1,135 @@
|
||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
! www.cs.sandia.gov/~sjplimp/lammps.html
|
||||
! Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
!
|
||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
! certain rights in this software. This software is distributed under
|
||||
! the GNU General Public License.
|
||||
!
|
||||
! See the README file in the top-level LAMMPS directory.
|
||||
|
||||
! f_driver = simple example of how an umbrella program
|
||||
! can invoke LAMMPS as a library on some subset of procs
|
||||
! Syntax: f_driver P in.lammps
|
||||
! P = # of procs to run LAMMPS on
|
||||
! must be <= # of procs the driver code itself runs on
|
||||
! in.lammps = LAMMPS input script
|
||||
! See README for compilation instructions
|
||||
|
||||
PROGRAM f_driver
|
||||
IMPLICIT NONE
|
||||
INCLUDE 'mpif.h'
|
||||
|
||||
INTEGER, PARAMETER :: fp=20
|
||||
INTEGER :: n, narg, ierr, me, nprocs, natoms
|
||||
INTEGER :: lammps, nprocs_lammps, comm_lammps
|
||||
INTEGER (kind=8) :: ptr
|
||||
|
||||
REAL (kind=8), ALLOCATABLE :: x(:)
|
||||
REAL (kind=8), PARAMETER :: epsilon=0.1
|
||||
|
||||
CHARACTER (len=64) :: arg
|
||||
CHARACTER (len=1024) :: line
|
||||
|
||||
! setup MPI and various communicators
|
||||
! driver runs on all procs in MPI_COMM_WORLD
|
||||
! comm_lammps only has 1st P procs (could be all or any subset)
|
||||
|
||||
CALL mpi_init(ierr)
|
||||
|
||||
narg = command_argument_count()
|
||||
|
||||
IF (narg /= 2) THEN
|
||||
PRINT *, 'Syntax: f_driver P in.lammps'
|
||||
CALL mpi_abort(MPI_COMM_WORLD,1,ierr)
|
||||
END IF
|
||||
|
||||
CALL mpi_comm_rank(MPI_COMM_WORLD,me,ierr);
|
||||
CALL mpi_comm_size(MPI_COMM_WORLD,nprocs,ierr);
|
||||
|
||||
CALL get_command_argument(1,arg)
|
||||
READ (arg,'(I10)') nprocs_lammps
|
||||
|
||||
IF (nprocs_lammps > nprocs) THEN
|
||||
IF (me == 0) THEN
|
||||
PRINT *, 'ERROR: LAMMPS cannot use more procs than available'
|
||||
CALL mpi_abort(MPI_COMM_WORLD,2,ierr)
|
||||
END IF
|
||||
END IF
|
||||
|
||||
lammps = 0
|
||||
IF (me < nprocs_lammps) THEN
|
||||
lammps = 1
|
||||
ELSE
|
||||
lammps = MPI_UNDEFINED
|
||||
END IF
|
||||
|
||||
CALL mpi_comm_split(MPI_COMM_WORLD,lammps,0,comm_lammps,ierr)
|
||||
|
||||
! open LAMMPS input script on rank zero
|
||||
|
||||
CALL get_command_argument(2,arg)
|
||||
OPEN(UNIT=fp, FILE=arg, ACTION='READ', STATUS='OLD', IOSTAT=ierr)
|
||||
IF (ierr /= 0) THEN
|
||||
PRINT *, 'ERROR: Could not open LAMMPS input script'
|
||||
CALL mpi_abort(MPI_COMM_WORLD,3,ierr);
|
||||
END IF
|
||||
|
||||
! run the input script thru LAMMPS one line at a time until end-of-file
|
||||
! driver proc 0 reads a line, Bcasts it to all procs
|
||||
! (could just send it to proc 0 of comm_lammps and let it Bcast)
|
||||
! all LAMMPS procs call lammps_command() on the line */
|
||||
|
||||
IF (lammps == 1) CALL lammps_open(comm_lammps,ptr)
|
||||
|
||||
n = 0
|
||||
DO
|
||||
IF (me == 0) THEN
|
||||
READ (UNIT=fp, FMT='(A)', IOSTAT=ierr) line
|
||||
n = 0
|
||||
IF (ierr == 0) THEN
|
||||
n = LEN(TRIM(line))
|
||||
IF (n == 0 ) THEN
|
||||
line = ' '
|
||||
n = 1
|
||||
END IF
|
||||
END IF
|
||||
END IF
|
||||
CALL mpi_bcast(n,1,MPI_INTEGER,0,MPI_COMM_WORLD,ierr)
|
||||
IF (n == 0) EXIT
|
||||
CALL mpi_bcast(line,n,MPI_CHARACTER,0,MPI_COMM_WORLD,ierr)
|
||||
IF (lammps == 1) CALL lammps_command(ptr,line,n)
|
||||
END DO
|
||||
CLOSE(UNIT=fp)
|
||||
|
||||
! run 10 more steps
|
||||
! get coords from LAMMPS
|
||||
! change coords of 1st atom
|
||||
! put coords back into LAMMPS
|
||||
! run a single step with changed coords */
|
||||
|
||||
IF (lammps == 1) THEN
|
||||
CALL lammps_command(ptr,'run 10',6)
|
||||
|
||||
CALL lammps_get_natoms(ptr,natoms)
|
||||
ALLOCATE(x(3*natoms))
|
||||
|
||||
CALL lammps_get_coords(ptr,x)
|
||||
x(1) = x(1) + epsilon
|
||||
CALL lammps_put_coords(ptr,x)
|
||||
|
||||
DEALLOCATE(x)
|
||||
|
||||
CALL lammps_command(ptr,'run 1',5);
|
||||
END IF
|
||||
|
||||
! free LAMMPS object
|
||||
|
||||
IF (lammps == 1) CALL lammps_close(ptr);
|
||||
|
||||
! close down MPI
|
||||
|
||||
CALL mpi_finalize(ierr)
|
||||
|
||||
END PROGRAM f_driver
|
||||
Reference in New Issue
Block a user