1LAMMPS.F90 defines a Fortran 2003 module, LAMMPS, which wraps all functions in
2src/library.h so they can be used directly from Fortran-encoded programs.
3
4All functions in src/library.h that use and/or return C-style pointers have
5Fortran wrapper functions that use Fortran-style arrays, pointers, and
6strings; all C-style memory management is handled internally with no user
7intervention. See --USE-- for notes on how this interface differs from the
8C interface (and the Python interface).
9
10This interface was created by Karl Hammond who you can contact with
11questions:
12
13Karl D. Hammond
14University of Tennessee, Knoxville
15karlh at ugcs.caltech.edu
16karlh at utk.edu
17
18-------------------------------------
19
20--COMPILATION--
21
22First, be advised that mixed-language programming is not trivial. It requires
23you to link in the required libraries of all languages you use (in this case,
24those for Fortran, C, and C++), as well as any other libraries required.
25You are also advised to read the --USE-- section below before trying to
26compile.
27
28The following steps will work to compile this module (replace ${LAMMPS_SRC}
29with the path to your LAMMPS source directory).
30
31Steps 3-5 are accomplished, possibly after some modifications to
32the makefile, by make using the attached makefile. Said makefile also builds
33the dynamically-linkable library (liblammps_fortran.so).
34
35** STATIC LIBRARY INSTRUCTIONS **
36 (1) Compile LAMMPS as a static library.
37 Call the resulting file ${LAMMPS_LIB}, which will have an actual name
38 like liblmp_openmpi.a. If compiling using the MPI stubs in
39 ${LAMMPS_SRC}/STUBS, you will need to know where libmpi_stubs.a
40 is as well (I'll call it ${MPI_STUBS} hereafter)
41 (2) Copy said library to your Fortran program's source directory or replace
42 ${LAMMPS_LIB} with its full path in the instructions below.
43 (3) Compile (but don't link!) LAMMPS.F90. Example:
44 mpif90 -c LAMMPS.f90
45 OR
46 gfortran -c LAMMPS.F90
47 NOTE: you may get a warning such as,
48 subroutine lammps_open_wrapper (argc, argv, communicator, ptr) &
49 Variable 'communicator' at (1) is a parameter to the BIND(C)
50 procedure 'lammps_open_wrapper' but may not be C interoperable
51 This is normal (see --IMPLEMENTATION NOTES--).
52
53 (4) Compile (but don't link) LAMMPS-wrapper.cpp. You will need its header
54 file as well. You will have to provide the locations of LAMMPS's
55 header files. For example,
56 mpicxx -c -I${LAMMPS_SRC} LAMMPS-wrapper.cpp
57 OR
58 g++ -c -I${LAMMPS_SRC} -I${LAMMPS_SRC}/STUBS LAMMPS-wrapper.cpp
59 OR
60 icpc -c -I${LAMMPS_SRC} -I${LAMMPS_SRC}/STUBS LAMMPS-wrapper.cpp
61 (5) OPTIONAL: Make a library from the object files so you can carry around
62 two files instead of three. Example:
63 ar rs liblammps_fortran.a LAMMPS.o LAMMPS-wrapper.o
64 This will create the file liblammps_fortran.a that you can use in place
65 of "LAMMPS.o LAMMPS-wrapper.o" later. Note that you will still
66 need to have the .mod file from part (3).
67
68 It is also possible to add LAMMPS.o and LAMMPS-wrapper.o into the
69 LAMMPS library (e.g., liblmp_openmpi.a) instead of creating a separate
70 library, like so:
71 ar rs ${LAMMPS_LIB} LAMMPS.o LAMMPS-wrapper.o
72 In this case, you can now use the Fortran wrapper functions as if they
73 were part of the usual LAMMPS library interface (if you have the module
74 file visible to the compiler, that is).
75 (6) Compile (but don't link) your Fortran program. Example:
76 mpif90 -c myfreeformatfile.f90
77 mpif90 -c myfixedformatfile.f
78 OR
79 gfortran -c myfreeformatfile.f90
80 gfortran -c myfixedformatfile.f
81 The object files generated by these steps are collectively referred to
82 as ${my_object_files} in the next step(s).
83
84 IMPORTANT: If the Fortran module from part (3) is not in the current
85 directory or in one searched by the compiler for module files, you will
86 need to include that location via the -I flag to the compiler, like so:
87 mpif90 -I${LAMMPS_SRC}/examples/COUPLE/fortran2 -c myfreeformatfile.f90
88
89 (7) Link everything together, including any libraries needed by LAMMPS (such
90 as the C++ standard library, the C math library, the JPEG library, fftw,
91 etc.) For example,
92 mpif90 LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
93 ${LAMMPS_LIB} -lmpi_cxx -lstdc++ -lm
94 OR
95 gfortran LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
96 ${LAMMPS_LIB} ${MPI_STUBS} -lstdc++ -lm
97 OR
98 ifort LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
99 ${LAMMPS_LIB} ${MPI_STUBS} -cxxlib -lm
100 Any other required libraries (e.g. -ljpeg, -lfftw) should be added to
101 the end of this line.
102
103You should now have a working executable.
104
105** DYNAMIC LIBRARY INSTRUCTIONS **
106 (1) Compile LAMMPS as a dynamic library
107 (make makeshlib && make -f Makefile.shlib [targetname]).
108 (2) Compile, but don't link, LAMMPS.F90 using the -fPIC flag, such as
109 mpif90 -fPIC -c LAMMPS.f90
110 (3) Compile, but don't link, LAMMPS-wrapper.cpp in the same manner, e.g.
111 mpicxx -fPIC -c LAMMPS-wrapper.cpp
112 (4) Make the dynamic library, like so:
113 mpif90 -fPIC -shared -o liblammps_fortran.so LAMMPS.o LAMMPS-wrapper.o
114 (5) Compile your program, such as,
115 mpif90 -I${LAMMPS_SRC}/examples/COUPLE/fortran2 -c myfreeformatfile.f90
116 where ${LAMMPS_SRC}/examples/COUPLE/fortran2 contains the .mod file from
117 step (3)
118 (6) Link everything together, such as
119 mpif90 ${my_object_files} -L${LAMMPS_SRC} \
120 -L${LAMMPS_SRC}/examples/COUPLE/fortran2 -llammps_fortran \
121 -llammps_openmpi -lmpi_cxx -lstdc++ -lm
122
123If you wish to avoid the -L flags, add the directories containing your
124shared libraries to the LIBRARY_PATH environment variable. At run time, you
125will have to add these directories to LD_LIBRARY_PATH as well; otherwise,
126your executable will not find the libraries it needs.
127
128-------------------------------------
129
130--USAGE--
131
132To use this API, your program unit (PROGRAM/SUBROUTINE/FUNCTION/MODULE/etc.)
133should look something like this:
134 program call_lammps
135 use LAMMPS
136 ! Other modules, etc.
137 implicit none
138 type (lammps_instance) :: lmp ! This is a pointer to your LAMMPS instance
139 real (C_double) :: fix
140 real (C_double), dimension(:), pointer :: fix2
141 ! Rest of declarations
142 call lammps_open_no_mpi ('lmp -in /dev/null -screen out.lammps',lmp)
143 ! Set up rest of program here
144 call lammps_file (lmp, 'in.example')
145 call lammps_extract_fix (fix, lmp, '2', 0, 1, 1, 1)
146 call lammps_extract_fix (fix2, lmp, '4', 0, 2, 1, 1)
147 call lammps_close (lmp)
148 end program call_lammps
149
150Important notes:
151 * Though I dislike the use of pointers, they are necessary when communicating
152 with C and C++, which do not support Fortran's ALLOCATABLE attribute.
153 * There is no need to deallocate C-allocated memory; this is done for you in
154 the cases when it is done (which are all cases when pointers are not
155 accepted, such as global fix data)
156 * All arguments which are char* variables in library.cpp are character (len=*)
157 variables here. For example,
158 call lammps_command (lmp, 'units metal')
159 will work as expected.
160 * The public functions (the only ones you can use) have interfaces as
161 described in the comments at the top of LAMMPS.F90. They are not always
162 the same as those in library.h, since C strings are replaced by Fortran
163 strings and the like.
164 * The module attempts to check whether you have done something stupid (such
165 as assign a 2D array to a scalar), but it's not perfect. For example, the
166 command
167 call lammps_extract_global (nlocal, ptr, 'nlocal')
168 will give nlocal correctly if nlocal is a pointer to type INTEGER, but it
169 will give the wrong answer if nlocal is a pointer to type REAL. This is a
170 feature of the (void*) type cast in library.cpp. There is no way I can
171 check this for you! It WILL catch you if you pass it an allocatable or
172 fixed-size array when it expects a pointer.
173 * Arrays constructed from temporary data from LAMMPS are ALLOCATABLE, and
174 represent COPIES of data, not the originals. Functions like
175 lammps_extract_atom, which return actual LAMMPS data, are pointers.
176 * IMPORTANT: Due to the differences between C and Fortran arrays (C uses
177 row-major vectors, Fortran uses column-major vectors), all arrays returned
178 from LAMMPS have their indices swapped.
179 * An example of a complete program, simple.f90, is included with this
180 package.
181
182-------------------------------------
183
184--TROUBLESHOOTING--
185
186Compile-time errors (when compiling LAMMPS.F90, that is) probably indicate
187that your compiler is not new enough to support Fortran 2003 features. For
188example, GCC 4.1.2 will not compile this module, but GCC 4.4.0 will.
189
190If your compiler balks at 'use, intrinsic :: ISO_C_binding,' try removing the
191intrinsic part so it looks like an ordinary module. However, it is likely
192that such a compiler will also have problems with everything else in the
193file as well.
194
195If you get a segfault as soon as the lammps_open call is made, check that you
196compiled your program AND LAMMPS-wrapper.cpp using the same MPI headers. Using
197the stubs for one and the actual MPI library for the other will cause Bad
198Things to happen.
199
200If you find run-time errors, please pass them along via the LAMMPS Users
201mailing list (please CC me as well; address above). Please provide a minimal
202working example along with the names and versions of the compilers you are
203using. Please make sure the error is repeatable and is in MY code, not yours
204(generating a minimal working example will usually ensure this anyway).
205
206-------------------------------------
207
208--IMPLEMENTATION NOTES--
209
210The Fortran procedures have the same names as the C procedures, and
211their purpose is the same, but they may take different arguments. Here are
212some of the important differences:
213 * lammps_open and lammps_open_no_mpi take a string instead of argc and
214 argv. This is necessary because C and C++ have a very different way
215 of treating strings than Fortran. If you want the command line to be
216 passed to lammps_open (as it often would be from C/C++), use the
217 GET_COMMAND intrinsic to obtain it.
218 * All C++ functions that accept char* pointers now accept Fortran-style
219 strings within this interface instead.
220 * All of the lammps_extract_[something] functions, which return void*
221 C-style pointers, have been replaced by generic subroutines that return
222 Fortran variables (which may be arrays). The first argument houses the
223 variable/pointer to be returned (pretend it's on the left-hand side); all
224 other arguments are identical except as stipulated above.
225 Note that it is not possible to declare generic functions that are selected
226 based solely on the type/kind/rank (TKR) signature of the return value,
227 only based on the TKR of the arguments.
228 * The SHAPE of the first argument to lammps_extract_[something] is checked
229 against the "shape" of the C array (e.g., double vs. double* vs. double**).
230 Calling a subroutine with arguments of inappropriate rank will result in an
231 error at run time.
232 * The indices i and j in lammps_extract_fix are used the same way they
233 are in f_ID[i][j] references in LAMMPS (i.e., starting from 1). This is
234 different than the way library.cpp uses these numbers, but is more
235 consistent with the way arrays are accessed in LAMMPS and in Fortran.
236 * The char* pointer normally returned by lammps_command is thrown away
237 in this version; note also that lammps_command is now a subroutine
238 instead of a function.
239 * The pointer to LAMMPS itself is of type(lammps_instance), which is itself
240 a synonym for type(C_ptr), part of ISO_C_BINDING. Type (C_ptr) is
241 C's void* data type.
242 * This module will almost certainly generate a compile-time warning,
243 such as,
244 subroutine lammps_open_wrapper (argc, argv, communicator, ptr) &
245 Variable 'communicator' at (1) is a parameter to the BIND(C)
246 procedure 'lammps_open_wrapper' but may not be C interoperable
247 This happens because lammps_open_wrapper actually takes a Fortran
248 INTEGER argument, whose type is defined by the MPI library itself. The
249 Fortran integer is converted to a C integer by the MPI library (if such
250 conversion is actually necessary).
251 * lammps_extract_global returns COPIES of the (scalar) data, as does the
252 C version.
253 * lammps_extract_atom, lammps_extract_compute, and lammps_extract_fix
254 have a first argument that will be associated with ACTUAL LAMMPS DATA.
255 This means the first argument must be:
256 * The right rank (via the DIMENSION modifier)
257 * A C-interoperable POINTER type (i.e., INTEGER (C_int) or
258 REAL (C_double)).
259 * lammps_extract_variable returns COPIES of the data, as the C library
260 interface does. There is no need to deallocate using lammps_free.
261 * The 'data' argument to lammps_gather_atoms and lammps_scatter atoms must
262 be ALLOCATABLE. It should be of type INTEGER or DOUBLE PRECISION. It
263 does NOT need to be C inter-operable (and indeed should not be).
264 * The 'count' argument of lammps_scatter_atoms is unnecessary; the shape of
265 the array determines the number of elements LAMMPS will read.
266