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Merge branch 'master' into lammps-icms

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Axel Kohlmeyer
2012-08-18 17:17:35 -04:00
parent ffc41c52c5 4cb989a2d3
commit 788b01cd71
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44
doc/Section_python.html
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@ -58,12 +58,13 @@ operations within LAMMPS, such as running a simulation for a
reasonable number of timesteps, then the overhead cost of invoking reasonable number of timesteps, then the overhead cost of invoking
LAMMPS thru Python will be negligible. LAMMPS thru Python will be negligible.
</P> </P>
<P>Before using LAMMPS from a Python script, you have to do two things. <P>Before using LAMMPS from a Python script, you need to do two things.
You need to set two environment variables. And you need to build You need to build LAMMPS as a dynamic shared library, so it can be
LAMMPS as a dynamic shared library, so it can be loaded by Python. loaded by Python. And you need to tell Python how to find the library
Both these steps are discussed below. If you wish to run LAMMPS in and the Python wrapper file python/lammps.py. Both these steps are
parallel from Python, you also need to extend your Python with MPI. discussed below. If you wish to run LAMMPS in parallel from Python,
This is also discussed below. you also need to extend your Python with MPI. This is also discussed
below.
</P> </P>
<P>The Python wrapper for LAMMPS uses the amazing and magical (to me) <P>The Python wrapper for LAMMPS uses the amazing and magical (to me)
"ctypes" package in Python, which auto-generates the interface code "ctypes" package in Python, which auto-generates the interface code
@ -131,7 +132,7 @@ python/lammps.py file.
</P> </P>
<P>You can invoke install.py from the python directory as <P>You can invoke install.py from the python directory as
</P> </P>
<PRE>% python install.py <B>libdir</B> <B>pydir</B> <PRE>% python install.py [libdir] [pydir]
</PRE> </PRE>
<P>The optional libdir is where to copy the LAMMPS shared library to; the <P>The optional libdir is where to copy the LAMMPS shared library to; the
default is /usr/local/lib. The optional pydir is where to copy the default is /usr/local/lib. The optional pydir is where to copy the
@ -146,12 +147,12 @@ non-standard locations, such as within your own user space, you will
need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables
accordingly, as above. accordingly, as above.
</P> </P>
<P>If the instally.py script does not allow you to copy files into system <P>If the install.py script does not allow you to copy files into system
directories, prefix the python command with "sudo". If you do this, directories, prefix the python command with "sudo". If you do this,
make sure that the Python that root runs is the same as the Python you make sure that the Python that root runs is the same as the Python you
run. E.g. you may need to do something like run. E.g. you may need to do something like
</P> </P>
<PRE>% sudo /usr/local/bin/python install.py <B>libdir</B> <B>pydir</B> <PRE>% sudo /usr/local/bin/python install.py [libdir] [pydir]
</PRE> </PRE>
<P>You can also invoke install.py from the make command in the src <P>You can also invoke install.py from the make command in the src
directory as directory as
@ -269,20 +270,27 @@ and type:
<PRE>>>> from lammps import lammps <PRE>>>> from lammps import lammps
>>> lmp = lammps() >>> lmp = lammps()
</PRE> </PRE>
<P>If you get no errors, you're ready to use LAMMPS from Python. <P>If you get no errors, you're ready to use LAMMPS from Python. If the
If the load fails, the most common error to see is 2nd command fails, the most common error to see is
</P> </P>
<PRE>OSError: Could not load LAMMPS dynamic library <PRE>OSError: Could not load LAMMPS dynamic library
</PRE> </PRE>
<P>which means Python was unable to load the LAMMPS shared library. This <P>which means Python was unable to load the LAMMPS shared library. This
typically occurs if the system can't find the LAMMMPS shared library typically occurs if the system can't find the LAMMPS shared library or
or one of the auxiliary shared libraries it depends on. one of the auxiliary shared libraries it depends on, or if something
about the library is incompatible with your Python. The error message
should give you an indication of what went wrong.
</P> </P>
<P>Python (actually the operating system) isn't verbose about telling you <P>You can also test the load directly in Python as follows, without
why the load failed, so carefully go through the steps above regarding first importing from the lammps.py file:
environment variables, and the instructions in <A HREF = "Section_start.html#start_5">Section_start </P>
5</A> about building a shared library and <PRE>>>> from ctypes import CDLL
about setting the LD_LIBRARY_PATH envirornment variable. >>> CDLL("liblammps.so")
</PRE>
<P>If an error occurs, carefully go thru the steps in <A HREF = "Section_start.html#start_5">Section_start
5</A> and above about building a shared
library and about insuring Python can find the necessary two files
it needs.
</P> </P>
<H5><B>Test LAMMPS and Python in serial:</B> <H5><B>Test LAMMPS and Python in serial:</B>
</H5> </H5>

44
doc/Section_python.txt
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@ -55,12 +55,13 @@ operations within LAMMPS, such as running a simulation for a
reasonable number of timesteps, then the overhead cost of invoking reasonable number of timesteps, then the overhead cost of invoking
LAMMPS thru Python will be negligible. LAMMPS thru Python will be negligible.
Before using LAMMPS from a Python script, you have to do two things. Before using LAMMPS from a Python script, you need to do two things.
You need to set two environment variables. And you need to build You need to build LAMMPS as a dynamic shared library, so it can be
LAMMPS as a dynamic shared library, so it can be loaded by Python. loaded by Python. And you need to tell Python how to find the library
Both these steps are discussed below. If you wish to run LAMMPS in and the Python wrapper file python/lammps.py. Both these steps are
parallel from Python, you also need to extend your Python with MPI. discussed below. If you wish to run LAMMPS in parallel from Python,
This is also discussed below. you also need to extend your Python with MPI. This is also discussed
below.
The Python wrapper for LAMMPS uses the amazing and magical (to me) The Python wrapper for LAMMPS uses the amazing and magical (to me)
"ctypes" package in Python, which auto-generates the interface code "ctypes" package in Python, which auto-generates the interface code
@ -127,7 +128,7 @@ python/lammps.py file.
You can invoke install.py from the python directory as You can invoke install.py from the python directory as
% python install.py [libdir] [pydir] :pre % python install.py \[libdir\] \[pydir\] :pre
The optional libdir is where to copy the LAMMPS shared library to; the The optional libdir is where to copy the LAMMPS shared library to; the
default is /usr/local/lib. The optional pydir is where to copy the default is /usr/local/lib. The optional pydir is where to copy the
@ -142,12 +143,12 @@ non-standard locations, such as within your own user space, you will
need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables
accordingly, as above. accordingly, as above.
If the instally.py script does not allow you to copy files into system If the install.py script does not allow you to copy files into system
directories, prefix the python command with "sudo". If you do this, directories, prefix the python command with "sudo". If you do this,
make sure that the Python that root runs is the same as the Python you make sure that the Python that root runs is the same as the Python you
run. E.g. you may need to do something like run. E.g. you may need to do something like
% sudo /usr/local/bin/python install.py [libdir] [pydir] :pre % sudo /usr/local/bin/python install.py \[libdir\] \[pydir\] :pre
You can also invoke install.py from the make command in the src You can also invoke install.py from the make command in the src
directory as directory as
@ -265,20 +266,27 @@ and type:
>>> from lammps import lammps >>> from lammps import lammps
>>> lmp = lammps() :pre >>> lmp = lammps() :pre
If you get no errors, you're ready to use LAMMPS from Python. If you get no errors, you're ready to use LAMMPS from Python. If the
If the load fails, the most common error to see is 2nd command fails, the most common error to see is
OSError: Could not load LAMMPS dynamic library :pre OSError: Could not load LAMMPS dynamic library :pre
which means Python was unable to load the LAMMPS shared library. This which means Python was unable to load the LAMMPS shared library. This
typically occurs if the system can't find the LAMMMPS shared library typically occurs if the system can't find the LAMMPS shared library or
or one of the auxiliary shared libraries it depends on. one of the auxiliary shared libraries it depends on, or if something
about the library is incompatible with your Python. The error message
should give you an indication of what went wrong.
Python (actually the operating system) isn't verbose about telling you You can also test the load directly in Python as follows, without
why the load failed, so carefully go through the steps above regarding first importing from the lammps.py file:
environment variables, and the instructions in "Section_start
5"_Section_start.html#start_5 about building a shared library and >>> from ctypes import CDLL
about setting the LD_LIBRARY_PATH envirornment variable. >>> CDLL("liblammps.so") :pre
If an error occurs, carefully go thru the steps in "Section_start
5"_Section_start.html#start_5 and above about building a shared
library and about insuring Python can find the necessary two files
it needs.
[Test LAMMPS and Python in serial:] :h5 [Test LAMMPS and Python in serial:] :h5

2
doc/Section_start.html
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@ -850,7 +850,7 @@ should be the file /usr/local/lib/libmpich.so.
the environment variable LD_LIBRARY_PATH. So you may wish to copy the the environment variable LD_LIBRARY_PATH. So you may wish to copy the
file src/liblammps.so or src/liblammps_g++.so (for example) to a place file src/liblammps.so or src/liblammps_g++.so (for example) to a place
the system can find it by default, such as /usr/local/lib, or you may the system can find it by default, such as /usr/local/lib, or you may
wish to add the lammps src directory to LD_LIBRARY_PATH, so that the wish to add the LAMMPS src directory to LD_LIBRARY_PATH, so that the
current version of the shared library is always available to programs current version of the shared library is always available to programs
that use it. that use it.
</P> </P>

2
doc/Section_start.txt
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@ -844,7 +844,7 @@ The operating system finds shared libraries to load at run-time using
the environment variable LD_LIBRARY_PATH. So you may wish to copy the the environment variable LD_LIBRARY_PATH. So you may wish to copy the
file src/liblammps.so or src/liblammps_g++.so (for example) to a place file src/liblammps.so or src/liblammps_g++.so (for example) to a place
the system can find it by default, such as /usr/local/lib, or you may the system can find it by default, such as /usr/local/lib, or you may
wish to add the lammps src directory to LD_LIBRARY_PATH, so that the wish to add the LAMMPS src directory to LD_LIBRARY_PATH, so that the
current version of the shared library is always available to programs current version of the shared library is always available to programs
that use it. that use it.

1
examples/COUPLE/fortran2/LAMMPS-wrapper.cpp
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@ -30,6 +30,7 @@
#include <compute.h> #include <compute.h>
#include <modify.h> #include <modify.h>
#include <error.h> #include <error.h>
#include <cstdlib>
using namespace LAMMPS_NS; using namespace LAMMPS_NS;

8
examples/COUPLE/fortran2/LAMMPS-wrapper.h
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@ -21,12 +21,6 @@
library.h. All prototypes herein COULD be added to library.h instead of library.h. All prototypes herein COULD be added to library.h instead of
including this as a separate file. See the README for instructions. */ including this as a separate file. See the README for instructions. */
/* These prototypes probably belong in mpi.h in the src/STUBS directory. */
#ifndef OPEN_MPI
#define MPI_Comm_f2c(a) a
#define MPI_Fint int
#endif
#ifdef __cplusplus #ifdef __cplusplus
extern "C" { extern "C" {
#endif #endif
@ -38,7 +32,7 @@ int lammps_extract_compute_vectorsize (void*, char*, int);
void lammps_extract_compute_arraysize (void*, char*, int, int*, int*); void lammps_extract_compute_arraysize (void*, char*, int, int*, int*);
int lammps_extract_fix_vectorsize (void*, char*, int); int lammps_extract_fix_vectorsize (void*, char*, int);
void lammps_extract_fix_arraysize (void*, char*, int, int*, int*); void lammps_extract_fix_arraysize (void*, char*, int, int*, int*);
void lammps_error_all (void *ptr, const char*, int, const char*); void lammps_error_all (void*, const char*, int, const char*);
#ifdef __cplusplus #ifdef __cplusplus
} }

212
examples/COUPLE/fortran2/LAMMPS.F90
View File

@ -39,8 +39,8 @@
!! subroutine lammps_extract_compute (compute, ptr, id, style, type) !! subroutine lammps_extract_compute (compute, ptr, id, style, type)
!! subroutine lammps_extract_variable (variable, ptr, name, group) !! subroutine lammps_extract_variable (variable, ptr, name, group)
!! function lammps_get_natoms (ptr) !! function lammps_get_natoms (ptr)
!! subroutine lammps_get_coords (ptr, coords) !! subroutine lammps_gather_atoms (ptr, name, count, data)
!! subroutine lammps_put_coords (ptr, coords) !! subroutine lammps_scatter_atoms (ptr, name, data)
#define FLERR __FILE__,__LINE__ #define FLERR __FILE__,__LINE__
! The above line allows for similar error checking as is done with standard ! The above line allows for similar error checking as is done with standard
@ -55,8 +55,9 @@ module LAMMPS
public :: lammps_open, lammps_open_no_mpi, lammps_close, lammps_file, & public :: lammps_open, lammps_open_no_mpi, lammps_close, lammps_file, &
lammps_command, lammps_free, lammps_extract_global, & lammps_command, lammps_free, lammps_extract_global, &
lammps_extract_atom, lammps_extract_compute, lammps_extract_fix, & lammps_extract_atom, lammps_extract_compute, lammps_extract_fix, &
lammps_extract_variable, lammps_get_natoms, lammps_get_coords, & lammps_extract_variable, lammps_get_natoms, lammps_gather_atoms, &
lammps_put_coords, lammps_instance lammps_scatter_atoms
public :: lammps_instance
!! Functions supplemental to the prototypes in library.h. {{{1 !! Functions supplemental to the prototypes in library.h. {{{1
!! The function definitions (in C++) are contained in LAMMPS-wrapper.cpp. !! The function definitions (in C++) are contained in LAMMPS-wrapper.cpp.
@ -204,18 +205,21 @@ module LAMMPS
integer (C_int) :: natoms integer (C_int) :: natoms
end function lammps_get_natoms end function lammps_get_natoms
subroutine lammps_actual_get_coords (ptr, coords) & subroutine lammps_actual_gather_atoms (ptr, name, type, count, data) &
bind (C, name='lammps_get_coords') bind (C, name='lammps_gather_atoms')
import :: C_ptr import :: C_ptr, C_int, C_char
type (C_ptr), value :: ptr, coords type (C_ptr), value :: ptr, data
end subroutine lammps_actual_get_coords character (kind=C_char), dimension(*) :: name
integer (C_int), value :: type, count
end subroutine lammps_actual_gather_atoms
subroutine lammps_actual_put_coords (ptr, coords) & subroutine lammps_actual_scatter_atoms (ptr, name, type, count, data) &
bind (C, name='lammps_put_coords') bind (C, name='lammps_scatter_atoms')
import :: C_ptr, C_double import :: C_ptr, C_int, C_char
type (C_ptr), value :: ptr type (C_ptr), value :: ptr, data
real (C_double), dimension(*) :: coords character (kind=C_char), dimension(*) :: name
end subroutine lammps_actual_put_coords integer (C_int), value :: type, count
end subroutine lammps_actual_scatter_atoms
end interface end interface
! Generic functions for the wrappers below {{{1 ! Generic functions for the wrappers below {{{1
@ -258,6 +262,16 @@ module LAMMPS
lammps_extract_variable_dpa lammps_extract_variable_dpa
end interface lammps_extract_variable end interface lammps_extract_variable
interface lammps_gather_atoms
module procedure lammps_gather_atoms_ia, lammps_gather_atoms_dpa, &
lammps_gather_atoms_ra
end interface lammps_gather_atoms
interface lammps_scatter_atoms
module procedure lammps_scatter_atoms_ia, lammps_scatter_atoms_dpa, &
lammps_scatter_atoms_ra
end interface lammps_scatter_atoms
contains !! Wrapper functions local to this module {{{1 contains !! Wrapper functions local to this module {{{1
subroutine lammps_open (command_line, communicator, ptr) subroutine lammps_open (command_line, communicator, ptr)
@ -374,7 +388,6 @@ contains !! Wrapper functions local to this module {{{1
integer (C_int), pointer :: Fptr integer (C_int), pointer :: Fptr
integer :: natoms integer :: natoms
natoms = lammps_get_natoms (ptr) natoms = lammps_get_natoms (ptr)
if ( allocated (atom) ) deallocate (atom)
allocate (atom(natoms)) allocate (atom(natoms))
Cptr = lammps_extract_atom_Cptr (ptr, name) Cptr = lammps_extract_atom_Cptr (ptr, name)
call C_F_pointer (Cptr, Fptr, (/natoms/)) call C_F_pointer (Cptr, Fptr, (/natoms/))
@ -399,7 +412,6 @@ contains !! Wrapper functions local to this module {{{1
! Everything else we can get is probably nlocal units long ! Everything else we can get is probably nlocal units long
call lammps_extract_global_i (nelements, ptr, 'nlocal') call lammps_extract_global_i (nelements, ptr, 'nlocal')
end if end if
if ( allocated (atom) ) deallocate (atom)
allocate (atom(nelements)) allocate (atom(nelements))
Cptr = lammps_extract_atom_Cptr (ptr, name) Cptr = lammps_extract_atom_Cptr (ptr, name)
if ( name == 'mass' ) then if ( name == 'mass' ) then
@ -417,7 +429,6 @@ contains !! Wrapper functions local to this module {{{1
character (len=*), intent(in) :: name character (len=*), intent(in) :: name
double precision, dimension(:), allocatable :: d_atom double precision, dimension(:), allocatable :: d_atom
call lammps_extract_atom_dpa (d_atom, ptr, name) call lammps_extract_atom_dpa (d_atom, ptr, name)
if ( allocated (atom) ) deallocate (atom)
allocate (atom(size(d_atom))) allocate (atom(size(d_atom)))
atom = real(d_atom) atom = real(d_atom)
deallocate (d_atom) deallocate (d_atom)
@ -428,7 +439,6 @@ contains !! Wrapper functions local to this module {{{1
character (len=*), intent(in) :: name character (len=*), intent(in) :: name
type (C_ptr) :: Cptr type (C_ptr) :: Cptr
integer :: nelements integer :: nelements
if ( allocated (atom) ) deallocate (atom)
if ( name /= 'x' .and. name /= 'v' .and. name /= 'f' ) then if ( name /= 'x' .and. name /= 'v' .and. name /= 'f' ) then
call lammps_error_all (ptr, FLERR, 'You cannot extract ' // name // & call lammps_error_all (ptr, FLERR, 'You cannot extract ' // name // &
' into a rank 2 array.') ' into a rank 2 array.')
@ -445,7 +455,6 @@ contains !! Wrapper functions local to this module {{{1
character (len=*), intent(in) :: name character (len=*), intent(in) :: name
double precision, dimension(:,:), allocatable :: d_atom double precision, dimension(:,:), allocatable :: d_atom
call lammps_extract_atom_dp2a (d_atom, ptr, name) call lammps_extract_atom_dp2a (d_atom, ptr, name)
if ( allocated (atom) ) deallocate (atom)
if ( allocated (d_atom) ) then if ( allocated (d_atom) ) then
allocate (atom(size(d_atom,1), size(d_atom,2))) allocate (atom(size(d_atom,1), size(d_atom,2)))
else else
@ -515,7 +524,6 @@ contains !! Wrapper functions local to this module {{{1
type (C_ptr) :: Cptr type (C_ptr) :: Cptr
real (C_double), dimension(:), pointer :: Fptr real (C_double), dimension(:), pointer :: Fptr
integer :: nelements integer :: nelements
if ( allocated (compute) ) deallocate (compute)
! Check for the correct dimensionality ! Check for the correct dimensionality
if ( type == 0 ) then if ( type == 0 ) then
call lammps_error_all (ptr, FLERR, 'You cannot extract a compute& call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
@ -541,7 +549,6 @@ contains !! Wrapper functions local to this module {{{1
integer, intent(in) :: style, type integer, intent(in) :: style, type
double precision, dimension(:), allocatable :: d_compute double precision, dimension(:), allocatable :: d_compute
call lammps_extract_compute_dpa (d_compute, ptr, id, style, type) call lammps_extract_compute_dpa (d_compute, ptr, id, style, type)
if ( allocated (compute) ) deallocate (compute)
allocate (compute(size(d_compute))) allocate (compute(size(d_compute)))
compute = real(d_compute) compute = real(d_compute)
deallocate (d_compute) deallocate (d_compute)
@ -554,7 +561,6 @@ contains !! Wrapper functions local to this module {{{1
type (C_ptr) :: Cptr type (C_ptr) :: Cptr
real (C_double), dimension(:,:), pointer :: Fptr real (C_double), dimension(:,:), pointer :: Fptr
integer :: nr, nc integer :: nr, nc
if ( allocated (compute) ) deallocate (compute)
! Check for the correct dimensionality ! Check for the correct dimensionality
if ( type == 0 ) then if ( type == 0 ) then
call lammps_error_all (ptr, FLERR, 'You cannot extract a compute& call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
@ -580,7 +586,6 @@ contains !! Wrapper functions local to this module {{{1
integer, intent(in) :: style, type integer, intent(in) :: style, type
double precision, dimension(:,:), allocatable :: d_compute double precision, dimension(:,:), allocatable :: d_compute
call lammps_extract_compute_dp2a (d_compute, ptr, id, style, type) call lammps_extract_compute_dp2a (d_compute, ptr, id, style, type)
if ( allocated (compute) ) deallocate (compute)
allocate (compute(size(d_compute,1), size(d_compute,2))) allocate (compute(size(d_compute,1), size(d_compute,2)))
compute = real(d_compute) compute = real(d_compute)
deallocate (d_compute) deallocate (d_compute)
@ -658,7 +663,6 @@ contains !! Wrapper functions local to this module {{{1
type (C_ptr) :: Cptr type (C_ptr) :: Cptr
real (C_double), dimension(:), pointer :: Fptr real (C_double), dimension(:), pointer :: Fptr
integer :: fix_len integer :: fix_len
if ( allocated (fix) ) deallocate (fix)
! Check for the correct dimensionality ! Check for the correct dimensionality
if ( style == 0 ) then if ( style == 0 ) then
call lammps_error_all (ptr, FLERR, 'You can''t extract the& call lammps_error_all (ptr, FLERR, 'You can''t extract the&
@ -692,7 +696,6 @@ contains !! Wrapper functions local to this module {{{1
integer, intent(in) :: style, type, i, j integer, intent(in) :: style, type, i, j
double precision, dimension(:), allocatable :: d_fix double precision, dimension(:), allocatable :: d_fix
call lammps_extract_fix_dpa (d_fix, ptr, id, style, type, i, j) call lammps_extract_fix_dpa (d_fix, ptr, id, style, type, i, j)
if ( allocated (fix) ) deallocate (fix)
allocate (fix(size(d_fix))) allocate (fix(size(d_fix)))
fix = real(d_fix) fix = real(d_fix)
deallocate (d_fix) deallocate (d_fix)
@ -705,7 +708,6 @@ contains !! Wrapper functions local to this module {{{1
type (C_ptr) :: Cptr type (C_ptr) :: Cptr
real (C_double), dimension(:,:), pointer :: Fptr real (C_double), dimension(:,:), pointer :: Fptr
integer :: nr, nc integer :: nr, nc
if ( allocated (fix) ) deallocate (fix)
! Check for the correct dimensionality ! Check for the correct dimensionality
if ( style == 0 ) then if ( style == 0 ) then
call lammps_error_all (ptr, FLERR, 'It is not possible to extract the& call lammps_error_all (ptr, FLERR, 'It is not possible to extract the&
@ -735,7 +737,6 @@ contains !! Wrapper functions local to this module {{{1
integer, intent(in) :: style, type, i, j integer, intent(in) :: style, type, i, j
double precision, dimension(:,:), allocatable :: d_fix double precision, dimension(:,:), allocatable :: d_fix
call lammps_extract_fix_dp2a (d_fix, ptr, id, style, type, i, j) call lammps_extract_fix_dp2a (d_fix, ptr, id, style, type, i, j)
if ( allocated (fix) ) deallocate (fix)
allocate (fix(size(d_fix,1), size(d_fix,2))) allocate (fix(size(d_fix,1), size(d_fix,2)))
fix = real(d_fix) fix = real(d_fix)
deallocate (d_fix) deallocate (d_fix)
@ -824,7 +825,6 @@ contains !! Wrapper functions local to this module {{{1
Cptr = lammps_extract_variable_Cptr (ptr, name) Cptr = lammps_extract_variable_Cptr (ptr, name)
end if end if
natoms = lammps_get_natoms (ptr) natoms = lammps_get_natoms (ptr)
if ( allocated (variable) ) deallocate (variable)
allocate (variable(natoms)) allocate (variable(natoms))
call C_F_pointer (Cptr, Fptr, (/natoms/)) call C_F_pointer (Cptr, Fptr, (/natoms/))
variable = Fptr variable = Fptr
@ -845,7 +845,6 @@ contains !! Wrapper functions local to this module {{{1
Cptr = lammps_extract_variable_Cptr (ptr, name) Cptr = lammps_extract_variable_Cptr (ptr, name)
end if end if
natoms = lammps_get_natoms (ptr) natoms = lammps_get_natoms (ptr)
if ( allocated (variable) ) deallocate (variable)
allocate (variable(natoms)) allocate (variable(natoms))
call C_F_pointer (Cptr, Fptr, (/natoms/)) call C_F_pointer (Cptr, Fptr, (/natoms/))
variable = Fptr variable = Fptr
@ -863,7 +862,6 @@ contains !! Wrapper functions local to this module {{{1
else else
call lammps_extract_variable_dpa (d_var, ptr, name) call lammps_extract_variable_dpa (d_var, ptr, name)
end if end if
if ( allocated (variable) ) deallocate (variable)
allocate (variable(size(d_var))) allocate (variable(size(d_var)))
variable = real(d_var) variable = real(d_var)
deallocate (d_var) deallocate (d_var)
@ -871,32 +869,146 @@ contains !! Wrapper functions local to this module {{{1
!-------------------------------------------------------------------------2}}} !-------------------------------------------------------------------------2}}}
subroutine lammps_get_coords (ptr, coords) subroutine lammps_gather_atoms_ia (ptr, name, count, data)
type (C_ptr) :: ptr type (C_ptr), intent(in) :: ptr
double precision, dimension(:), allocatable :: coords character (len=*), intent(in) :: name
real (C_double), dimension(:), allocatable, target :: C_coords integer, intent(in) :: count
integer :: natoms integer, dimension(:), allocatable, intent(out) :: data
type (C_ptr) :: Cdata
integer (C_int), dimension(:), pointer :: Fdata
integer (C_int) :: natoms
character (kind=C_char), dimension(len_trim(name)) :: Cname
integer (C_int), parameter :: Ctype = 0
integer (C_int) :: Ccount
natoms = lammps_get_natoms (ptr) natoms = lammps_get_natoms (ptr)
if ( allocated(coords) ) deallocate (coords) Cname = string2Cstring (name)
allocate (coords(3*natoms)) if ( count /= 1 .and. count /= 3 ) then
allocate (C_coords(3*natoms)) call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
call lammps_actual_get_coords (ptr, C_loc(C_coords)) & count to be either 1 or 3')
coords = C_coords else
deallocate (C_coords) Ccount = count
end subroutine lammps_get_coords end if
allocate ( Fdata(count*natoms) )
allocate ( data(count*natoms) )
Cdata = C_loc (Fdata(1))
call lammps_actual_gather_atoms (ptr, Cname, Ctype, Ccount, Cdata)
data = Fdata
deallocate (Fdata)
end subroutine lammps_gather_atoms_ia
subroutine lammps_gather_atoms_dpa (ptr, name, count, data)
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: name
integer, intent(in) :: count
double precision, dimension(:), allocatable, intent(out) :: data
type (C_ptr) :: Cdata
real (C_double), dimension(:), pointer :: Fdata
integer (C_int) :: natoms
character (kind=C_char), dimension(len_trim(name)) :: Cname
integer (C_int), parameter :: Ctype = 1
integer (C_int) :: Ccount
natoms = lammps_get_natoms (ptr)
Cname = string2Cstring (name)
if ( count /= 1 .and. count /= 3 ) then
call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
& count to be either 1 or 3')
else
Ccount = count
end if
allocate ( Fdata(count*natoms) )
allocate ( data(count*natoms) )
Cdata = C_loc (Fdata(1))
call lammps_actual_gather_atoms (ptr, Cname, Ctype, Ccount, Cdata)
data = Fdata(:)
deallocate (Fdata)
end subroutine lammps_gather_atoms_dpa
subroutine lammps_gather_atoms_ra (ptr, name, count, data)
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: name
integer, intent(in) :: count
real, dimension(:), allocatable, intent(out) :: data
double precision, dimension(:), allocatable :: d_data
call lammps_gather_atoms_dpa (ptr, name, count, d_data)
allocate (data(size(d_data)))
data = d_data
deallocate (d_data)
end subroutine lammps_gather_atoms_ra
!----------------------------------------------------------------------------- !-----------------------------------------------------------------------------
subroutine lammps_put_coords (ptr, coords) subroutine lammps_scatter_atoms_ia (ptr, name, data)
type (C_ptr) :: ptr type (C_ptr), intent(in) :: ptr
double precision, dimension(:) :: coords character (len=*), intent(in) :: name
real (C_double), dimension(size(coords)) :: C_coords integer, dimension(:), intent(in) :: data
C_coords = coords integer (kind=C_int) :: natoms, Ccount
call lammps_actual_put_coords (ptr, C_coords) integer (kind=C_int), parameter :: Ctype = 0
end subroutine lammps_put_coords character (kind=C_char), dimension(len_trim(name)) :: Cname
integer, dimension(size(data)), target :: Fdata
type (C_ptr) :: Cdata
natoms = lammps_get_natoms (ptr)
Cname = string2Cstring (name)
Ccount = size(data) / natoms
if ( Ccount /= 1 .and. Ccount /= 3 ) &
call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
& count to be either 1 or 3')
Fdata = data
Cdata = C_loc (Fdata(1))
call lammps_actual_scatter_atoms (ptr, Cname, Ctype, Ccount, Cdata)
end subroutine lammps_scatter_atoms_ia
subroutine lammps_scatter_atoms_dpa (ptr, name, data)
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: name
double precision, dimension(:), intent(in) :: data
integer (kind=C_int) :: natoms, Ccount
integer (kind=C_int), parameter :: Ctype = 0
character (kind=C_char), dimension(len_trim(name)) :: Cname
double precision, dimension(size(data)), target :: Fdata
type (C_ptr) :: Cdata
natoms = lammps_get_natoms (ptr)
Cname = string2Cstring (name)
Ccount = size(data) / natoms
if ( Ccount /= 1 .and. Ccount /= 3 ) &
call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
& count to be either 1 or 3')
Fdata = data
Cdata = C_loc (Fdata(1))
call lammps_actual_scatter_atoms (ptr, Cname, Ctype, Ccount, Cdata)
end subroutine lammps_scatter_atoms_dpa
subroutine lammps_scatter_atoms_ra (ptr, name, data)
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: name
real, dimension(:), intent(out) :: data
double precision, dimension(size(data)) :: d_data
d_data = real (data, kind(d_data))
call lammps_scatter_atoms_dpa (ptr, name, d_data)
end subroutine lammps_scatter_atoms_ra
!----------------------------------------------------------------------------- !-----------------------------------------------------------------------------
! subroutine lammps_get_coords (ptr, coords)
! type (C_ptr) :: ptr
! double precision, dimension(:), allocatable, intent(out) :: coords
! real (C_double), dimension(:), allocatable, target :: C_coords
! integer :: natoms
! natoms = lammps_get_natoms (ptr)
! allocate (coords(3*natoms))
! allocate (C_coords(3*natoms))
! call lammps_actual_get_coords (ptr, C_loc(C_coords))
! coords = C_coords
! deallocate (C_coords)
! end subroutine lammps_get_coords
!
!!-----------------------------------------------------------------------------
!
! subroutine lammps_put_coords (ptr, coords)
! type (C_ptr) :: ptr
! double precision, dimension(:) :: coords
! real (C_double), dimension(size(coords)) :: C_coords
! C_coords = coords
! call lammps_actual_put_coords (ptr, C_coords)
! end subroutine lammps_put_coords
!
!!-----------------------------------------------------------------------------
function lammps_extract_compute_vectorsize (ptr, id, style) & function lammps_extract_compute_vectorsize (ptr, id, style) &
result (vectorsize) result (vectorsize)
integer :: vectorsize integer :: vectorsize

6
examples/COUPLE/fortran2/README
View File

@ -12,7 +12,7 @@ questions:
Karl D. Hammond Karl D. Hammond
University of Tennessee, Knoxville University of Tennessee, Knoxville
karlh at ugcs.caltech.edu karlh at ugcs.caltech.edu
karlh atutk.edu karlh at utk.edu
------------------------------------- -------------------------------------
@ -27,7 +27,7 @@ compile.
The following steps will work to compile this module (replace ${LAMMPS_SRC} The following steps will work to compile this module (replace ${LAMMPS_SRC}
with the path to your LAMMPS source directory): with the path to your LAMMPS source directory):
(1) Compile LAMMPS as a static library. Call the resulting file ${LAMMPS_LIB}, (1) Compile LAMMPS as a static library. Call the resulting file ${LAMMPS_LIB},
which will have an actual name lake liblammps_openmpi.a. If compiling which will have an actual name lake liblmp_openmpi.a. If compiling
using the MPI stubs in ${LAMMPS_SRC}/STUBS, you will need to know where using the MPI stubs in ${LAMMPS_SRC}/STUBS, you will need to know where
libmpi.a is as well (I'll call it ${MPI_STUBS} hereafter) libmpi.a is as well (I'll call it ${MPI_STUBS} hereafter)
(2) Copy said library to your Fortran program's source directory or include (2) Copy said library to your Fortran program's source directory or include
@ -61,7 +61,7 @@ with the path to your LAMMPS source directory):
need to have the .mod file from part (3). need to have the .mod file from part (3).
It is also possible to add LAMMPS.o and LAMMPS-wrapper.o into the It is also possible to add LAMMPS.o and LAMMPS-wrapper.o into the
LAMMPS library (e.g., liblammps_openmpi.a) instead of creating a separate LAMMPS library (e.g., liblmp_openmpi.a) instead of creating a separate
library, like so: library, like so:
ar rs ${LAMMPS_LIB} LAMMPS.o LAMMPS-wrapper.o ar rs ${LAMMPS_LIB} LAMMPS.o LAMMPS-wrapper.o
In this case, you can now use the Fortran wrapper functions as if they In this case, you can now use the Fortran wrapper functions as if they

2
examples/COUPLE/fortran2/makefile
View File

@ -1,7 +1,7 @@
SHELL = /bin/sh SHELL = /bin/sh
# Path to LAMMPS extraction directory # Path to LAMMPS extraction directory
LAMMPS_ROOT = ../svn-dist LAMMPS_ROOT = ../../..
LAMMPS_SRC = $(LAMMPS_ROOT)/src LAMMPS_SRC = $(LAMMPS_ROOT)/src
# Remove the line below if using mpicxx/mpic++ as your C++ compiler # Remove the line below if using mpicxx/mpic++ as your C++ compiler

66
python/install.py
View File

@ -1,35 +1,67 @@
#!/usr/local/bin/python #!/usr/local/bin/python
# copy LAMMPS shared library src/liblammps.so and lammps.py to system dirs # copy LAMMPS src/liblammps.so and lammps.py to system dirs
# Syntax: python install.py [libdir] [pydir]
# libdir = target dir for src/liblammps.so, default = /usr/local/lib
# pydir = target dir for lammps.py, default = Python site-packages dir
import sys,commands instructions = """
Syntax: python install.py [-h] [libdir] [pydir]
libdir = target dir for src/liblammps.so, default = /usr/local/lib
pydir = target dir for lammps.py, default = Python site-packages dir
"""
if len(sys.argv) > 3: import sys,os,commands
print "Syntax: python install.py [libdir] [pydir]"
if (len(sys.argv) > 1 and sys.argv[1] == "-h") or len(sys.argv) > 3:
print instructions
sys.exit() sys.exit()
if len(sys.argv) >= 2: libdir = sys.argv[1] if len(sys.argv) >= 2: libdir = sys.argv[1]
else: libdir = "/usr/local/lib" else: libdir = "/usr/local/lib"
if len(sys.argv) == 3: pydir = sys.argv[2] if len(sys.argv) == 3: pydir = sys.argv[2]
else: pydir = ""
# copy C lib to libdir if it exists
# warn if not in LD_LIBRARY_PATH or LD_LIBRARY_PATH is undefined
if not os.path.isdir(libdir):
print "ERROR: libdir %s does not exist" % libdir
sys.exit()
if "LD_LIBRARY_PATH" not in os.environ:
print "WARNING: LD_LIBRARY_PATH undefined, cannot check libdir %s" % libdir
else: else:
paths = sys.path libpaths = os.environ['LD_LIBRARY_PATH'].split(':')
for i,path in enumerate(paths): if libdir not in libpaths:
index = path.rfind("site-packages") print "WARNING: libdir %s not in LD_LIBRARY_PATH" % libdir
if index < 0: continue
if index == len(path) - len("site-packages"): break
pydir = paths[i]
str = "cp ../src/liblammps.so %s" % libdir str = "cp ../src/liblammps.so %s" % libdir
print str print str
outstr = commands.getoutput(str) outstr = commands.getoutput(str)
if len(outstr.strip()): print outstr if len(outstr.strip()): print outstr
str = "cp ../python/lammps.py %s" % pydir # copy lammps.py to pydir if it exists
print str # if pydir not specified, install in site-packages via distutils setup()
outstr = commands.getoutput(str)
if len(outstr.strip()): print outstr
if pydir:
if not os.path.isdir(pydir):
print "ERROR: pydir %s does not exist" % pydir
sys.exit()
str = "cp ../python/lammps.py %s" % pydir
print str
outstr = commands.getoutput(str)
if len(outstr.strip()): print outstr
sys.exit()
print "installing lammps.py in Python site-packages dir"
os.chdir('../python') # in case invoked via make in src dir
from distutils.core import setup
sys.argv = ["setup.py","install"] # as if had run "python setup.py install"
setup(name = "lammps",
version = "15Aug12",
author = "Steve Plimpton",
author_email = "sjplimp@sandia.gov",
url = "http://lammps.sandia.gov",
description = "LAMMPS molecular dynamics library",
py_modules = ["lammps"])

4
python/lammps.py
View File

@ -13,7 +13,7 @@
# Python wrapper on LAMMPS library via ctypes # Python wrapper on LAMMPS library via ctypes
import types import sys,traceback,types
from ctypes import * from ctypes import *
import os.path import os.path
@ -27,6 +27,8 @@ class lammps:
if not name: self.lib = CDLL("liblammps.so") if not name: self.lib = CDLL("liblammps.so")
else: self.lib = CDLL("liblammps_%s.so" % name) else: self.lib = CDLL("liblammps_%s.so" % name)
except: except:
type,value,tb = sys.exc_info()
traceback.print_exception(type,value,tb)
raise OSError,"Could not load LAMMPS dynamic library" raise OSError,"Could not load LAMMPS dynamic library"
# create an instance of LAMMPS # create an instance of LAMMPS

4
src/KSPACE/fft3d_wrap.h
View File

@ -39,6 +39,8 @@ class FFT3d : protected Pointers {
E: Could not create 3d FFT plan E: Could not create 3d FFT plan
The FFT setup in pppm failed. The FFT setup for the PPPM solver failed, typically due
to lack of memory. This is an unusual error. Check the
size of the FFT grid you are requesting.
*/ */

1
src/KSPACE/pppm.cpp
View File

@ -100,7 +100,6 @@ PPPM::PPPM(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
// see JCP 109, pg 7698 for derivation of coefficients // see JCP 109, pg 7698 for derivation of coefficients
// higher order coefficients may be computed if needed // higher order coefficients may be computed if needed
memory->destroy(acons);
memory->create(acons,8,7,"pppm:acons"); memory->create(acons,8,7,"pppm:acons");
acons[1][0] = 2.0 / 3.0; acons[1][0] = 2.0 / 3.0;
acons[2][0] = 1.0 / 50.0; acons[2][0] = 1.0 / 50.0;

3
src/MAKE/Makefile.g++
View File

@ -85,9 +85,6 @@ $(EXE): $(OBJ)
lib: $(OBJ) lib: $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
#shlib: $(OBJ)
# $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
shlib: $(OBJ) shlib: $(OBJ)
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
$(OBJ) $(EXTRA_LIB) $(LIB) $(OBJ) $(EXTRA_LIB) $(LIB)

4
src/Make.sh
View File

@ -1,6 +1,8 @@
# Make.sh = update Makefile.lib or Makefile.list or style_*.h files # Make.sh = update Makefile.lib, Makefile.shlib, Makefile.list
# or style_*.h files
# Syntax: sh Make.sh style # Syntax: sh Make.sh style
# sh Make.sh Makefile.lib # sh Make.sh Makefile.lib
# sh Make.sh Makefile.shlib
# sh Make.sh Makefile.list # sh Make.sh Makefile.list
# function to create one style_*.h file # function to create one style_*.h file

2
src/Makefile
View File

@ -130,7 +130,7 @@ makelist:
@$(SHELL) Make.sh style @$(SHELL) Make.sh style
@$(SHELL) Make.sh Makefile.list @$(SHELL) Make.sh Makefile.list
# install LAMMPS shared lib and Python wrapper in Python # install LAMMPS shared lib and Python wrapper for Python usage
install-python: install-python:
@python ../python/install.py @python ../python/install.py

3
src/Makefile.lib
View File

@ -21,9 +21,6 @@ help:
@files="`ls MAKE/Makefile.*`"; \ @files="`ls MAKE/Makefile.*`"; \
for file in $$files; do head -1 $$file; done for file in $$files; do head -1 $$file; done
clean:
rm -rf Obj_*
.DEFAULT: .DEFAULT:
@test -f MAKE/Makefile.$@ @test -f MAKE/Makefile.$@
@if [ ! -d Obj_$@ ]; then mkdir Obj_$@; fi @if [ ! -d Obj_$@ ]; then mkdir Obj_$@; fi

3
src/Makefile.list
View File

@ -21,9 +21,6 @@ help:
@files="`ls MAKE/Makefile.*`"; \ @files="`ls MAKE/Makefile.*`"; \
for file in $$files; do head -1 $$file; done for file in $$files; do head -1 $$file; done
clean:
rm -rf Obj_*
.DEFAULT: .DEFAULT:
@test -f MAKE/Makefile.$@ @test -f MAKE/Makefile.$@
@if [ ! -d Obj_$@ ]; then mkdir Obj_$@; fi @if [ ! -d Obj_$@ ]; then mkdir Obj_$@; fi

6
src/Makefile.shlib
View File

File diff suppressed because one or more lines are too long

2
src/USER-CUDA/cuda.cpp
View File

@ -410,6 +410,8 @@ void Cuda::setDomainParams()
cu_domain->boxlo_lamda[i] = domain->boxlo_lamda[i]; cu_domain->boxlo_lamda[i] = domain->boxlo_lamda[i];
cu_domain->boxhi_lamda[i] = domain->boxhi_lamda[i]; cu_domain->boxhi_lamda[i] = domain->boxhi_lamda[i];
cu_domain->prd_lamda[i] = domain->prd_lamda[i]; cu_domain->prd_lamda[i] = domain->prd_lamda[i];
cu_domain->sublo[i] = domain->sublo_lamda[i];
cu_domain->subhi[i] = domain->subhi_lamda[i];
} }
cu_domain->xy = domain->xy; cu_domain->xy = domain->xy;

2
src/USER-OMP/pair_lj_expand_omp.h
View File

@ -17,7 +17,7 @@
#ifdef PAIR_CLASS #ifdef PAIR_CLASS
PairStyle(lj/cut/omp,PairLJExpandOMP) PairStyle(lj/expand/omp,PairLJExpandOMP)
#else #else

23
src/library.cpp
View File

@ -30,7 +30,9 @@
#include "modify.h" #include "modify.h"
#include "compute.h" #include "compute.h"
#include "fix.h" #include "fix.h"
#include "comm.h"
#include "memory.h" #include "memory.h"
#include "error.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -383,8 +385,13 @@ void lammps_gather_atoms(void *ptr, char *name,
// error if tags are not defined or not consecutive // error if tags are not defined or not consecutive
if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) return; int flag = 0;
if (lmp->atom->natoms > MAXSMALLINT) return; if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) flag = 1;
if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (flag && lmp->comm->me == 0) {
lmp->error->warning(FLERR,"Library error in lammps_gather_atoms");
return;
}
int natoms = static_cast<int> (lmp->atom->natoms); int natoms = static_cast<int> (lmp->atom->natoms);
@ -464,10 +471,16 @@ void lammps_scatter_atoms(void *ptr, char *name,
{ {
LAMMPS *lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
// error if tags are not defined or not consecutive // error if tags are not defined or not consecutive or no atom map
if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) return; int flag = 0;
if (lmp->atom->natoms > MAXSMALLINT) return; if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) flag = 1;
if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (lmp->atom->map_style == 0) flag = 1;
if (flag && lmp->comm->me == 0) {
lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms");
return;
}
int natoms = static_cast<int> (lmp->atom->natoms); int natoms = static_cast<int> (lmp->atom->natoms);