you have not pre-built the necessary add-on LAMMPS library
+- you are including a package that needs an extra library, but have not pre-built the necessary package library
- you are linking to a library that doesn't exist on your system
- you are not linking to the necessary system library
@@ -166,40 +166,64 @@
Editing a new low-level Makefile.foo:
These are the issues you need to address when editing a low-level
-Makefile for your machine. The only portion of the file you should
-need to edit is the first line and the "System-specific Settings"
-section, which has two parts. The first part lists additional system
-libraries needed by certain LAMMPS libraries; see (2). The second
-part is compiler and linker settings, as well as MPI and FFT settings;
-see (3-9).
+Makefile for your machine. The portions of the file you typically
+need to edit are the first line, the "compiler/linker settings"
+section, and the "system-specific settings" section.
(1) Change the first line of Makefile.foo to list the word "foo" after
the "#", and whatever other options you set. This is the line you
will see if you just type "make".
-(2) The system library section can be ignored unless you are building
-LAMMPS with one or more of the listed LAMMPS packages that use these
-libraries. See the section below for more details. The
-SYSLIB settings are the libraries themselves. The SYSLIBPATH settings
-are where they are located on your machine, which is typically only
-needed if they are in some non-standard place, that is not in your
-library search path.
-
-(3) Set the paths and flags for your C++ compiler, including
-optimization flags. You can use g++, the open-source GNU compiler,
-which is available on all Unix systems. Vendor compilers often
-produce faster code. On boxes with Intel CPUs, we suggest using the
-free Intel icc compiler, which you can download from Intel's compiler
-site.
+
(3) The "compiler/linker settings" section lists compiler and linker
+settings for your C++ compiler, including optimization flags. You can
+use g++, the open-source GNU compiler, which is available on all Unix
+systems. You can also use mpicc which will typically be available if
+MPI is installed on your system, though you should check which actual
+compiler it wraps. Vendor compilers often produce faster code. On
+boxes with Intel CPUs, we suggest using the free Intel icc compiler,
+which you can download from Intel's compiler site.
-(4) If you want LAMMPS to run in parallel, you must have an MPI
-library installed on your platform. If you do not use "mpicc" as your
-compiler/linker, then Makefile.foo needs to specify where the mpi.h
-file (-I switch) and the libmpi.a library (-L switch) is found. If
-you are installing MPI yourself, we recommend Argonne's MPICH 1.2
-which can be downloaded from the Argonne MPI
+If building a C++ code on your machine requires additional libraries,
+then you should list them as part of the LIB variable.
+
+The DEPFLAGS setting is what triggers the C++ compiler to create a
+dependency list for a source file. This speeds re-compilation when
+source (*.cpp) or header (*.h) files are edited. Some compilers do
+not support dependency file creation, or may use a different switch
+than -D. GNU g++ works with -D. If your compiler can't create
+dependency files (a long list of errors involving *.d files), then
+you'll need to create a Makefile.foo patterned after Makefile.storm,
+which uses different rules that do not involve dependency files.
+
+(3) The "system-specific settings" section has 4 parts.
+
+(3.a) The LMP_INC variable is used to include options that turn on
+system-dependent ifdefs within the LAMMPS code.
+
+The read_data and dump commands will read/write gzipped files if you
+compile with -DLAMMPS_GZIP. It requires that your Unix support the
+"popen" command. Using one of the -DPACK_ARRAY, -DPACK_POINTER, and
+-DPACK_MEMCPY options can make for faster parallel FFTs (in the PPPM
+solver) on some platforms. The -DPACK_ARRAY setting is the default.
+If you use -DLAMMPS_XDR, the build will include XDR compatibility
+files for doing particle dumps in XTC format. This is only necessary
+if your platform does have its own XDR files available. See the
+Restrictions section of the dump command for details.
+
+(3.b) The 3 MPI variables are used to specify an MPI library to build
+LAMMPS with.
+
+If you want LAMMPS to run in parallel, you must have an MPI library
+installed on your platform. If you use an MPI-wrapped compiler, such
+as "mpicc" to build LAMMPS, you can probably leave these 3 variables
+blank. If you do not use "mpicc" as your compiler/linker, then you
+need to specify where the mpi.h file (MPI_INC) and the MPI library
+(MPI_PATH) is found and its name (MPI_LIB).
+
+If you are installing MPI yourself, we recommend Argonne's MPICH 1.2
+or 2.0 which can be downloaded from the Argonne MPI
site. LAM MPI should also work. If
you are running on a big parallel platform, your system people or the
vendor should have already installed a version of MPI, which will be
@@ -207,16 +231,16 @@
If you use MPICH or LAM, you will have to configure and build it for
your platform. The MPI configure script should have compiler options
to enable you to use the same compiler you are using for the LAMMPS
-build, which can avoid problems that may arise when linking LAMMPS to
+build, which can avoid problems that can arise when linking LAMMPS to
the MPI library.
-(5) If you just want LAMMPS to run on a single processor, you can use
-the STUBS library in place of MPI, since you don't need an MPI library
+
If you just want LAMMPS to run on a single processor, you can use the
+STUBS library in place of MPI, since you don't need an MPI library
installed on your system. See the Makefile.serial file for how to
-specify the -I and -L switches. You will also need to build the STUBS
+specify the 3 MPI variables. You will also need to build the STUBS
library for your platform before making LAMMPS itself. From the STUBS
dir, type "make" and it will hopefully create a libmpi.a suitable for
-linking to LAMMPS. If the build fails, you will need to edit the
+linking to LAMMPS. If this build fails, you will need to edit the
STUBS/Makefile for your platform.
The file STUBS/mpi.cpp has a CPU timer function MPI_Wtime() that calls
@@ -225,52 +249,46 @@
ANSI-standard function clock() rolls over after an hour or so, and is
therefore insufficient for timing long LAMMPS simulations.
-(6) If you want to use the particle-particle particle-mesh (PPPM)
-option in LAMMPS for long-range Coulombics, you must have a 1d FFT
-library installed on your platform. This is specified by a switch of
-the form -DFFT_XXX where XXX = INTEL, DEC, SGI, SCSL, or FFTW. All
-but the last one are native vendor-provided libraries. FFTW is a
-fast, portable library that should work on any platform. You can
-download it from www.fftw.org. Use version
-2.1.X, not the newer 3.0.X. Building FFTW for your box should be as
-simple as ./configure; make. Whichever FFT library you have on your
-platform, you'll need to set the appropriate -I and -L switches in
+
(3.c) The 3 FFT variables are used to specify an FFT library which
+LAMMPS uses when using the particle-particle particle-mesh (PPPM)
+option in LAMMPS for long-range Coulombics via the
+kspace_style command.
+
+To use this option, you must have a 1d FFT library installed on your
+platform. This is specified by a switch of the form -DFFT_XXX where
+XXX = INTEL, DEC, SGI, SCSL, or FFTW. All but the last one are native
+vendor-provided libraries. FFTW is a fast, portable library that
+should work on any platform. You can download it from
+www.fftw.org. Use version 2.1.X, not the newer
+3.0.X. Building FFTW for your box should be as simple as ./configure;
+make. Whichever FFT library you have on your platform, you'll need to
+set the appropriate FFT_INC, FFT_PATH, and FFT_LIB variables in
Makefile.foo.
-If you examine fft3d.c and fft3d.h you'll see it's possible to add
-other vendor FFT libraries via #ifdef statements in the appropriate
-places. If you successfully add a new FFT option, like -DFFT_IBM,
-please send the developers an email; we'd
-like to add it to LAMMPS.
-
-(7) If you don't plan to use PPPM, you don't need an FFT library. Use
-a -DFFT_NONE switch in the CCFLAGS setting of Makefile.foo, or exclude
-the KSPACE package (see below).
-
-(8) There are a few other -D compiler switches you can set as part of
-CCFLAGS. The read_data and dump commands will read/write gzipped
-files if you compile with -DLAMMPS_GZIP. It requires that your Unix
-support the "popen" command. Using one of the -DPACK_ARRAY,
--DPACK_POINTER, and -DPACK_MEMCPY options can make for faster parallel
-FFTs (in the PPPM solver) on some platforms. The -DPACK_ARRAY setting
-is the default. If you compile with -DLAMMPS_XDR, the build will
-include XDR compatibility files for doing particle dumps in XTC
-format. This is only necessary if your platform does have its own XDR
-files available. See the Restrictions section of the dump
-command for details.
-
-(9) The DEPFLAGS setting is how the C++ compiler creates a dependency
-file for each source file. This speeds re-compilation when source
-(*.cpp) or header (*.h) files are edited. Some compilers do not
-support dependency file creation, or may use a different switch than
--D. GNU g++ works with -D. If your compiler can't create dependency
-files (a long list of errors involving *.d files), then you'll need to
-create a Makefile.foo patterned after Makefile.tflop, which uses
-different rules that do not involve dependency files.
+
If you examine src/fft3d.c and src.fft3d.h you'll see it's possible to
+add other vendor FFT libraries via #ifdef statements in the
+appropriate places. If you successfully add a new FFT option, like
+-DFFT_IBM, please send the LAMMPS developers an email; we'd like to
+add it to LAMMPS.
+
+If you don't plan to use PPPM, you don't need an FFT library. In this
+case you can set FFT_INC to -DFFT_NONE and leave the other 2 FFT
+variables blank. Or you can exclude the KSPACE package when you build
+LAMMPS (see below).
+
+(3.d) The several SYSLIB and SYSPATH variables can be ignored unless
+you are building LAMMPS with one or more of the LAMMPS packages that
+require these extra system libraries. The names of these packages are
+the prefixes on the SYSLIB and SYSPATH variables. See the section
+below for more details. The SYSLIB variables list the system
+libraries. The SYSPATH variables are where they are located on your
+machine, which is typically only needed if they are in some
+non-standard place, that is not in your library search path.
That's it. Once you have a correct Makefile.foo and you have
-pre-built the MPI and FFT libraries it will use, all you need to do
-from the src directory is type one of these 2 commands:
+pre-built any other libraries it will use (e.g. MPI, FFT, package
+libraries), all you need to do from the src directory is type one of
+these 2 commands:
make foo
gmake foo
@@ -289,8 +307,9 @@
(2) Cleaning up.
-Typing "make clean" will delete all *.o object files created when
-LAMMPS is built.
+
Typing "make clean-all" or "make clean-foo" will delete *.o object
+files created when LAMMPS is built, for either all builds or for a
+particular machine.
(3) On some machines with some compiler options, the Coulomb tabling
option that is enabled by default for "long" pair
@@ -321,11 +340,17 @@
(4) Building for a Mac.
-OS X is BSD Unix, so it already works. See the Makefile.mac file.
+
OS X is BSD Unix, so it should just work. See the Makefile.mac file.
(5) Building for MicroSoft Windows.
-I've never done this, but LAMMPS is just standard C++ with MPI and FFT
+
The LAMMPS download page has an option to download a pre-built Windows
+exeutable. See below for instructions for running this executable on
+a Windows box.
+
+If the pre-built executable doesn't have the options you want, then
+you should be able to build LAMMPS from source files on a Windows box.
+I've never done this, but LAMMPS is just standard C++ with MPI and FFT
calls. You can use cygwin to build LAMMPS with a Unix make; see
Makefile.cygwin. Or you should be able to pull all the source files
into Visual C++ (ugh) or some similar development environment and
@@ -402,8 +427,8 @@
Any or all packages can be included or excluded independently BEFORE
LAMMPS is built.
-Note: The two exceptions to this are the "gpu" and "opt" packages.
-Some of the files in these packages require other packages to also be
+
The two exceptions to this are the "gpu" and "opt" packages. Some of
+the files in these packages require other packages to also be
included. If this is not the case, then those subsidiary files in
"gpu" and "opt" will not be installed either. To install all the
files in package "gpu", the "asphere" package must also be installed.
@@ -416,8 +441,7 @@
which may run a bit faster.
By default, LAMMPS includes only the "kspace", "manybody", and
-"molecule" packages. As described below, some standard packages
-require LAMMPS be linked to separately built libraries.
+"molecule" packages.
Packages are included or excluded by typing "make yes-name" or "make
no-name", where "name" is the name of the package. You can also type
@@ -449,16 +473,16 @@
Packages that require extra LAMMPS libraries:
-
A few packages (standard or user) require that add-on libraries be
+
A few packages (standard or user) require that additional libraries be
compiled first, which LAMMPS will link to when it builds. The source
code for these libraries are included in the LAMMPS distribution under
the "lib" directory. Look at the README files in the lib directories
(e.g. lib/reax/README) for instructions on how to build each library.
-IMPORTANT NOTE: If you have included a package that uses
-one of the libraries, then you must build the library BEFORE
-building LAMMPS itself, as the LAMMPS build will link with
-the library file.
+
IMPORTANT NOTE: If you are including a package in your LAMMPS build
+that uses one of these libraries, then you must build the library
+BEFORE building LAMMPS itself, since the LAMMPS build will attempt to
+link with the library file.
Here is a bit of information about each library:
@@ -526,37 +550,37 @@
After the desired library or libraries are built, and the package has
been included, you can build LAMMPS itself. For example, from the
lammps/src directory you would type this, to build LAMMPS with ReaxFF.
-Note that the library itself, namely lib/reax/libreax.a, must already
-have been built, as dicussed in the preceding section, for the
-LAMMPS build to be successful.
+Note that as discussed in the preceding section, the package library
+itself, namely lib/reax/libreax.a, must already have been built, for
+the LAMMPS build to be successful.
make yes-reax
make g++
-Note that simply building the library is not sufficient to use it from
-LAMMPS. You must also include the package that uses and wraps the
-library before you build LAMMPS itself.
+
Also note that simply building the library is not sufficient to use it
+from LAMMPS. As in this example, you must also include the package
+that uses and wraps the library before you build LAMMPS itself.
-As discussed in point (2) of this section above, there are
+
As discussed in point (2.4) of this section above, there are
settings in the low-level Makefile that specify additional system
libraries needed by individual LAMMPS add-on libraries. These are the
settings you must specify correctly in your low-level Makefile in
lammps/src/MAKE, such as Makefile.foo:
To use the gpu package and library, the settings for gpu_SYSLIB and
-gpu_SYSLIBPATH must be correct. These are specific to the NVIDIA CUDA
+gpu_SYSPATH must be correct. These are specific to the NVIDIA CUDA
software which must be installed on your system.
To use the meam or reax packages and their libraries which are Fortran
-based, the settings for meam_SYSLIB, reax_SYSLIB, meam_SYSLIBPATH, and
-reax_SYSLIBPATH must be correct. This is so that the C++ compiler can
+based, the settings for meam_SYSLIB, reax_SYSLIB, meam_SYSPATH, and
+reax_SYSPATH must be correct. This is so that the C++ compiler can
perform a cross-language link using the appropriate system Fortran
libraries.
To use the user-atc package and library, the settings for
-user-atc_SYSLIB and user-atc_SYSLIBPATH must be correct. This is so
-that the appropriate BLAS and LAPACK libs, used by the user-atc
-library, can be found.
+user-atc_SYSLIB and user-atc_SYSPATH must be correct. This is so that
+the appropriate BLAS and LAPACK libs, used by the user-atc library,
+can be found.
diff -Naur lammps-25Oct09/doc/Section_start.txt lammps-29Oct09/doc/Section_start.txt
--- lammps-25Oct09/doc/Section_start.txt 2009-10-26 17:21:50.000000000 -0600
+++ lammps-29Oct09/doc/Section_start.txt 2009-10-29 15:37:40.000000000 -0600
@@ -49,8 +49,8 @@
lmp_windows.exe :pre
-Skip to the "Running LAMMPS"_#2_5 section, to learn how to launch it
-on a Windows box.
+Skip to the "Running LAMMPS"_#2_5 section, to learn how to launch this
+executable on a Windows box.
Note that this executable does not include an MPI or FFT library, so
it can only be run on a single processor and it cannot perform
@@ -61,8 +61,8 @@
bug-fixes/upgrades listed on "this
page"_http://lammps.sandia.gov/bug.html up to a certain date, as
stated on the download page. If you want something with more packages
-or more current, you'll have to download the source tarball and build
-it yourself, as described in the next section.
+or that is more current, you'll have to download the source tarball
+and build it yourself, as described in the next section.
:line
@@ -72,7 +72,7 @@
"Read this first"_#2_2_1
"Building a LAMMPS executable"_#2_2_2
-"Errors that can occur when making LAMMPS"_#2_2_3
+"Common errors that can occur when making LAMMPS"_#2_2_3
"Editing a new low-level Makefile"_#2_2_4
"Additional build tips"_#2_2_5 :ul
@@ -95,9 +95,9 @@
please send an email to the
"developers"_http://lammps.sandia.gov/authors.html.
-If you succeed in building LAMMPS on a new kind of machine (which
-there isn't a similar Makefile for in the distribution), send it to
-the developers and we'll include it in future LAMMPS releases.
+If you succeed in building LAMMPS on a new kind of machine, for which
+there isn't a similar Makefile for in the src/MAKE directory, send it
+to the developers and we'll include it in future LAMMPS releases.
:line
@@ -115,14 +115,14 @@
Note that on a multi-processor or multi-core platform you can launch a
parallel make, by using the "-j" switch with the make command, which
-will typically build LAMMPS more quickly.
+will build LAMMPS more quickly.
If you get no errors and an executable like lmp_linux or lmp_mac is
produced, you're done; it's your lucky day.
:line
-[{Errors that can occur when making LAMMPS:}] :link(2_2_3)
+[{Common errors that can occur when making LAMMPS:}] :link(2_2_3)
(1) If the make command breaks immediately with errors that indicate
it can't find files with a "*" in their names, this can be because
@@ -141,14 +141,14 @@
(2) Other errors typically occur because the low-level Makefile isn't
setup correctly for your machine. If your platform is named "foo",
-you need to create a Makefile.foo in the MAKE sub-directory. Use
+you will need to create a Makefile.foo in the MAKE sub-directory. Use
whatever existing file is closest to your platform as a starting
point. See the next section for more instructions.
(3) If you get a link-time error about missing libraries or missing
dependencies, then it can be because:
-you have not pre-built the necessary "add-on LAMMPS library"_#2_3_3
+you are including a package that needs an extra library, but have not pre-built the necessary "package library"_#2_3_3
you are linking to a library that doesn't exist on your system
you are not linking to the necessary system library :ul
@@ -161,40 +161,64 @@
[{Editing a new low-level Makefile.foo:}] :link(2_2_4)
These are the issues you need to address when editing a low-level
-Makefile for your machine. The only portion of the file you should
-need to edit is the first line and the "System-specific Settings"
-section, which has two parts. The first part lists additional system
-libraries needed by certain LAMMPS libraries; see (2). The second
-part is compiler and linker settings, as well as MPI and FFT settings;
-see (3-9).
+Makefile for your machine. The portions of the file you typically
+need to edit are the first line, the "compiler/linker settings"
+section, and the "system-specific settings" section.
(1) Change the first line of Makefile.foo to list the word "foo" after
the "#", and whatever other options you set. This is the line you
will see if you just type "make".
-(2) The system library section can be ignored unless you are building
-LAMMPS with one or more of the listed LAMMPS packages that use these
-libraries. See the "section below"_#2_3_4 for more details. The
-SYSLIB settings are the libraries themselves. The SYSLIBPATH settings
-are where they are located on your machine, which is typically only
-needed if they are in some non-standard place, that is not in your
-library search path.
-
-(3) Set the paths and flags for your C++ compiler, including
-optimization flags. You can use g++, the open-source GNU compiler,
-which is available on all Unix systems. Vendor compilers often
-produce faster code. On boxes with Intel CPUs, we suggest using the
-free Intel icc compiler, which you can download from "Intel's compiler
-site"_intel.
+(3) The "compiler/linker settings" section lists compiler and linker
+settings for your C++ compiler, including optimization flags. You can
+use g++, the open-source GNU compiler, which is available on all Unix
+systems. You can also use mpicc which will typically be available if
+MPI is installed on your system, though you should check which actual
+compiler it wraps. Vendor compilers often produce faster code. On
+boxes with Intel CPUs, we suggest using the free Intel icc compiler,
+which you can download from "Intel's compiler site"_intel.
:link(intel,http://www.intel.com/software/products/noncom)
-(4) If you want LAMMPS to run in parallel, you must have an MPI
-library installed on your platform. If you do not use "mpicc" as your
-compiler/linker, then Makefile.foo needs to specify where the mpi.h
-file (-I switch) and the libmpi.a library (-L switch) is found. If
-you are installing MPI yourself, we recommend Argonne's MPICH 1.2
-which can be downloaded from the "Argonne MPI
+If building a C++ code on your machine requires additional libraries,
+then you should list them as part of the LIB variable.
+
+The DEPFLAGS setting is what triggers the C++ compiler to create a
+dependency list for a source file. This speeds re-compilation when
+source (*.cpp) or header (*.h) files are edited. Some compilers do
+not support dependency file creation, or may use a different switch
+than -D. GNU g++ works with -D. If your compiler can't create
+dependency files (a long list of errors involving *.d files), then
+you'll need to create a Makefile.foo patterned after Makefile.storm,
+which uses different rules that do not involve dependency files.
+
+(3) The "system-specific settings" section has 4 parts.
+
+(3.a) The LMP_INC variable is used to include options that turn on
+system-dependent ifdefs within the LAMMPS code.
+
+The read_data and dump commands will read/write gzipped files if you
+compile with -DLAMMPS_GZIP. It requires that your Unix support the
+"popen" command. Using one of the -DPACK_ARRAY, -DPACK_POINTER, and
+-DPACK_MEMCPY options can make for faster parallel FFTs (in the PPPM
+solver) on some platforms. The -DPACK_ARRAY setting is the default.
+If you use -DLAMMPS_XDR, the build will include XDR compatibility
+files for doing particle dumps in XTC format. This is only necessary
+if your platform does have its own XDR files available. See the
+Restrictions section of the "dump"_dump.html command for details.
+
+(3.b) The 3 MPI variables are used to specify an MPI library to build
+LAMMPS with.
+
+If you want LAMMPS to run in parallel, you must have an MPI library
+installed on your platform. If you use an MPI-wrapped compiler, such
+as "mpicc" to build LAMMPS, you can probably leave these 3 variables
+blank. If you do not use "mpicc" as your compiler/linker, then you
+need to specify where the mpi.h file (MPI_INC) and the MPI library
+(MPI_PATH) is found and its name (MPI_LIB).
+
+If you are installing MPI yourself, we recommend Argonne's MPICH 1.2
+or 2.0 which can be downloaded from the "Argonne MPI
site"_http://www-unix.mcs.anl.gov/mpi. LAM MPI should also work. If
you are running on a big parallel platform, your system people or the
vendor should have already installed a version of MPI, which will be
@@ -202,16 +226,16 @@
If you use MPICH or LAM, you will have to configure and build it for
your platform. The MPI configure script should have compiler options
to enable you to use the same compiler you are using for the LAMMPS
-build, which can avoid problems that may arise when linking LAMMPS to
+build, which can avoid problems that can arise when linking LAMMPS to
the MPI library.
-(5) If you just want LAMMPS to run on a single processor, you can use
-the STUBS library in place of MPI, since you don't need an MPI library
+If you just want LAMMPS to run on a single processor, you can use the
+STUBS library in place of MPI, since you don't need an MPI library
installed on your system. See the Makefile.serial file for how to
-specify the -I and -L switches. You will also need to build the STUBS
+specify the 3 MPI variables. You will also need to build the STUBS
library for your platform before making LAMMPS itself. From the STUBS
dir, type "make" and it will hopefully create a libmpi.a suitable for
-linking to LAMMPS. If the build fails, you will need to edit the
+linking to LAMMPS. If this build fails, you will need to edit the
STUBS/Makefile for your platform.
The file STUBS/mpi.cpp has a CPU timer function MPI_Wtime() that calls
@@ -220,52 +244,46 @@
ANSI-standard function clock() rolls over after an hour or so, and is
therefore insufficient for timing long LAMMPS simulations.
-(6) If you want to use the particle-particle particle-mesh (PPPM)
-option in LAMMPS for long-range Coulombics, you must have a 1d FFT
-library installed on your platform. This is specified by a switch of
-the form -DFFT_XXX where XXX = INTEL, DEC, SGI, SCSL, or FFTW. All
-but the last one are native vendor-provided libraries. FFTW is a
-fast, portable library that should work on any platform. You can
-download it from "www.fftw.org"_http://www.fftw.org. Use version
-2.1.X, not the newer 3.0.X. Building FFTW for your box should be as
-simple as ./configure; make. Whichever FFT library you have on your
-platform, you'll need to set the appropriate -I and -L switches in
+(3.c) The 3 FFT variables are used to specify an FFT library which
+LAMMPS uses when using the particle-particle particle-mesh (PPPM)
+option in LAMMPS for long-range Coulombics via the
+"kspace_style"_kspace_style.html command.
+
+To use this option, you must have a 1d FFT library installed on your
+platform. This is specified by a switch of the form -DFFT_XXX where
+XXX = INTEL, DEC, SGI, SCSL, or FFTW. All but the last one are native
+vendor-provided libraries. FFTW is a fast, portable library that
+should work on any platform. You can download it from
+"www.fftw.org"_http://www.fftw.org. Use version 2.1.X, not the newer
+3.0.X. Building FFTW for your box should be as simple as ./configure;
+make. Whichever FFT library you have on your platform, you'll need to
+set the appropriate FFT_INC, FFT_PATH, and FFT_LIB variables in
Makefile.foo.
-If you examine fft3d.c and fft3d.h you'll see it's possible to add
-other vendor FFT libraries via #ifdef statements in the appropriate
-places. If you successfully add a new FFT option, like -DFFT_IBM,
-please send the "developers"_http://lammps.sandia.gov an email; we'd
-like to add it to LAMMPS.
-
-(7) If you don't plan to use PPPM, you don't need an FFT library. Use
-a -DFFT_NONE switch in the CCFLAGS setting of Makefile.foo, or exclude
-the KSPACE package (see below).
-
-(8) There are a few other -D compiler switches you can set as part of
-CCFLAGS. The read_data and dump commands will read/write gzipped
-files if you compile with -DLAMMPS_GZIP. It requires that your Unix
-support the "popen" command. Using one of the -DPACK_ARRAY,
--DPACK_POINTER, and -DPACK_MEMCPY options can make for faster parallel
-FFTs (in the PPPM solver) on some platforms. The -DPACK_ARRAY setting
-is the default. If you compile with -DLAMMPS_XDR, the build will
-include XDR compatibility files for doing particle dumps in XTC
-format. This is only necessary if your platform does have its own XDR
-files available. See the Restrictions section of the "dump"_dump.html
-command for details.
-
-(9) The DEPFLAGS setting is how the C++ compiler creates a dependency
-file for each source file. This speeds re-compilation when source
-(*.cpp) or header (*.h) files are edited. Some compilers do not
-support dependency file creation, or may use a different switch than
--D. GNU g++ works with -D. If your compiler can't create dependency
-files (a long list of errors involving *.d files), then you'll need to
-create a Makefile.foo patterned after Makefile.tflop, which uses
-different rules that do not involve dependency files.
+If you examine src/fft3d.c and src.fft3d.h you'll see it's possible to
+add other vendor FFT libraries via #ifdef statements in the
+appropriate places. If you successfully add a new FFT option, like
+-DFFT_IBM, please send the LAMMPS developers an email; we'd like to
+add it to LAMMPS.
+
+If you don't plan to use PPPM, you don't need an FFT library. In this
+case you can set FFT_INC to -DFFT_NONE and leave the other 2 FFT
+variables blank. Or you can exclude the KSPACE package when you build
+LAMMPS (see below).
+
+(3.d) The several SYSLIB and SYSPATH variables can be ignored unless
+you are building LAMMPS with one or more of the LAMMPS packages that
+require these extra system libraries. The names of these packages are
+the prefixes on the SYSLIB and SYSPATH variables. See the "section
+below"_#2_3_4 for more details. The SYSLIB variables list the system
+libraries. The SYSPATH variables are where they are located on your
+machine, which is typically only needed if they are in some
+non-standard place, that is not in your library search path.
That's it. Once you have a correct Makefile.foo and you have
-pre-built the MPI and FFT libraries it will use, all you need to do
-from the src directory is type one of these 2 commands:
+pre-built any other libraries it will use (e.g. MPI, FFT, package
+libraries), all you need to do from the src directory is type one of
+these 2 commands:
make foo
gmake foo :pre
@@ -284,8 +302,9 @@
(2) Cleaning up.
-Typing "make clean" will delete all *.o object files created when
-LAMMPS is built.
+Typing "make clean-all" or "make clean-foo" will delete *.o object
+files created when LAMMPS is built, for either all builds or for a
+particular machine.
(3) On some machines with some compiler options, the Coulomb tabling
option that is enabled by default for "long" "pair
@@ -316,10 +335,16 @@
(4) Building for a Mac.
-OS X is BSD Unix, so it already works. See the Makefile.mac file.
+OS X is BSD Unix, so it should just work. See the Makefile.mac file.
(5) Building for MicroSoft Windows.
+The LAMMPS download page has an option to download a pre-built Windows
+exeutable. See below for instructions for running this executable on
+a Windows box.
+
+If the pre-built executable doesn't have the options you want, then
+you should be able to build LAMMPS from source files on a Windows box.
I've never done this, but LAMMPS is just standard C++ with MPI and FFT
calls. You can use cygwin to build LAMMPS with a Unix make; see
Makefile.cygwin. Or you should be able to pull all the source files
@@ -395,8 +420,8 @@
Any or all packages can be included or excluded independently BEFORE
LAMMPS is built.
-Note: The two exceptions to this are the "gpu" and "opt" packages.
-Some of the files in these packages require other packages to also be
+The two exceptions to this are the "gpu" and "opt" packages. Some of
+the files in these packages require other packages to also be
included. If this is not the case, then those subsidiary files in
"gpu" and "opt" will not be installed either. To install all the
files in package "gpu", the "asphere" package must also be installed.
@@ -409,8 +434,7 @@
which may run a bit faster.
By default, LAMMPS includes only the "kspace", "manybody", and
-"molecule" packages. As described below, some standard packages
-require LAMMPS be linked to separately built libraries.
+"molecule" packages.
Packages are included or excluded by typing "make yes-name" or "make
no-name", where "name" is the name of the package. You can also type
@@ -442,16 +466,16 @@
[{Packages that require extra LAMMPS libraries:}] :link(2_3_3)
-A few packages (standard or user) require that add-on libraries be
+A few packages (standard or user) require that additional libraries be
compiled first, which LAMMPS will link to when it builds. The source
code for these libraries are included in the LAMMPS distribution under
the "lib" directory. Look at the README files in the lib directories
(e.g. lib/reax/README) for instructions on how to build each library.
-IMPORTANT NOTE: If you have included a package that uses
-one of the libraries, then you must build the library BEFORE
-building LAMMPS itself, as the LAMMPS build will link with
-the library file.
+IMPORTANT NOTE: If you are including a package in your LAMMPS build
+that uses one of these libraries, then you must build the library
+BEFORE building LAMMPS itself, since the LAMMPS build will attempt to
+link with the library file.
Here is a bit of information about each library:
@@ -519,37 +543,37 @@
After the desired library or libraries are built, and the package has
been included, you can build LAMMPS itself. For example, from the
lammps/src directory you would type this, to build LAMMPS with ReaxFF.
-Note that the library itself, namely lib/reax/libreax.a, must already
-have been built, as dicussed in the preceding section, for the
-LAMMPS build to be successful.
+Note that as discussed in the preceding section, the package library
+itself, namely lib/reax/libreax.a, must already have been built, for
+the LAMMPS build to be successful.
make yes-reax
make g++ :pre
-Note that simply building the library is not sufficient to use it from
-LAMMPS. You must also include the package that uses and wraps the
-library before you build LAMMPS itself.
+Also note that simply building the library is not sufficient to use it
+from LAMMPS. As in this example, you must also include the package
+that uses and wraps the library before you build LAMMPS itself.
-As discussed in point (2) of "this section"_#2_2_4 above, there are
+As discussed in point (2.4) of "this section"_#2_2_4 above, there are
settings in the low-level Makefile that specify additional system
libraries needed by individual LAMMPS add-on libraries. These are the
settings you must specify correctly in your low-level Makefile in
lammps/src/MAKE, such as Makefile.foo:
To use the gpu package and library, the settings for gpu_SYSLIB and
-gpu_SYSLIBPATH must be correct. These are specific to the NVIDIA CUDA
+gpu_SYSPATH must be correct. These are specific to the NVIDIA CUDA
software which must be installed on your system.
To use the meam or reax packages and their libraries which are Fortran
-based, the settings for meam_SYSLIB, reax_SYSLIB, meam_SYSLIBPATH, and
-reax_SYSLIBPATH must be correct. This is so that the C++ compiler can
+based, the settings for meam_SYSLIB, reax_SYSLIB, meam_SYSPATH, and
+reax_SYSPATH must be correct. This is so that the C++ compiler can
perform a cross-language link using the appropriate system Fortran
libraries.
To use the user-atc package and library, the settings for
-user-atc_SYSLIB and user-atc_SYSLIBPATH must be correct. This is so
-that the appropriate BLAS and LAPACK libs, used by the user-atc
-library, can be found.
+user-atc_SYSLIB and user-atc_SYSPATH must be correct. This is so that
+the appropriate BLAS and LAPACK libs, used by the user-atc library,
+can be found.
:line
diff -Naur lammps-25Oct09/doc/fix_rigid.html lammps-29Oct09/doc/fix_rigid.html
--- lammps-25Oct09/doc/fix_rigid.html 2009-07-02 09:09:14.000000000 -0600
+++ lammps-29Oct09/doc/fix_rigid.html 2009-10-29 10:10:55.000000000 -0600
@@ -121,14 +121,17 @@
separate rigid body. Only atoms that are also in the fix group are
included in each rigid body.
-By default, each rigid body is acted on by other atoms which induce a
-force and torque on its center of mass, causing it to translate and
-rotate. Components of the center-of-mass force and torque can be
-turned off by the force and torque keywords. This may be useful
-if you wish a body to rotate but not translate, or vice versa. Note
-that if you expect a rigid body not to move or rotate by using these
-keywords, you must insure its initial center-of-mass translational or
-angular velocity is 0.0.
+
By default, each rigid body is acted on by other atoms which induce an
+external force and torque on its center of mass, causing it to
+translate and rotate. Components of the external center-of-mass force
+and torque can be turned off by the force and torque keywords.
+This may be useful if you wish a body to rotate but not translate, or
+vice versa, or if you wish it to rotate or translate continuously
+unaffected by interactions with other particles. Note that if you
+expect a rigid body not to move or rotate by using these keywords, you
+must insure its initial center-of-mass translational or angular
+velocity is 0.0. Otherwise the initial translational or angular
+momentum the body has will persist.
An xflag, yflag, or zflag set to off means turn off the component of
force of torque in that dimension. A setting of on means turn on
diff -Naur lammps-25Oct09/doc/fix_rigid.txt lammps-29Oct09/doc/fix_rigid.txt
--- lammps-25Oct09/doc/fix_rigid.txt 2009-07-02 09:09:14.000000000 -0600
+++ lammps-29Oct09/doc/fix_rigid.txt 2009-10-29 10:10:55.000000000 -0600
@@ -112,14 +112,17 @@
separate rigid body. Only atoms that are also in the fix group are
included in each rigid body.
-By default, each rigid body is acted on by other atoms which induce a
-force and torque on its center of mass, causing it to translate and
-rotate. Components of the center-of-mass force and torque can be
-turned off by the {force} and {torque} keywords. This may be useful
-if you wish a body to rotate but not translate, or vice versa. Note
-that if you expect a rigid body not to move or rotate by using these
-keywords, you must insure its initial center-of-mass translational or
-angular velocity is 0.0.
+By default, each rigid body is acted on by other atoms which induce an
+external force and torque on its center of mass, causing it to
+translate and rotate. Components of the external center-of-mass force
+and torque can be turned off by the {force} and {torque} keywords.
+This may be useful if you wish a body to rotate but not translate, or
+vice versa, or if you wish it to rotate or translate continuously
+unaffected by interactions with other particles. Note that if you
+expect a rigid body not to move or rotate by using these keywords, you
+must insure its initial center-of-mass translational or angular
+velocity is 0.0. Otherwise the initial translational or angular
+momentum the body has will persist.
An xflag, yflag, or zflag set to {off} means turn off the component of
force of torque in that dimension. A setting of {on} means turn on
diff -Naur lammps-25Oct09/doc/pair_gayberne.html lammps-29Oct09/doc/pair_gayberne.html
--- lammps-25Oct09/doc/pair_gayberne.html 2009-08-13 11:27:39.000000000 -0600
+++ lammps-29Oct09/doc/pair_gayberne.html 2009-10-29 09:41:27.000000000 -0600
@@ -63,8 +63,9 @@
The variable names utilized as potential parameters are for the most
part taken from (Everaers) in order to be consistent with
-its RE-squared potential fix. Details on the upsilon and mu
-parameters are given here.
+the RE-squared pair potential. Details on the
+upsilon and mu parameters are given
+here.
More details of the Gay-Berne formulation are given in the references
listed below and in this supplementary
diff -Naur lammps-25Oct09/doc/pair_gayberne.txt lammps-29Oct09/doc/pair_gayberne.txt
--- lammps-25Oct09/doc/pair_gayberne.txt 2009-08-13 11:27:39.000000000 -0600
+++ lammps-29Oct09/doc/pair_gayberne.txt 2009-10-29 09:41:27.000000000 -0600
@@ -58,8 +58,9 @@
The variable names utilized as potential parameters are for the most
part taken from "(Everaers)"_#Everaers in order to be consistent with
-its RE-squared potential fix. Details on the upsilon and mu
-parameters are given "here"_gbdoc.
+the "RE-squared pair potential"_pair_resquared.html. Details on the
+upsilon and mu parameters are given
+"here"_PDF/pair_resquared_extra.pdf.
More details of the Gay-Berne formulation are given in the references
listed below and in "this supplementary
diff -Naur lammps-25Oct09/src/GPU/Install.csh lammps-29Oct09/src/GPU/Install.csh
--- lammps-25Oct09/src/GPU/Install.csh 2009-09-28 10:08:11.000000000 -0600
+++ lammps-29Oct09/src/GPU/Install.csh 2009-10-29 14:55:35.000000000 -0600
@@ -6,10 +6,10 @@
sed -i -e 's/[^ \t]*gpu //' ../Makefile.package
sed -i -e 's/[^ \t]*gpu_[^ \t]*) //' ../Makefile.package
- sed -i -e 's|^PKGPATH =[ \t]*|&-L../../lib/gpu |' ../Makefile.package
- sed -i -e 's|^PKGLIB =[ \t]*|&-lgpu |' ../Makefile.package
- sed -i -e 's|^PKGPATHSYS =[ \t]*|&$(gpu_SYSLIBPATH) |' ../Makefile.package
- sed -i -e 's|^PKGLIBSYS =[ \t]*|&$(gpu_SYSLIB) |' ../Makefile.package
+ sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/gpu |' ../Makefile.package
+ sed -i -e 's|^PKG_LIB =[ \t]*|&-lgpu |' ../Makefile.package
+ sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(gpu_SYSPATH) |' ../Makefile.package
+ sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(gpu_SYSLIB) |' ../Makefile.package
cp style_gpu.h tmp.h
if (! -e ../pair_gayberne.cpp) then
diff -Naur lammps-25Oct09/src/MAKE/Makefile.altix lammps-29Oct09/src/MAKE/Makefile.altix
--- lammps-25Oct09/src/MAKE/Makefile.altix 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.altix 2009-10-29 15:32:55.000000000 -0600
@@ -1,59 +1,93 @@
# altix = SGI Altix, Intel icc, MPI, FFTs from SGI SCSL library
SHELL = /bin/sh
-#.IGNORE:
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
+# specify flags and libraries needed for your compiler
CC = icc
-CCFLAGS = $(PKGINC) -O2 -DFFT_SCSL -w
+CCFLAGS = -O2
DEPFLAGS = -M
-# one user needed icpc to link
LINK = icc
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB)
-SYSLIB = $(PKGLIBSYS)
+LINKFLAGS = -O2
+LIB = -lstdc++
+ARCHIVE = ar
+ARFLAGS = -rc
SIZE = size
-# Link rule
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+
+# LAMMPS ifdef options, see doc/Section_start.html
+
+LMP_INC = -DLAMMPS_GZIP
+
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC =
+MPI_PATH =
+MPI_LIB = -lmpi
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_SCSL
+FFT_PATH =
+FFT_LIB =
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
+
+# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
+# Library target
+
+lib: $(OBJ)
+ $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
DEPENDS = $(OBJ:.o=.d)
include $(DEPENDS)
-
diff -Naur lammps-25Oct09/src/MAKE/Makefile.bgl lammps-29Oct09/src/MAKE/Makefile.bgl
--- lammps-25Oct09/src/MAKE/Makefile.bgl 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.bgl 2009-10-29 15:32:55.000000000 -0600
@@ -2,64 +2,98 @@
SHELL = /bin/sh
.SUFFIXES: .cpp .u
-.IGNORE:
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
-
-CC = /opt/ibmcmp/vacpp/7.0/bin/blrts_xlC \
- -I/bgl/BlueLight/ppcfloor/bglsys/include \
- -I/bgl/local/bglfftwgel-2.1.5.pre5/include
-CCFLAGS = $(PKGINC) -O3 -DFFT_FFTW -DMPICH_IGNORE_CXX_SEEK
+# specify flags and libraries needed for your compiler
+
+CC = /opt/ibmcmp/vacpp/7.0/bin/blrts_xlC
+CCFLAGS = -O3
DEPFLAGS = -M
-LINK = /opt/ibmcmp/vacpp/7.0/bin/blrts_xlC
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
+LINK = /opt/ibmcmp/vacpp/7.0/bin/blrts_xlC
+LINKFLAGS = -O \
-L/opt/ibmcmp/xlf/9.1/blrts_lib \
-L/opt/ibmcmp/vacpp/7.0/blrts_lib \
-L/bgl/local/lib \
-L/bgl/local/bglfftwgel-2.1.5.pre5/lib
-USRLIB = $(PKGLIB) -lxlopt -lxlomp_ser -lxl -lxlfmath -lm -lfftw \
- -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts -lmassv
-SYSLIB =$(PKGLIBSYS)
+LIB = -lxlopt -lxlomp_ser -lxl -lxlfmath -lm \
+ -lmsglayer.rts -lrts.rts -ldevices.rts -lmassv
+ARCHIVE = ar
+ARFLAGS = -rc
SIZE = size
-# Link rule
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+
+# LAMMPS ifdef options, see doc/Section_start.html
+
+LMP_INC = -DLAMMPS_GZIP
+
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC = -DMPICH_IGNORE_CXX_SEEK
+MPI_PATH =
+MPI_LIB = -lmpich.rts
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_FFTW
+FFT_PATH =
+FFT_LIB = -lfftw
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
+
+# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
+# Library target
+
+lib: $(OBJ)
+ $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
-%.u:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) -c $<
+%.d:%.cpp
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
-DEPENDS = $(OBJ:.o=.u)
+DEPENDS = $(OBJ:.o=.d)
include $(DEPENDS)
diff -Naur lammps-25Oct09/src/MAKE/Makefile.cheetah lammps-29Oct09/src/MAKE/Makefile.cheetah
--- lammps-25Oct09/src/MAKE/Makefile.cheetah 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.cheetah 1969-12-31 17:00:00.000000000 -0700
@@ -1,71 +0,0 @@
-# cheetah = ORNL IBM machine, mpCC, native MPI, FFTW
-
-SHELL = /bin/sh
-.SUFFIXES: .cpp .u
-.IGNORE:
-
-# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
-# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
-
-CC = mpCC_r
-CCFLAGS = $(PKGINC) -O4 -qnoipa -I/usr/apps/include -DFFT_FFTW
-DEPFLAGS = -M
-LINK = mpCC_r
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -lfftw
-SYSLIB = $(PKGLIBSYS)
-SIZE = size
-
-# Link rule
-
-$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
- $(SIZE) $(EXE)
-
-# --------- old section -------------
-
-# Compilation rules
-
-#.cpp.o:
-# $(CC) $(CCFLAGS) -c $<
-
-# Individual dependencies
-
-#$(OBJ): $(INC)
-
-# --------- new section -------------
-
-# Compilation rules
-
-%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
-
-%.u:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) -c $<
-
-# Individual dependencies
-
-DEPENDS = $(OBJ:.o=.u)
-include $(DEPENDS)
diff -Naur lammps-25Oct09/src/MAKE/Makefile.crockett lammps-29Oct09/src/MAKE/Makefile.crockett
--- lammps-25Oct09/src/MAKE/Makefile.crockett 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.crockett 1969-12-31 17:00:00.000000000 -0700
@@ -1,53 +0,0 @@
-# crockett = RedHat Linux box, mpiCC, LAM MPI, no FFTs
-
-SHELL = /bin/sh
-#.IGNORE:
-
-# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
-# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
-
-CC = mpiCC
-CCFLAGS = $(PKGINC) -g -O -DFFT_NONE -DLAMMPS_GZIP
-DEPFLAGS = -M
-LINK = mpiCC
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB =$(PKGLIB)
-SYSLIB = $(PKGLIBSYS)
-SIZE = size
-
-# Link rule
-
-$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
- $(SIZE) $(EXE)
-
-# Compilation rules
-
-.cpp.o:
- $(CC) $(CCFLAGS) -c $<
-
-# Individual dependencies
-
-$(OBJ): $(INC)
diff -Naur lammps-25Oct09/src/MAKE/Makefile.cygwin lammps-29Oct09/src/MAKE/Makefile.cygwin
--- lammps-25Oct09/src/MAKE/Makefile.cygwin 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.cygwin 2009-10-29 15:32:55.000000000 -0600
@@ -1,56 +1,91 @@
-# cygwin = Windows Cygwin, mpicxx, FFTW
+# cygwin = Windows Cygwin, mpicxx, MPICH, FFTW
SHELL = /bin/sh
-#.IGNORE:
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
+# compiler/linker settings
+# specify flags and libraries needed for your compiler
+
+CC = mpicxx
+CCFLAGS = -O
+DEPFLAGS = -M
+LINK = mpicxx
+LINKFLAGS = -O
+LIB =
+ARCHIVE = ar
+ARFLAGS = -rc
+SIZE = size
+
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+
+# LAMMPS ifdef options, see doc/Section_start.html
+
+LMP_INC = -DLAMMPS_GZIP
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC = -DMPICH_IGNORE_CXX_SEEK
+MPI_PATH = -L/cygdrive/c/cygwin/mpich2-1.0.4p1/lib
+MPI_LIB = -lmpich
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_FFTW -I/cygdrive/c/cygwin/fftw/include
+FFT_PATH = -L/cygdrive/c/cygwin/fftw/lib
+FFT_LIB = -lfftw
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
include Makefile.package
-# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
-
-CC = mpicxx
-CCFLAGS = $(PKGINC) -O -g -I/cygdrive/c/cygwin/fftw/include -DFFT_FFTW -DMPICH_IGNORE_CXX_SEEK
-DEPFLAGS = -M
-LINK = mpicxx
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -lfftw -lmpich
-SYSLIB = $(PKGLIBSYS)
-SIZE = size
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
-# Link rule
+# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
- $(SIZE) $(EXE).exe
- mv $(EXE).exe ../lmp
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
+ $(SIZE) $(EXE)
+
+# Library target
+
+lib: $(OBJ)
+ $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
diff -Naur lammps-25Oct09/src/MAKE/Makefile.debian lammps-29Oct09/src/MAKE/Makefile.debian
--- lammps-25Oct09/src/MAKE/Makefile.debian 2009-10-12 09:31:17.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.debian 1969-12-31 17:00:00.000000000 -0700
@@ -1,67 +0,0 @@
-# debian = Debian, g++, MPICH, FFTW
-
-SHELL = /bin/sh
-#.IGNORE:
-
-# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
-# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
-
-CC = g++
-CCFLAGS = $(PKGINC) -g -O -I/usr/lib/mpich/include/ -DFFT_FFTW -DLAMMPS_GZIP
-DEPFLAGS = -M
-LINK = g++
-LINKFLAGS = -g -O -L/usr/lib/mpich/lib $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -lfftw -lmpich
-SYSLIB = $(PKGLIBSYS)
-ARCHIVE = ar
-ARFLAGS = -rc
-SIZE = size
-
-# ---------------------------------------------------------------------
-# no need to edit below here
-
-# Link target
-
-$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
- $(SIZE) $(EXE)
-
-# Library target
-
-lib: $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
-
-# Compilation rules
-
-%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
-
-%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# Individual dependencies
-
-DEPENDS = $(OBJ:.o=.d)
-include $(DEPENDS)
diff -Naur lammps-25Oct09/src/MAKE/Makefile.diesel lammps-29Oct09/src/MAKE/Makefile.diesel
--- lammps-25Oct09/src/MAKE/Makefile.diesel 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.diesel 1969-12-31 17:00:00.000000000 -0700
@@ -1,62 +0,0 @@
-# diesel = SGI Origin 350, 64-bit, SGI MIPSpro CC, SGI MPT, SGI SCSL MP FFTs
-
-SHELL = /bin/sh
-#.IGNORE:
-
-# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
-# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
-
-CC = CC
-CCFLAGS = $(PKGINC) -64 -O -mp -DFFT_SCSL
-DEPFLAGS = -M
-LINK = CC
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB)
-SYSLIB = $(PKGLIBSYS)
-SIZE = size
-
-# Link rule
-
-$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
- $(SIZE) $(EXE)
-
-# Library target
-
-lib: $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
-
-# Compilation rules
-
-%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
-
-%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# Individual dependencies
-
-DEPENDS = $(OBJ:.o=.d)
-include $(DEPENDS)
diff -Naur lammps-25Oct09/src/MAKE/Makefile.encanto lammps-29Oct09/src/MAKE/Makefile.encanto
--- lammps-25Oct09/src/MAKE/Makefile.encanto 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.encanto 2009-10-29 15:32:55.000000000 -0600
@@ -1,63 +1,91 @@
# encanto = NM cluster with dual quad-core Xeons, mpicxx, native MPI, FFTW
SHELL = /bin/sh
-.IGNORE:
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
+# specify flags and libraries needed for your compiler
CC = mpicxx
-CCFLAGS = $(PKGINC) -O -DFFT_FFTW -I/home/jlane/fftw-2.1.5/fftw
+CCFLAGS = -O
DEPFLAGS = -M
LINK = mpicxx
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -lstdc++ -lfftw
-SYSLIB = $(PKGLIBSYS)
+LINKFLAGS = -O
+LIB = -lstdc++
+ARCHIVE = ar
+ARFLAGS = -rc
SIZE = size
-ARCHIVE = ar
-ARFLAGS = -rc
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+
+# LAMMPS ifdef options, see doc/Section_start.html
+
+LMP_INC = -DLAMMPS_GZIP
-# Link rule
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC = -DMPICH_IGNORE_CXX_SEEK
+MPI_PATH =
+MPI_LIB = -lmpich -lpthread
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_FFTW -I/home/jlane/fftw-2.1.5/fftw
+FFT_PATH = -L/home/jlane/fftw-2.1.5/fftw/.libs
+FFT_LIB = -lfftw
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
+
+# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
# Library target
-
-lib: $(OBJ)
+
+lib: $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
diff -Naur lammps-25Oct09/src/MAKE/Makefile.fink lammps-29Oct09/src/MAKE/Makefile.fink
--- lammps-25Oct09/src/MAKE/Makefile.fink 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.fink 2009-10-29 15:32:55.000000000 -0600
@@ -1,57 +1,93 @@
-# fink = Mac OS-X w/ fink installed libraries, c++, no MPI, FFTW 2.1.5
+# fink = Mac OS-X w/ fink libraries, c++, no MPI, FFTW 2.1.5
SHELL = /bin/sh
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
+# specify flags and libraries needed for your compiler
CC = c++
-CCFLAGS = $(PKGINC) -O -I../STUBS -I/sw/include -DFFT_FFTW
+CCFLAGS = -O
DEPFLAGS = -M
LINK = c++
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -lfftw -lmpi
-SYSLIB = $(PKGLIBSYS)
+LINKFLAGS = -O
+LIB = -lstdc++
+ARCHIVE = ar
+ARFLAGS = -rc
SIZE = size
-# Link rule
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+
+# LAMMPS ifdef options, see doc/Section_start.html
+
+LMP_INC = -DLAMMPS_GZIP
+
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC = -I../STUBS
+MPI_PATH = -L../STUBS
+MPI_LIB = -lmpi
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_FFTW -I/sw/include
+FFT_PATH = -L/sw/lib
+FFT_LIB = -lfftw
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
+
+# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
+# Library target
+
+lib: $(OBJ)
+ $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
DEPENDS = $(OBJ:.o=.d)
include $(DEPENDS)
-
diff -Naur lammps-25Oct09/src/MAKE/Makefile.freebsd lammps-29Oct09/src/MAKE/Makefile.freebsd
--- lammps-25Oct09/src/MAKE/Makefile.freebsd 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.freebsd 1969-12-31 17:00:00.000000000 -0700
@@ -1,56 +0,0 @@
-# freebsd = FreeBSD box, 7.0-RELEASE, LAM/MPI, FFTW
-
-SHELL = /bin/sh
-
-# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
-# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
-
-CC = mpic++
-CCFLAGS = $(PKGINC) -O3 -DFFT_FFTW
-DEPFLAGS = -M
-LINK = mpic++
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -lfftw -lmpi
-SYSLIB = $(PKGLIBSYS)
-SIZE = size
-
-# Link rule
-
-$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
- $(SIZE) $(EXE)
-
-# Compilation rules
-
-%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
-
-%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# Individual dependencies
-
-DEPENDS = $(OBJ:.o=.d)
-include $(DEPENDS)
diff -Naur lammps-25Oct09/src/MAKE/Makefile.g++ lammps-29Oct09/src/MAKE/Makefile.g++
--- lammps-25Oct09/src/MAKE/Makefile.g++ 2009-09-28 09:26:47.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.g++ 2009-10-29 15:32:55.000000000 -0600
@@ -1,50 +1,77 @@
-# g++ = RedHat Linux box, g++, MPICH, FFTW
+# g++ = RedHat Linux box, g++, MPICH2, FFTW
SHELL = /bin/sh
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
+# specify flags and libraries needed for your compiler
CC = g++
-CCFLAGS = -g -O -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK $(PKGINC)
+CCFLAGS = -g -O
DEPFLAGS = -M
LINK = g++
-LINKFLAGS = -g -O $(PKGPATH) $(PKGPATHSYS)
-USRLIB = -lfftw -lmpich $(PKGLIB)
-SYSLIB = -lpthread $(PKGLIBSYS)
+LINKFLAGS = -g -O
+LIB =
ARCHIVE = ar
ARFLAGS = -rc
SIZE = size
# ---------------------------------------------------------------------
-# no need to edit below here
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+
+# LAMMPS ifdef options, see doc/Section_start.html
+
+LMP_INC = -DLAMMPS_GZIP
+
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC = -DMPICH_IGNORE_CXX_SEEK
+MPI_PATH =
+MPI_LIB = -lmpich -lpthread
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_FFTW
+FFT_PATH =
+FFT_LIB = -lfftw
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
# Library target
@@ -55,10 +82,10 @@
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
diff -Naur lammps-25Oct09/src/MAKE/Makefile.glory lammps-29Oct09/src/MAKE/Makefile.glory
--- lammps-25Oct09/src/MAKE/Makefile.glory 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.glory 2009-10-29 15:32:55.000000000 -0600
@@ -20,59 +20,89 @@
# either interactively or via a batch script
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
+# specify flags and libraries needed for your compiler
CC = mpicxx
-CCFLAGS = $(PKGINC) -O -DFFT_FFTW -I${FFTW_INCLUDE}
+CCFLAGS = -O
DEPFLAGS = -M
LINK = mpicxx
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -lfftw -lstdc++
-SYSLIB = $(PKGLIBSYS)
+LINKFLAGS = -O
+LIB = -lstdc++ -lm
+ARCHIVE = ar
+ARFLAGS = -rc
SIZE = size
-ARCHIVE = ar
-ARFLAGS = -rc
-# Link rule
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+
+# LAMMPS ifdef options, see doc/Section_start.html
+
+LMP_INC = -DLAMMPS_GZIP
+
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC =
+MPI_PATH =
+MPI_LIB =
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_FFTW -I${FFTW_INCLUDE}
+FFT_PATH = -L${FFTW_LIB}
+FFT_LIB = -lfftw
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
+
+# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
# Library target
-
-lib: $(OBJ)
+
+lib: $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
diff -Naur lammps-25Oct09/src/MAKE/Makefile.intel lammps-29Oct09/src/MAKE/Makefile.intel
--- lammps-25Oct09/src/MAKE/Makefile.intel 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.intel 1969-12-31 17:00:00.000000000 -0700
@@ -1,110 +0,0 @@
-# intel = Fedora Core 6, intel icc 9.1, FFTW2, no MPI
-
-SHELL = /bin/sh
-#.IGNORE:
-
-# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
-# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
-
-CC = icpc
-CCFLAGS = $(PKGINC) -O2 -unroll -DFFT_FFTW -DLAMMPS_GZIP \
- -fstrict-aliasing -I../STUBS
-NOALIAS = -fno-strict-aliasing
-DEPFLAGS = -M
-LINK = icpc
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -L../STUBS -lmpi -lfftw
-SYSLIB = $(PKGLIBSYS)
-ARCHIVE = ar
-ARFLAGS = -rcsv
-SIZE = size
-
-# ---------------------------------------------------------------------
-# no need to edit below here
-
-# Link target
-
-$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
- $(SIZE) $(EXE)
-
-# Library target
-
-lib: $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
-
-# Compilation rules
-
-%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
-
-%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# explicit overrides for files that violate ansi aliasing rules
-
-pair.o : pair.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_table.o : pair_table.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_eam_alloy_opt.o : pair_eam_alloy_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_eam_fs_opt.o : pair_eam_fs_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_eam_opt.o : pair_eam_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_lj_charmm_coul_long_opt.o : pair_lj_charmm_coul_long_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_lj_cut_opt.o : pair_lj_cut_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_morse_opt.o : pair_morse_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_lj_cut_coul_long.o : pair_lj_cut_coul_long.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_cg_cut_coul_cut.o : pair_cg_cut_coul_cut.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_cg_cut_coul_long.o : pair_cg_cut_coul_long.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_lj_charmm_coul_long.o : pair_lj_charmm_coul_long.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_lj_cut_coul_long_tip4p.o : pair_lj_cut_coul_long_tip4p.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-# Individual dependencies
-
-DEPENDS = $(OBJ:.o=.d)
-include $(DEPENDS)
diff -Naur lammps-25Oct09/src/MAKE/Makefile.intel_mkl lammps-29Oct09/src/MAKE/Makefile.intel_mkl
--- lammps-25Oct09/src/MAKE/Makefile.intel_mkl 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.intel_mkl 1969-12-31 17:00:00.000000000 -0700
@@ -1,73 +0,0 @@
-# intel_mkl = Intel Cluster Tools with MKL library for FFTs and MPI
-
-# Intel C++, Intel MPI, Intel MKL FFTs
-# Intel recommends Intel Cluster Tools Compiler Edition
-# to build libfftw2xc_intel.a:
-# > cd /opt/intel/mkl/10.0.011/interfaces/fftw2xc
-# > become root via su
-# > gmake libem64t
-
-SHELL = /bin/sh
-
-# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
-# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
-
-CC = mpiicc
-CCFLAGS = $(PKGINC) -O3 -fno-alias -ip -unroll0 -g -DMPICH_IGNORE_CXX_SEEK -DLAMMPS_GZIP -DFFT_FFTW -I/opt/intel/mkl/10.0.011/include/fftw
-DEPFLAGS = -M
-LINK = mpiicc
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) /opt/intel/mkl/10.0.011/lib/em64t/libfftw2xc_intel.a
-SYSLIB = $(PKGLIBSYS)
-ARCHIVE = ar
-ARFLAGS = -rc
-SIZE = size
-
-# ---------------------------------------------------------------------
-# no need to edit below here
-
-# Link target
-
-$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
- $(SIZE) $(EXE)
-
-# Library target
-
-lib: $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
-
-# Compilation rules
-
-%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
-
-%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# Individual dependencies
-
-DEPENDS = $(OBJ:.o=.d)
-include $(DEPENDS)
diff -Naur lammps-25Oct09/src/MAKE/Makefile.liberty lammps-29Oct09/src/MAKE/Makefile.liberty
--- lammps-25Oct09/src/MAKE/Makefile.liberty 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.liberty 1969-12-31 17:00:00.000000000 -0700
@@ -1,72 +0,0 @@
-# liberty = HP cluster with dual 3.0 GHz Xeons, mpiCC, native MPI, FFTW
-
-SHELL = /bin/sh
-.IGNORE:
-
-# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
-# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
-
-# Note: this Makefile builds LAMMPS according to what modules you've loaded
-# by default this is openmpi MPI
-# you still need this line in your .cshrc to load FFTW
-# module load libraries/fftw-2.1.5_openmpi-1.2.3_mx_intel-8.1-f034-c038
-# if you want to build with mpich MPI instead, put this in your .cshrc
-# module switch mpi mpi/mpich-mx-1.2.7..4_intel-10.0-f025-c025
-# module load libraries/fftw-2.1.5_mpich-mx-1.2.7..4_intel-9.1-f040-c046
-# whichever mode you build LAMMPS (openmpi or mpich),
-# your qsub environment needs these same modules
-# this will occur if you use qsub -V to inherit from your login shell
-
-#FFTW = /home/sjplimp/fftw/fftw_liberty
-
-CC = mpiCC
-#CCFLAGS = $(PKGINC) -O -DFFT_FFTW -I${FFTW}/fftw
-CCFLAGS = $(PKGINC) -O -DFFT_FFTW -I${FFTW_INCLUDE}
-DEPFLAGS = -M
-LINK = mpiCC
-#LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -lfftw
-SYSLIB = $(PKGLIBSYS)
-SIZE = size
-
-# Link rule
-
-$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
- $(SIZE) $(EXE)
-
-# Compilation rules
-
-%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
-
-%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# Individual dependencies
-
-DEPENDS = $(OBJ:.o=.d)
-include $(DEPENDS)
diff -Naur lammps-25Oct09/src/MAKE/Makefile.linux lammps-29Oct09/src/MAKE/Makefile.linux
--- lammps-25Oct09/src/MAKE/Makefile.linux 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.linux 2009-10-29 15:32:55.000000000 -0600
@@ -3,48 +3,75 @@
SHELL = /bin/sh
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
+# specify flags and libraries needed for your compiler
CC = icc
-CCFLAGS = -O -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK $(PKGINC)
+CCFLAGS = -O
DEPFLAGS = -M
LINK = icc
-LINKFLAGS = -O $(PKGPATH) $(PKGPATHSYS)
-USRLIB = -lfftw -lmpich $(PKGLIB)
-SYSLIB = -lpthread -lstdc++ $(PKGLIBSYS)
+LINKFLAGS = -O
+LIB = -lstdc++
ARCHIVE = ar
ARFLAGS = -rc
SIZE = size
# ---------------------------------------------------------------------
-# no need to edit below here
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+
+# LAMMPS ifdef options, see doc/Section_start.html
+
+LMP_INC = -DLAMMPS_GZIP
+
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC = -DMPICH_IGNORE_CXX_SEEK
+MPI_PATH =
+MPI_LIB = -lmpich -lpthread
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_FFTW
+FFT_PATH =
+FFT_LIB = -lfftw
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
# Library target
@@ -55,10 +82,10 @@
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
diff -Naur lammps-25Oct09/src/MAKE/Makefile.mac lammps-29Oct09/src/MAKE/Makefile.mac
--- lammps-25Oct09/src/MAKE/Makefile.mac 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.mac 2009-10-29 15:32:55.000000000 -0600
@@ -3,52 +3,89 @@
SHELL = /bin/sh
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
+# specify flags and libraries needed for your compiler
CC = c++
-CCFLAGS = -O -DFFT_FFTW -I../STUBS $(PKGINC)
+CCFLAGS = -O
DEPFLAGS = -M
LINK = c++
-LINKFLAGS = -O $(PKGPATH) $(PKGPATHSYS)
-USRLIB = -lfftw ../STUBS/mpi.o $(PKGLIB)
-SYSLIB = $(PKGLIBSYS)
+LINKFLAGS = -O
+LIB =
+ARCHIVE = ar
+ARFLAGS = -rc
SIZE = size
-# Link rule
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+
+# LAMMPS ifdef options, see doc/Section_start.html
+
+LMP_INC = -DLAMMPS_GZIP
+
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC = -I../STUBS
+MPI_PATH = -L../STUBS
+MPI_LIB = -lmpi
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_FFTW
+FFT_PATH =
+FFT_LIB = -lfftw
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
+
+# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
+# Library target
+
+lib: $(OBJ)
+ $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
diff -Naur lammps-25Oct09/src/MAKE/Makefile.mac_mpi lammps-29Oct09/src/MAKE/Makefile.mac_mpi
--- lammps-25Oct09/src/MAKE/Makefile.mac_mpi 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.mac_mpi 2009-10-29 15:32:55.000000000 -0600
@@ -1,55 +1,96 @@
-# mac_mpi = Apple PowerBook G4 laptop, Finked LAM/MPI, Finked FFTW 2.1.5
+# mac_mpi = Apple PowerBook G4 laptop, mpic++, fink LAM/MPI, fink FFTW 2.1.5
SHELL = /bin/sh
# ---------------------------------------------------------------------
-# System-specific settings
+# compiler/linker settings
+# generally no need to edit this section
+# unless additional compiler/linker flags or libraries needed for your machine
+
+CC = mpic++
+CCFLAGS = -O -MMD -MG
+DEPFLAGS = -M
+LINK = mpic++
+LINKFLAGS = -O
+LIB =
+ARCHIVE = ar
+ARFLAGS = -rc
+SIZE = size
+
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings
# edit as needed for your machine
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
+# LAMMPS ifdef options, see doc/Section_start.html
-include Makefile.package
+LMP_INC = -DLAMMPS_GZIP
-# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC = -DOMPI_SKIP_MPICXX
+MPI_PATH =
+MPI_LIB =
+
+# FFT library, can be -DFFT_NONE if not using PPPM from kspace package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
FFTW = /sw
-CC = mpic++
-CCFLAGS = -O -MMD -MG -DFFT_FFTW \
- -I${FFTW}/include -DOMPI_SKIP_MPICXX $(PKGINC)
-LINK = mpic++
-LINKFLAGS = -O -L${FFTW}/lib $(PKGPATH) $(PKGPATHSYS)
-USRLIB = -lfftw $(PKGLIB)
-SYSLIB = $(PKGLIBSYS)
-SIZE = size
+FFT_INC = -DFFT_FFTW -I${FFTW}/include
+FFT_PATH = -L${FFTW}/lib
+FFT_LIB = -lfftw
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
-# Link rule
+# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
+# Library target
+
+lib: $(OBJ)
+ $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
+
+%.d:%.cpp
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
DEPENDS = $(OBJ:.o=.d)
--include $(DEPENDS)
+include $(DEPENDS)
diff -Naur lammps-25Oct09/src/MAKE/Makefile.odin lammps-29Oct09/src/MAKE/Makefile.odin
--- lammps-25Oct09/src/MAKE/Makefile.odin 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.odin 2009-10-29 15:32:55.000000000 -0600
@@ -1,51 +1,77 @@
# odin = 1400 cluster, g++, MPICH, no FFTs
SHELL = /bin/sh
-#.IGNORE:
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
+# specify flags and libraries needed for your compiler
CC = g++
-CCFLAGS = $(PKGINC) -O -I/opt/mpich-mx/include -DFFT_NONE -DLAMMPS_GZIP
+CCFLAGS = -O
DEPFLAGS = -M
-LINK = g++
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -lmpich -lmyriexpress
-SYSLIB =$(PKGLIBSYS)
+LINK = G++
+LINKFLAGS = -O
+LIB =
ARCHIVE = ar
ARFLAGS = -rc
SIZE = size
# ---------------------------------------------------------------------
-# no need to edit below here
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+
+# LAMMPS ifdef options, see doc/Section_start.html
+
+LMP_INC = -DLAMMPS_GZIP
+
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC = -I/opt/mpich-mx/include
+MPI_PATH = -L/opt/mpich-mx/lib -L/opt/mx/lib
+MPI_LIB = -lmpich -lmyriexpress
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_NONE
+FFT_PATH =
+FFT_LIB =
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
# Library target
@@ -56,10 +82,10 @@
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
diff -Naur lammps-25Oct09/src/MAKE/Makefile.openmpi lammps-29Oct09/src/MAKE/Makefile.openmpi
--- lammps-25Oct09/src/MAKE/Makefile.openmpi 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.openmpi 2009-10-29 15:32:55.000000000 -0600
@@ -1,53 +1,78 @@
-# openmpi = Fedora Core 6, gcc/g++ 4.1, OpenMPI-1.1 , FFTW2, Open MPI
+# openmpi = Fedora Core 6, mpic++, OpenMPI-1.1, FFTW2
SHELL = /bin/sh
-#.IGNORE:
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
+# specify flags and libraries needed for your compiler
CC = mpic++
-CCFLAGS = $(PKGINC) -O2 -funroll-loops -DFFT_FFTW -DLAMMPS_GZIP \
- -fstrict-aliasing -Wall -W -Wno-uninitialized
-NOALIAS = -fno-strict-aliasing
+CCFLAGS = -O2 \
+ -funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized
DEPFLAGS = -M
LINK = mpic++
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -lfftw
-SYSLIB = $(PKGLIBSYS)
+LINKFLAGS = -O
+LIB = -lstdc++
ARCHIVE = ar
ARFLAGS = -rcsv
SIZE = size
# ---------------------------------------------------------------------
-# no need to edit below here
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+
+# LAMMPS ifdef options, see doc/Section_start.html
+
+LMP_INC = -DLAMMPS_GZIP
+
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC =
+MPI_PATH =
+MPI_LIB =
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_FFTW
+FFT_PATH =
+FFT_LIB = -lfftw
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
# Library target
@@ -58,51 +83,10 @@
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# explicit overrides for files that violate ansi aliasing rules
-
-pair.o : pair.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_table.o : pair_table.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_eam_alloy_opt.o : pair_eam_alloy_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_eam_fs_opt.o : pair_eam_fs_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_eam_opt.o : pair_eam_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_lj_charmm_coul_long_opt.o : pair_lj_charmm_coul_long_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_lj_cut_opt.o : pair_lj_cut_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_morse_opt.o : pair_morse_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_lj_cut_coul_long.o : pair_lj_cut_coul_long.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_cg_cut_coul_cut.o : pair_cg_cut_coul_cut.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_cg_cut_coul_long.o : pair_cg_cut_coul_long.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_lj_charmm_coul_long.o : pair_lj_charmm_coul_long.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_lj_cut_coul_long_tip4p.o : pair_lj_cut_coul_long_tip4p.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
diff -Naur lammps-25Oct09/src/MAKE/Makefile.opensuse lammps-29Oct09/src/MAKE/Makefile.opensuse
--- lammps-25Oct09/src/MAKE/Makefile.opensuse 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.opensuse 1969-12-31 17:00:00.000000000 -0700
@@ -1,66 +0,0 @@
-# opensuse = openSUSE linux, g++, MPICH, FFTW
-
-SHELL = /bin/sh
-
-# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
-# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
-
-CC = g++
-CCFLAGS = $(PKGINC) -O3 -I /opt/mpich/include/ -DFFT_FFTW -DLAMMPS_GZIP
-DEPFLAGS = -M
-LINK = g++
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -ldfftw -lmpich
-SYSLIB =$(PKGLIBSYS)
-ARCHIVE = ar
-ARFLAGS = -rc
-SIZE = size
-
-# ---------------------------------------------------------------------
-# no need to edit below here
-
-# Link target
-
-$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
- $(SIZE) $(EXE)
-
-# Library target
-
-lib: $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
-
-# Compilation rules
-
-%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
-
-%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# Individual dependencies
-
-DEPENDS = $(OBJ:.o=.d)
-include $(DEPENDS)
diff -Naur lammps-25Oct09/src/MAKE/Makefile.pg lammps-29Oct09/src/MAKE/Makefile.pg
--- lammps-25Oct09/src/MAKE/Makefile.pg 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.pg 1969-12-31 17:00:00.000000000 -0700
@@ -1,70 +0,0 @@
-# pg = Portland Group compiler, MPICH, FFTW
-
-SHELL = /bin/sh
-#.IGNORE:
-
-# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
-# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
-
-CC = pgCC -fast
-CCFLAGS = $(PKGINC) -I/usr/local/mpich-1.2.6/pg/include \
- -I/usr/local/include \
- -DFFT_FFTW -DLAMMPS_GZIP
-DEPFLAGS = -M
-LINK = pgCC
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
- -L/usr/local/lib
-USRLIB = $(PKGLIB) -lfftw -lmpich
-SYSLIB = $(PKGLIBSYS)
-ARCHIVE = ar
-ARFLAGS = -rc
-SIZE = size
-
-# ---------------------------------------------------------------------
-# no need to edit below here
-
-# Link target
-
-$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
- $(SIZE) $(EXE)
-
-# Library target
-
-lib: $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
-
-# Compilation rules
-
-%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
-
-%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# Individual dependencies
-
-DEPENDS = $(OBJ:.o=.d)
-include $(DEPENDS)
diff -Naur lammps-25Oct09/src/MAKE/Makefile.power5 lammps-29Oct09/src/MAKE/Makefile.power5
--- lammps-25Oct09/src/MAKE/Makefile.power5 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.power5 2009-10-29 15:32:55.000000000 -0600
@@ -1,57 +1,94 @@
-# power5 = IBM Power5+ machine, mpCC, FFTW
+# power5 = IBM Power5+, mpCC_r, native MPI, FFTW
SHELL = /bin/sh
.SUFFIXES: .cpp .u
-.IGNORE:
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
+# specify flags and libraries needed for your compiler
CC = mpCC_r
-CCFLAGS = $(PKGINC) -O3 -qnoipa -qlanglvl=oldmath \
- -I/scr/oppe/LAMMPS/fftw-2.1.5/include -DFFT_FFTW
+CCFLAGS = -O3 -qnoipa -qlanglvl=oldmath
DEPFLAGS = -M
LINK = mpCC_r
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -L/scr/oppe/LAMMPS/fftw-2.1.5/lib -lfftw
-SYSLIB = $(PKGLIBSYS)
+LINKFLAGS = -O -qnoipa -qlanglvl=oldmath -bmaxdata:0x70000000
+LIB = -lm
+ARCHIVE = ar
+ARFLAGS = -rc
SIZE = size
# ---------------------------------------------------------------------
-# no need to edit below here
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+
+# LAMMPS ifdef options, see doc/Section_start.html
+
+LMP_INC = -DLAMMPS_GZIP
+
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC =
+MPI_PATH =
+MPI_LIB =
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_FFTW -I/scr/oppe/LAMMPS/fftw-2.1.5/include
+FFT_PATH = -L/scr/oppe/LAMMPS/fftw-2.1.5/lib
+FFT_LIB = -lfftw
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
+# Library target
+
+lib: $(OBJ)
+ $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
+
+%.d:%.cpp
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
+
+# Individual dependencies
-pppm.o: pppm.cpp
- $(CC) $(CCFLAGS) -D_ANSI_C_SOURCE -c $<
+DEPENDS = $(OBJ:.o=.d)
+include $(DEPENDS)
diff -Naur lammps-25Oct09/src/MAKE/Makefile.qed lammps-29Oct09/src/MAKE/Makefile.qed
--- lammps-25Oct09/src/MAKE/Makefile.qed 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.qed 2009-10-29 15:32:55.000000000 -0600
@@ -1,50 +1,77 @@
-# qed = CSRI cluster, Intel Xeons + Ethernet, mpiCC, MPICH, no FFTs
+# qed = CSRI cluster, mpiCC, MPICH, no FFTs
SHELL = /bin/sh
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
+# specify flags and libraries needed for your compiler
CC = mpiCC
-CCFLAGS = $(PKGINC) -O -I/usr/local/mpich-1.2.6-eth/include -DFFT_NONE
+CCFLAGS = -O
DEPFLAGS = -M
LINK = mpiCC
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -lmpich
-SYSLIB = $(PKGLIBSYS)
+LINKFLAGS = -O
+LIB =
ARCHIVE = ar
ARFLAGS = -rc
SIZE = size
# ---------------------------------------------------------------------
-# no need to edit below here
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+
+# LAMMPS ifdef options, see doc/Section_start.html
+
+LMP_INC = -DLAMMPS_GZIP
+
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC = -I/usr/local/mpich-1.2.6-eth/include
+MPI_PATH = -L/usr/local/mpich-1.2.6-eth/lib
+MPI_LIB = -lmpich
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_NONE
+FFT_PATH =
+FFT_LIB =
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
# Library target
@@ -55,13 +82,12 @@
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
DEPENDS = $(OBJ:.o=.d)
include $(DEPENDS)
-
diff -Naur lammps-25Oct09/src/MAKE/Makefile.ross lammps-29Oct09/src/MAKE/Makefile.ross
--- lammps-25Oct09/src/MAKE/Makefile.ross 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.ross 1969-12-31 17:00:00.000000000 -0700
@@ -1,57 +0,0 @@
-# ross = CPlant cluster (compile on taylor), c++, native MPI, DEC FFTs
-
-SHELL = /bin/sh
-.IGNORE:
-
-# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
-# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
-
-CC = /usr/local/cplant/ross/current/bin/c++
-CCFLAGS = $(PKGINC) -O -DFFT_DEC
-DEPFLAGS = -M
-LINK = /usr/local/cplant/ross/current/bin/c++
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -lmpi -lcxml
-SYSLIB = $(PKGLIBSYS)
-SIZE = size
-
-# Link rule
-
-$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
- $(SIZE) $(EXE)
-
-# Compilation rules
-
-%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
-
-%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# Individual dependencies
-
-DEPENDS = $(OBJ:.o=.d)
-include $(DEPENDS)
diff -Naur lammps-25Oct09/src/MAKE/Makefile.sdsc lammps-29Oct09/src/MAKE/Makefile.sdsc
--- lammps-25Oct09/src/MAKE/Makefile.sdsc 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.sdsc 2009-10-29 15:32:55.000000000 -0600
@@ -2,103 +2,95 @@
SHELL = /bin/sh
.SUFFIXES: .cpp .u
-.IGNORE:
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
-
-CC = blrts_xlC \
- -I/bgl/BlueLight/ppcfloor/bglsys/include \
- -I//usr/local/apps/V1R3/fftw-2.1.5d/include/
-CCFLAGS = $(PKGINC) -O2 -qarch=440 -qtune=440 \
- -DFFT_FFTW -DMPICH_IGNORE_CXX_SEEK -DLAMMPS_XDR
-NOALIAS = -qalias=noansi
+# specify flags and libraries needed for your compiler
+
+CC = blrts_xlC
+CCFLAGS = -I/bgl/BlueLight/ppcfloor/bglsys/include \
+ -O2 -qarch=440 -qtune=440
DEPFLAGS = -M -qmakedep=gcc
-LINK = blrts_xlC
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
+LINK = blrts_xlC
+LINKFLAGS = -O \
+ -L/bgl/BlueLight/ppcfloor/bglsys/lib \
-L/opt/ibmcmp/xlf/bg/10.1/blrts_lib \
- -L/opt/ibmcmp/vacpp/bg/8.0/blrts_lib \
- -L/usr/local/apps/V1R3/fftw-2.1.5d/lib
-USRLIB = $(PKGLIB) -lfftw -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts -lm
-SYSLIB = $(PKGLIBSYS)
+ -L/opt/ibmcmp/vacpp/bg/8.0/blrts_lib
+LIB = -lm
+ARCHIVE = ar
+ARFLAGS = -rc
SIZE = size
-# Link rule
-
-$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
- $(SIZE) $(EXE)
-
-# Compilation rules
-
-%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
-
-%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) -MF$@ -c $<
-
-# explicit overrides for files that violate ansi aliasing rules
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
-pair.o : pair.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
+# LAMMPS ifdef options, see doc/Section_start.html
-pair_table.o : pair_table.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
+LMP_INC = -DLAMMPS_GZIP -DLAMMPS_XDR
-pair_eam_alloy_opt.o : pair_eam_alloy_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC = -DMPICH_IGNORE_CXX_SEEK
+MPI_PATH =
+MPI_LIB = -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_FFTW -I//usr/local/apps/V1R3/fftw-2.1.5d/include
+FFT_PATH = -L/usr/local/apps/V1R3/fftw-2.1.5d/lib
+FFT_LIB = -lfftw
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
-pair_eam_fs_opt.o : pair_eam_fs_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
-pair_eam_opt.o : pair_eam_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
+include Makefile.package
-pair_lj_charmm_coul_long_opt.o : pair_lj_charmm_coul_long_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
-pair_lj_cut_opt.o : pair_lj_cut_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
+# Link target
-pair_morse_opt.o : pair_morse_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
+$(EXE): $(OBJ)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
+ $(SIZE) $(EXE)
-pair_lj_cut_coul_long.o : pair_lj_cut_coul_long.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
+# Library target
-pair_cg_cmm_coul_long.o : pair_cg_cmm_coul_long.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
+lib: $(OBJ)
+ $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
-pair_coul_long.o: pair_coul_long.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
+# Compilation rules
-pair_lj_charmm_coul_long.o : pair_lj_charmm_coul_long.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
+%.o:%.cpp
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
-pair_lj_cut_coul_long_tip4p.o : pair_lj_cut_coul_long_tip4p.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
+%.d:%.cpp
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
diff -Naur lammps-25Oct09/src/MAKE/Makefile.seaborg lammps-29Oct09/src/MAKE/Makefile.seaborg
--- lammps-25Oct09/src/MAKE/Makefile.seaborg 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.seaborg 2009-10-29 15:32:55.000000000 -0600
@@ -2,71 +2,93 @@
SHELL = /bin/sh
.SUFFIXES: .cpp .u
-.IGNORE:
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
+# specify flags and libraries needed for your compiler
CC = mpCC_r
-CCFLAGS = $(PKGINC) -O2 -qnoipa -I/usr/common/usg/fftw/2.1.5/include -DFFT_FFTW
+CCFLAGS = -O2 -qnoipa
DEPFLAGS = -M
LINK = mpCC_r
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -lfftw -lfftw_mpi
-SYSLIB = $(PKGLIBSYS)
+LINKFLAGS = -O -L/usr/lib
+LIB = -lm
+ARCHIVE = ar
+ARFLAGS = -rc
SIZE = size
-# Link rule
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
-$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
- $(SIZE) $(EXE)
+# LAMMPS ifdef options, see doc/Section_start.html
-# --------- old section -------------
+LMP_INC = -DLAMMPS_GZIP
-# Compilation rules
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC = -DMPICH_IGNORE_CXX_SEEK
+MPI_PATH =
+MPI_LIB = -lmpich -lpthread
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_FFTW -I/usr/common/usg/fftw/2.1.5/include
+FFT_PATH = -L/usr/common/usg/fftw/2.1.5/lib
+FFT_LIB = -lfftw -lfftw_mpi
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
-#.cpp.o:
-# $(CC) $(CCFLAGS) -c $<
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
-# Individual dependencies
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
+
+# Link target
-#$(OBJ): $(INC)
+$(EXE): $(OBJ)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
+ $(SIZE) $(EXE)
-# --------- new section -------------
+# Library target
+
+lib: $(OBJ)
+ $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
-%.u:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) -c $<
+%.d:%.cpp
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
-DEPENDS = $(OBJ:.o=.u)
+DEPENDS = $(OBJ:.o=.d)
include $(DEPENDS)
-
diff -Naur lammps-25Oct09/src/MAKE/Makefile.serial lammps-29Oct09/src/MAKE/Makefile.serial
--- lammps-25Oct09/src/MAKE/Makefile.serial 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.serial 2009-10-29 15:32:55.000000000 -0600
@@ -3,48 +3,76 @@
SHELL = /bin/sh
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
+# generally no need to edit this section
+# unless additional compiler/linker flags or libraries needed for your machine
CC = g++
-CCFLAGS = -O -DFFT_NONE -I../STUBS $(PKGINC)
+CCFLAGS = -O
DEPFLAGS = -M
LINK = g++
-LINKFLAGS = -O -L../STUBS $(PKGPATH) $(PKGPATHSYS)
-USRLIB = -lmpi $(PKGLIB)
-SYSLIB = $(PKGLIBSYS)
+LINKFLAGS = -O
+LIB =
ARCHIVE = ar
ARFLAGS = -rc
SIZE = size
# ---------------------------------------------------------------------
-# no need to edit below here
+# LAMMPS-specific settings
+# edit as needed for your machine
+
+# LAMMPS ifdef options, see doc/Section_start.html
+
+LMP_INC = -DLAMMPS_GZIP
+
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC = -I../STUBS
+MPI_PATH = -L../STUBS
+MPI_LIB = -lmpi
+
+# FFT library, can be -DFFT_NONE if not using PPPM from kspace package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_NONE
+FFT_PATH =
+FFT_LIB =
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
# Library target
@@ -55,10 +83,10 @@
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
diff -Naur lammps-25Oct09/src/MAKE/Makefile.serial_debug lammps-29Oct09/src/MAKE/Makefile.serial_debug
--- lammps-25Oct09/src/MAKE/Makefile.serial_debug 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.serial_debug 2009-10-29 15:32:55.000000000 -0600
@@ -1,53 +1,77 @@
-# serial_debug = Fedora Core 6, GNU gcc/g++ 4.1, FFTW2, no MPI, debug info
+# serial_debug = RedHat Linux box, g++, no MPI, no FFTs
SHELL = /bin/sh
-#.IGNORE:
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
-
-CC = gcc
-CCFLAGS = $(PKGINC) -g -Wall -W -O2 -funroll-loops \
- -DFFT_FFTW -DLAMMPS_GZIP -fstrict-aliasing -I../STUBS
-NOALIAS = -fno-strict-aliasing
+# specify flags and libraries needed for your compiler
+
+CC = g++
+CCFLAGS = -O -Wall -W -O2 -funroll-loops -fstrict-aliasing
DEPFLAGS = -M
LINK = g++
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -L../STUBS -lmpi -lfftw
-SYSLIB = $(PKGLIBSYS)
+LINKFLAGS = -O
+LIB =
ARCHIVE = ar
ARFLAGS = -rcsv
SIZE = size
# ---------------------------------------------------------------------
-# no need to edit below here
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+
+# LAMMPS ifdef options, see doc/Section_start.html
+
+LMP_INC = -DLAMMPS_GZIP
+
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC = -I../STUBS
+MPI_PATH = -L../STUBS
+MPI_LIB = -lmpi
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_NONE
+FFT_PATH =
+FFT_LIB =
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
# Library target
@@ -58,51 +82,10 @@
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# explicit overrides for files that violate ansi aliasing rules
-
-pair.o : pair.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_table.o : pair_table.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_eam_alloy_opt.o : pair_eam_alloy_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_eam_fs_opt.o : pair_eam_fs_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_eam_opt.o : pair_eam_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_lj_charmm_coul_long_opt.o : pair_lj_charmm_coul_long_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_lj_cut_opt.o : pair_lj_cut_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_morse_opt.o : pair_morse_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_lj_cut_coul_long.o : pair_lj_cut_coul_long.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_cg_cut_coul_long.o : pair_cg_cut_coul_long.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_cg_cut_coul_cut.o : pair_cg_cut_coul_cut.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_lj_charmm_coul_long.o : pair_lj_charmm_coul_long.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_lj_cut_coul_long_tip4p.o : pair_lj_cut_coul_long_tip4p.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
diff -Naur lammps-25Oct09/src/MAKE/Makefile.serial_icc lammps-29Oct09/src/MAKE/Makefile.serial_icc
--- lammps-25Oct09/src/MAKE/Makefile.serial_icc 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.serial_icc 1969-12-31 17:00:00.000000000 -0700
@@ -1,66 +0,0 @@
-# serial_icc = RedHat Linux box, icc, no MPI, no FFTs
-
-SHELL = /bin/sh
-
-# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
-# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
-
-CC = icc
-CCFLAGS = $(PKGINC) -O -I../STUBS -DFFT_NONE
-DEPFLAGS = -M
-LINK = icc
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -lmpi
-SYSLIB = $(PKGLIBSYS)
-ARCHIVE = ar
-ARFLAGS = -rc
-SIZE = size
-
-# ---------------------------------------------------------------------
-# no need to edit below here
-
-# Link target
-
-$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
- $(SIZE) $(EXE)
-
-# Library target
-
-lib: $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
-
-# Compilation rules
-
-%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
-
-%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# Individual dependencies
-
-DEPENDS = $(OBJ:.o=.d)
-include $(DEPENDS)
diff -Naur lammps-25Oct09/src/MAKE/Makefile.solaris lammps-29Oct09/src/MAKE/Makefile.solaris
--- lammps-25Oct09/src/MAKE/Makefile.solaris 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.solaris 2009-10-29 15:32:55.000000000 -0600
@@ -3,64 +3,91 @@
SHELL = /bin/sh
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
+# specify flags and libraries needed for your compiler
CC = c++
-CCFLAGS = $(PKGINC) -O -I../STUBS -DFFT_NONE
+CCFLAGS = -O
DEPFLAGS = -M
LINK = c++
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -lmpi
-SYSLIB =$(PKGLIBSYS)
+LINKFLAGS = -O
+LIB =
ARCHIVE = ar
ARFLAGS = -rc
SIZE = size
# ---------------------------------------------------------------------
-# no need to edit below here
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+
+# LAMMPS ifdef options, see doc/Section_start.html
+
+LMP_INC = -DLAMMPS_GZIP
+
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC = -I../STUBS
+MPI_PATH = -L../STUBS
+MPI_LIB = -lmpi
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_NONE
+FFT_PATH =
+FFT_LIB =
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
# Library target
-lib: $(OBJ)
+lib: $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
-$(OBJ): $(INC)
-#include $(DEPENDS)
+DEPENDS = $(OBJ:.o=.d)
+include $(DEPENDS)
diff -Naur lammps-25Oct09/src/MAKE/Makefile.spirit lammps-29Oct09/src/MAKE/Makefile.spirit
--- lammps-25Oct09/src/MAKE/Makefile.spirit 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.spirit 2009-10-29 15:32:55.000000000 -0600
@@ -1,67 +1,101 @@
-# spirit = HP cluster with dual 3.4 GHz EM64T (64 bit), mpiCC, native MPI, FFTW
+# spirit = HP cluster 64-bit, mpicxx, native MPI, FFTW
-# users may wish to add the following (uncommented) to their .bashrc or equivalent:
+SHELL = /bin/sh
+
+# users may wish to add the following lines to their .bashrc or equivalent:
# if [ "$SNLCLUSTER" = "spirit" ]; then
# source /opt/modules/default/init/bash
# module load libraries/fftw-2.1.5_openmpi-1.2.2_mx_intel-9.1-f040-c045
# fi;
-SHELL = /bin/sh
-.IGNORE:
+# ---------------------------------------------------------------------
+# compiler/linker settings
+# specify flags and libraries needed for your compiler
+
+CC = mpicxx
+CCFLAGS = -O
+DEPFLAGS = -M
+LINK = mpicxx
+LINKFLAGS = -O
+LIB = -lm
+ARCHIVE = ar
+ARFLAGS = -rc
+SIZE = size
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
+# LAMMPS ifdef options, see doc/Section_start.html
-include Makefile.package
+LMP_INC = -DLAMMPS_GZIP
-# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC =
+MPI_PATH =
+MPI_LIB =
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
FFTW = /apps/x86_64/libraries/fftw/openmpi-1.2.2_mx_intel-9.1-f040-c045/fftw-2.1.5
-CC = mpicxx
-OPTIMIZE = -O
-CCFLAGS = $(PKGINC) $(OPTIMIZE) -DFFT_FFTW -I$(FFTW)/include
-DEPFLAGS = -M
-LINK = mpicxx
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -lfftw -lstdc++
-SYSLIB = $(PKGLIBSYS)
-SIZE = size
+FFT_INC = -DFFT_FFTW -I$(FFTW)/include
+FFT_PATH = -L$(FFTW)/lib
+FFT_LIB = -lfftw
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
-# Link rule
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
+
+# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
+# Library target
+
+lib: $(OBJ)
+ $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
DEPENDS = $(OBJ:.o=.d)
include $(DEPENDS)
-
diff -Naur lammps-25Oct09/src/MAKE/Makefile.squall lammps-29Oct09/src/MAKE/Makefile.squall
--- lammps-25Oct09/src/MAKE/Makefile.squall 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.squall 1969-12-31 17:00:00.000000000 -0700
@@ -1,64 +0,0 @@
-# squall = Red Squall (compile on srnsquall), pgiCC, MPI, FFTW
-#
-# To use this, first do:
-#
-# module unload compilers/gnu
-# module load compilers/pgi-6.0
-# module unload mpich/mpich-gnu
-# module load mpich/mpich-pgi-6.0
-#
-
-SHELL = /bin/sh
-
-# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
-# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
-
-CC = mpiCC
-CCFLAGS = $(PKGINC) -DFFT_FFTW -I/home/athomps/tools/fftw-2.1.5/fftw
-DEPFLAGS = -O2 -M
-LINK = mpiCC
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -lfftw -lmpi
-SYSLIB = $(PKGLIBSYS)
-SIZE = size
-
-# Link rule
-
-$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
- $(SIZE) $(EXE)
-
-# Compilation rules
-
-%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
-
-%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# Individual dependencies
-
-DEPENDS = $(OBJ:.o=.d)
-include $(DEPENDS)
diff -Naur lammps-25Oct09/src/MAKE/Makefile.storm lammps-29Oct09/src/MAKE/Makefile.storm
--- lammps-25Oct09/src/MAKE/Makefile.storm 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.storm 2009-10-29 15:32:55.000000000 -0600
@@ -1,48 +1,78 @@
-# storm = Cray Red Storm, Cray mpicxx, native MPI, FFTW
+# storm = Cray Red Storm XT3, Cray CC, native MPI, FFTW
SHELL = /bin/sh
.SUFFIXES: .cpp .d
-.IGNORE:
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
+# specify flags and libraries needed for your compiler
CC = CC
-CCFLAGS = $(PKGINC) -fastsse -DFFT_FFTW -DMPICH_IGNORE_CXX_SEEK \
- -I/projects/fftw/fftw-2.1.5/include
+CCFLAGS = -fastsse
DEPFLAGS = -M
LINK = CC
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -lfftw
-SYSLIB =$(PKGLIBSYS)
+LINKFLAGS = -O
+LIB = -lstdc++
+ARCHIVE = ar
+ARFLAGS = -rc
SIZE = size
-# Link rule
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+
+# LAMMPS ifdef options, see doc/Section_start.html
+
+LMP_INC = -DLAMMPS_GZIP
+
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC = -DMPICH_IGNORE_CXX_SEEK
+MPI_PATH =
+MPI_LIB =
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_FFTW -I/projects/fftw/fftw-2.1.5/include
+FFT_PATH =
+FFT_LIB = -lfftw
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
+
+# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
# Library target
@@ -53,7 +83,7 @@
# Compilation rules
.cpp.o:
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
# Individual dependencies
diff -Naur lammps-25Oct09/src/MAKE/Makefile.tacc lammps-29Oct09/src/MAKE/Makefile.tacc
--- lammps-25Oct09/src/MAKE/Makefile.tacc 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.tacc 2009-10-29 15:32:55.000000000 -0600
@@ -1,52 +1,80 @@
-# g++ = UT Lonestar TACC machine, mpiCC, MPI, FFTW
+# tacc = UT Lonestar TACC machine, mpiCC, MPI, FFTW
SHELL = /bin/sh
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
-
-FFTW_INC = ${TACC_FFTW2_INC}
-FFTW_LIB = ${TACC_FFTW2_LIB}
+# specify flags and libraries needed for your compiler
CC = mpiCC
-CCFLAGS = -O -DFFT_FFTW -I${FFTW_INC} $(PKGINC)
+CCFLAGS = -O
DEPFLAGS = -M
LINK = mpiCC
-LINKFLAGS = -O -L${FFTW_LIB} $(PKGPATH) $(PKGPATHSYS)
-USRLIB = ${FFTW_LIB}/libfftw.a $(PKGLIB)
-SYSLIB = $(PKGLIBSYS)
+LINKFLAGS = -O
+LIB =
+ARCHIVE = ar
ARFLAGS = -rc
SIZE = size
# ---------------------------------------------------------------------
-# no need to edit below here
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+
+# LAMMPS ifdef options, see doc/Section_start.html
+
+LMP_INC = -DLAMMPS_GZIP
+
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC = -DMPICH_IGNORE_CXX_SEEK
+MPI_PATH =
+MPI_LIB = -lmpich -lpthread
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFTW_INC = ${TACC_FFTW2_INC}
+FFTW_LIB = ${TACC_FFTW2_LIB}
+
+FFT_INC = -DFFT_FFTW -I${FFTW_INC}
+FFT_PATH = -L${FFTW_LIB}
+FFT_LIB = ${FFTW_LIB}/libfftw.a
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore
+reax_SYSLIB = -lifcore
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/apps/intel/10.1/fc/lib
+reax_SYSPATH = -L/opt/apps/intel/10.1/fc/lib
+user-atc_SYSPATH =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
# Library target
@@ -57,10 +85,10 @@
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
diff -Naur lammps-25Oct09/src/MAKE/Makefile.tbird lammps-29Oct09/src/MAKE/Makefile.tbird
--- lammps-25Oct09/src/MAKE/Makefile.tbird 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.tbird 2009-10-29 15:32:55.000000000 -0600
@@ -1,7 +1,6 @@
-# tbird = Dell cluster with dual 3.6 GHz Xeons, Intel mpicxx, native MPI, FFTW
+# tbird = Dell cluster with Xeons, Intel mpicxx, native MPI, FFTW
SHELL = /bin/sh
-.IGNORE:
# this Makefile builds LAMMPS for openMPI running on Tbird
# as of April 09, you want these modules loaded, which are not the default:
@@ -23,58 +22,89 @@
# either interactively or via a batch script
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
+# specify flags and libraries needed for your compiler
CC = mpicxx
-CCFLAGS = -O -DFFT_FFTW -I$(FFTW_INCLUDE) $(PKGINC)
+CCFLAGS = -O
DEPFLAGS = -M
LINK = mpicxx
-LINKFLAGS = -O $(PKGPATH) $(PKGPATHSYS)
-SYSLIB = -lm $(PKGLIBSYS)
+LINKFLAGS = -O
+LIB = -lstdc++ -lm
+ARCHIVE = ar
+ARFLAGS = -rc
SIZE = size
-ARCHIVE = ar
-ARFLAGS = -rc
-# Link rule
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+
+# LAMMPS ifdef options, see doc/Section_start.html
+
+LMP_INC = -DLAMMPS_GZIP
+
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC = -DMPICH_IGNORE_CXX_SEEK
+MPI_PATH =
+MPI_LIB = -lmpich -lpthread
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_FFTW -I$(FFTW_INCLUDE)
+FFT_PATH =
+FFT_LIB = $(BLASLIB) $(FFTW_LINK_LINE)
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
+
+# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
# Library target
-
-lib: $(OBJ)
+
+lib: $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
diff -Naur lammps-25Oct09/src/MAKE/Makefile.tesla lammps-29Oct09/src/MAKE/Makefile.tesla
--- lammps-25Oct09/src/MAKE/Makefile.tesla 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.tesla 2009-10-29 15:32:55.000000000 -0600
@@ -1,58 +1,93 @@
# tesla = 16-proc SGI Onyx3, g++, no MPI, SGI FFTs
SHELL = /bin/sh
-#.IGNORE:
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
+# specify flags and libraries needed for your compiler
CC = g++
-CCFLAGS = $(PKGINC) -O -I../STUBS -DFFT_SGI
+CCFLAGS = -O
DEPFLAGS = -M
LINK = g++
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -lmpi
-SYSLIB = $(PKGLIBSYS)
+LINKFLAGS = -O
+LIB = -lm -lcomplib.sgimath
+ARCHIVE = ar
+ARFLAGS = -rc
SIZE = size
-# Link rule
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+
+# LAMMPS ifdef options, see doc/Section_start.html
+
+LMP_INC = -DLAMMPS_GZIP
+
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC = -I../STUBS
+MPI_PATH = -L../STUBS
+MPI_LIB = -lmpi
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_SGI
+FFT_PATH =
+FFT_LIB = -lcomplib.sgimath
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
+
+# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
+# Library target
+
+lib: $(OBJ)
+ $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
DEPENDS = $(OBJ:.o=.d)
include $(DEPENDS)
-
diff -Naur lammps-25Oct09/src/MAKE/Makefile.tflop lammps-29Oct09/src/MAKE/Makefile.tflop
--- lammps-25Oct09/src/MAKE/Makefile.tflop 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.tflop 1969-12-31 17:00:00.000000000 -0700
@@ -1,54 +0,0 @@
-# tflop = Intel Tflops (compile on sasn100), ciCC, native MPI, Intel FFTs
-
-SHELL = /bin/sh
-.SUFFIXES: .cpp .d
-.IGNORE:
-
-# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
-# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
-
-CC = ciCC
-CCFLAGS = $(PKGINC) -O4 -Knoieee -DFFT_INTEL
-DEPFLAGS = -M
-LINK = ciCC
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -lmpi -lkmath
-SYSLIB =$(PKGLIBSYS)
-SIZE = xsize
-
-# Link rule
-
-$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
- $(SIZE) $(EXE)
-
-# Compilation rules
-
-.cpp.o:
- $(CC) $(CCFLAGS) -c $<
-
-# Individual dependencies
-
-$(OBJ): $(INC)
diff -Naur lammps-25Oct09/src/MAKE/Makefile.valor lammps-29Oct09/src/MAKE/Makefile.valor
--- lammps-25Oct09/src/MAKE/Makefile.valor 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.valor 1969-12-31 17:00:00.000000000 -0700
@@ -1,59 +0,0 @@
-# valor = HP cluster with dual Xeons, mpiCC, native MPI, FFTW
-
-SHELL = /bin/sh
-.IGNORE:
-
-# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
-# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
-
-FFTW = /apps/libraries/fftw-2.1.5
-
-CC = mpiCC
-CCFLAGS = $(PKGINC) -O -DFFT_FFTW -I${FFTW}/include
-DEPFLAGS = -M
-LINK = mpiCC
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -lfftw -lstdc++
-SYSLIB = $(PKGLIBSYS)
-SIZE = size
-
-# Link rule
-
-$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
- $(SIZE) $(EXE)
-
-# Compilation rules
-
-%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
-
-%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# Individual dependencies
-
-DEPENDS = $(OBJ:.o=.d)
-include $(DEPENDS)
diff -Naur lammps-25Oct09/src/MAKE/Makefile.xt3 lammps-29Oct09/src/MAKE/Makefile.xt3
--- lammps-25Oct09/src/MAKE/Makefile.xt3 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.xt3 2009-10-29 15:32:55.000000000 -0600
@@ -1,54 +1,80 @@
-# xt3 = PSC BigBen Cray XT3, GCC, native MPI, FFTW
+# xt3 = PSC BigBen Cray XT3, CC, native MPI, FFTW
SHELL = /bin/sh
-#.IGNORE:
# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
+# compiler/linker settings
+# specify flags and libraries needed for your compiler
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
+CC = CC
+CCFLAGS = -O3 --target=catamount \
+CCFLAGS = -fomit-frame-pointer -finline-functions \
+ -Wall -Wno-unused -funroll-all-loops
+DEPFLAGS = -M
+LINK = CC
+LINKFLAGS = --target=catamount -O
+LIB = -lgmalloc
+ARCHIVE = ar
+ARFLAGS = -rc
+SIZE = size
-include Makefile.package
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
-# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
-
-CC = CC --target=catamount
-CCFLAGS = $(PKGINC) -O3 -fomit-frame-pointer -finline-functions \
- -Wall -Wno-unused -funroll-all-loops \
- -DFFT_FFTW -DMPICH_IGNORE_CXX_SEEK -DLAMMPS_XDR -I$(FFTW_INC)
-NOALIAS = -fno-strict-aliasing
-DEPFLAGS = -M
-LINK = CC --target=catamount
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
-USRLIB = $(PKGLIB) -ldfftw -lgmalloc
-SYSLIB =$(PKGLIBSYS)
-SIZE = size
+# LAMMPS ifdef options, see doc/Section_start.html
+
+LMP_INC = -DLAMMPS_GZIP -DLAMMPS_XDR
+
+# MPI library, can be src/STUBS dummy lib
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC = -DMPICH_IGNORE_CXX_SEEK
+MPI_PATH =
+MPI_LIB = -lmpich -lpthread
+
+# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
+# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_FFTW -I$(FFTW_INC)
+FFT_PATH = -L$(FFTW_LIB)
+FFT_LIB = -ldfftw
+
+# additional system libraries needed by LAMMPS package libraries
+# these settings are IGNORED if the corresponding LAMMPS package
+# (e.g. gpu, meam) is NOT included in the LAMMPS build
+# SYSLIB = names of libraries
+# SYSPATH = paths of libraries
+
+gpu_SYSLIB = -lcudart
+meam_SYSLIB = -lifcore -lsvml -lompstub -limf
+reax_SYSLIB = -lifcore -lsvml -lompstub -limf
+user-atc_SYSLIB = -lblas -llapack
+
+gpu_SYSPATH = -L/usr/local/cuda/lib64
+meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+reax_SYSPATH = -L/opt/intel/fce/10.0.023/lib
+user-atc_SYSPATH =
# ---------------------------------------------------------------------
-# no need to edit below here
+# build rules and dependencies
+# no need to edit this section
+
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(PKG_SYSLIB)
# Link target
$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
- @echo Run $(EXE) with yod/pbsyod -small_pages for maximum performance.
# Library target
@@ -58,51 +84,10 @@
# Compilation rules
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# explicit overrides for files that violate ansi aliasing rules
-
-pair.o : pair.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_table.o : pair_table.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_eam_alloy_opt.o : pair_eam_alloy_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_eam_fs_opt.o : pair_eam_fs_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_eam_opt.o : pair_eam_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_lj_charmm_coul_long_opt.o : pair_lj_charmm_coul_long_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_lj_cut_opt.o : pair_lj_cut_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_morse_opt.o : pair_morse_opt.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_lj_cut_coul_long.o : pair_lj_cut_coul_long.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_cg_cut_coul_cut.o : pair_cg_cut_coul_cut.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_cg_cut_coul_long.o : pair_cg_cut_coul_long.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_lj_charmm_coul_long.o : pair_lj_charmm_coul_long.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
-
-pair_lj_cut_coul_long_tip4p.o : pair_lj_cut_coul_long_tip4p.cpp
- $(CC) $(CCFLAGS) $(NOALIAS) -c $<
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
diff -Naur lammps-25Oct09/src/MAKE/Makefile.ydl lammps-29Oct09/src/MAKE/Makefile.ydl
--- lammps-25Oct09/src/MAKE/Makefile.ydl 2009-09-28 09:27:14.000000000 -0600
+++ lammps-29Oct09/src/MAKE/Makefile.ydl 1969-12-31 17:00:00.000000000 -0700
@@ -1,65 +0,0 @@
-# ydl = Yellow Dog Linux box, xlc -q64, MPICH, FFTW
-
-SHELL = /bin/sh
-#.IGNORE:
-
-# ---------------------------------------------------------------------
-# System-specific settings
-# edit as needed for your machine
-
-# additional system libs needed by LAMMPS libs
-# NOTE: these settings are ignored if the LAMMPS package (e.g. gpu, meam)
-# which needs these libs is not included in the LAMMPS build
-
-gpu_SYSLIB = -lcudart
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-reax_SYSLIB = -lifcore -lsvml -lompstub -limf
-user-atc_SYSLIB = -lblas -llapack
-
-gpu_SYSLIBPATH = -L/usr/local/cuda/lib64
-meam_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-reax_SYSLIBPATH = -L/opt/intel/fce/10.0.023/lib
-user-atc_SYSLIBPATH =
-
-include Makefile.package
-
-# compiler/linker settings
-# NOTE: specify how to compile/link with MPI
-# either an MPI installed on your machine, or the src/STUBS dummy lib
-# NOTE: specify an FFT option, e.g. -DFFT_NONE, -DFFT_FFTW, etc
-
-CC = xlc -q64
-CCFLAGS = $(PKGINC) -g -O -I/opt/mpich/include \
- -I/usr/local/include -L/opt/mpich/lib64 \
- -DFFT_FFTW -DLAMMPS_LAMMPS_GZIP
-DEPFLAGS = -M
-LINK = xlc -q64
-LINKFLAGS = $(PKGPATH) $(PKGPATHSYS)
- -L/usr/local/lib -lstdc++ -lc
-USRLIB = $(PKGLIB) -lfftw -lmpich
-SYSLIB =$(PKGLIBSYS)
-SIZE = size
-
-# Link rule
-
-$(EXE): $(OBJ)
- $(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
- $(SIZE) $(EXE)
-
-# Library target
-
-lib: $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
-
-# Compilation rules
-
-%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
-
-%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# Individual dependencies
-
-DEPENDS = $(OBJ:.o=.d)
-include $(DEPENDS)
diff -Naur lammps-25Oct09/src/MEAM/Install.csh lammps-29Oct09/src/MEAM/Install.csh
--- lammps-25Oct09/src/MEAM/Install.csh 2009-09-28 10:08:11.000000000 -0600
+++ lammps-29Oct09/src/MEAM/Install.csh 2009-10-29 14:55:35.000000000 -0600
@@ -5,11 +5,11 @@
sed -i -e 's/[^ \t]*meam //' ../Makefile.package
sed -i -e 's/[^ \t]*meam_[^ \t]*) //' ../Makefile.package
- sed -i -e 's|^PKGINC =[ \t]*|&-I../../lib/meam |' ../Makefile.package
- sed -i -e 's|^PKGPATH =[ \t]*|&-L../../lib/meam |' ../Makefile.package
- sed -i -e 's|^PKGLIB =[ \t]*|&-lmeam |' ../Makefile.package
- sed -i -e 's|^PKGPATHSYS =[ \t]*|&$(meam_SYSLIBPATH) |' ../Makefile.package
- sed -i -e 's|^PKGLIBSYS =[ \t]*|&$(meam_SYSLIB) |' ../Makefile.package
+ sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/meam |' ../Makefile.package
+ sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/meam |' ../Makefile.package
+ sed -i -e 's|^PKG_LIB =[ \t]*|&-lmeam |' ../Makefile.package
+ sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(meam_SYSPATH) |' ../Makefile.package
+ sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(meam_SYSLIB) |' ../Makefile.package
cp style_meam.h ..
diff -Naur lammps-25Oct09/src/Makefile.package lammps-29Oct09/src/Makefile.package
--- lammps-25Oct09/src/Makefile.package 2009-10-29 15:38:59.000000000 -0600
+++ lammps-29Oct09/src/Makefile.package 2009-10-29 15:39:23.000000000 -0600
@@ -1,9 +1,9 @@
# Settings for libraries used by specific LAMMPS packages
# this file is auto-edited when those packages are included/excluded
-PKGINC =
-PKGPATH =
-PKGLIB =
+PKG_INC =
+PKG_PATH =
+PKG_LIB =
-PKGPATHSYS =
-PKGLIBSYS =
+PKG_SYSPATH =
+PKG_SYSLIB =
diff -Naur lammps-25Oct09/src/POEMS/Install.csh lammps-29Oct09/src/POEMS/Install.csh
--- lammps-25Oct09/src/POEMS/Install.csh 2009-08-13 15:36:58.000000000 -0600
+++ lammps-29Oct09/src/POEMS/Install.csh 2009-10-29 14:55:35.000000000 -0600
@@ -4,9 +4,9 @@
if ($1 == 1) then
sed -i -e 's/[^ \t]*poems //' ../Makefile.package
- sed -i -e 's|^PKGINC =[ \t]*|&-I../../lib/poems |' ../Makefile.package
- sed -i -e 's|^PKGPATH =[ \t]*|&-L../../lib/poems |' ../Makefile.package
- sed -i -e 's|^PKGLIB =[ \t]*|&-lpoems |' ../Makefile.package
+ sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/poems |' ../Makefile.package
+ sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/poems |' ../Makefile.package
+ sed -i -e 's|^PKG_LIB =[ \t]*|&-lpoems |' ../Makefile.package
cp style_poems.h ..
diff -Naur lammps-25Oct09/src/REAX/Install.csh lammps-29Oct09/src/REAX/Install.csh
--- lammps-25Oct09/src/REAX/Install.csh 2009-09-28 10:08:11.000000000 -0600
+++ lammps-29Oct09/src/REAX/Install.csh 2009-10-29 14:55:35.000000000 -0600
@@ -5,11 +5,11 @@
sed -i -e 's/[^ \t]*reax //' ../Makefile.package
sed -i -e 's/[^ \t]*reax_[^ \t]*) //' ../Makefile.package
- sed -i -e 's|^PKGINC =[ \t]*|&-I../../lib/reax |' ../Makefile.package
- sed -i -e 's|^PKGPATH =[ \t]*|&-L../../lib/reax |' ../Makefile.package
- sed -i -e 's|^PKGLIB =[ \t]*|&-lreax |' ../Makefile.package
- sed -i -e 's|^PKGPATHSYS =[ \t]*|&$(reax_SYSLIBPATH) |' ../Makefile.package
- sed -i -e 's|^PKGLIBSYS =[ \t]*|&$(reax_SYSLIB) |' ../Makefile.package
+ sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/reax |' ../Makefile.package
+ sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/reax |' ../Makefile.package
+ sed -i -e 's|^PKG_LIB =[ \t]*|&-lreax |' ../Makefile.package
+ sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(reax_SYSPATH) |' ../Makefile.package
+ sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(reax_SYSLIB) |' ../Makefile.package
cp style_reax.h ..
diff -Naur lammps-25Oct09/src/USER-ATC/Install.csh lammps-29Oct09/src/USER-ATC/Install.csh
--- lammps-25Oct09/src/USER-ATC/Install.csh 2009-09-28 10:08:11.000000000 -0600
+++ lammps-29Oct09/src/USER-ATC/Install.csh 2009-10-29 14:55:35.000000000 -0600
@@ -5,11 +5,11 @@
sed -i -e 's/[^ \t]*atc //' ../Makefile.package
sed -i -e 's/[^ \t]*atc_[^ \t]*) //' ../Makefile.package
- sed -i -e 's|^PKGINC =[ \t]*|&-I../../lib/atc |' ../Makefile.package
- sed -i -e 's|^PKGPATH =[ \t]*|&-L../../lib/atc |' ../Makefile.package
- sed -i -e 's|^PKGLIB =[ \t]*|&-latc |' ../Makefile.package
- sed -i -e 's|^PKGPATHSYS =[ \t]*|&$(user-atc_SYSLIBPATH) |' ../Makefile.package
- sed -i -e 's|^PKGLIBSYS =[ \t]*|&$(user-atc_SYSLIB) |' ../Makefile.package
+ sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/atc |' ../Makefile.package
+ sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/atc |' ../Makefile.package
+ sed -i -e 's|^PKG_LIB =[ \t]*|&-latc |' ../Makefile.package
+ sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(user-atc_SYSPATH) |' ../Makefile.package
+ sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(user-atc_SYSLIB) |' ../Makefile.package
cp style_user_atc.h ..
diff -Naur lammps-25Oct09/src/shell.cpp lammps-29Oct09/src/shell.cpp
--- lammps-25Oct09/src/shell.cpp 2007-01-29 17:22:05.000000000 -0700
+++ lammps-29Oct09/src/shell.cpp 2009-10-27 08:33:19.000000000 -0600
@@ -36,9 +36,11 @@
} else if (strcmp(arg[0],"mkdir") == 0) {
if (narg < 2) error->all("Illegal shell command");
+#ifndef WINDOWS
if (comm->me == 0)
for (int i = 1; i < narg; i++)
mkdir(arg[i], S_IRWXU | S_IRGRP | S_IXGRP);
+#endif
} else if (strcmp(arg[0],"mv") == 0) {
if (narg != 3) error->all("Illegal shell command");