LAMMPS + TDM-GCC-64 + Win7 + MATLAB R2015b + Gnumex
By R.L. Carino (carino@cavs.msstate.edu)


A. Software setup

1. MinGW, download installer from http://sourceforge.net/projects/mingw/?source=directory. Install gcc, g++, gfortran and MSYS. We do not use the compilers (these are 32-bit), but we need MSYS for a Unix-like compilation environment. Install to C:\Mingw. Add C:\MinGW\msys\1.0\bin to PATH environment variable.

2. TDM-GCC-64 (install to C:\TDM-GCC-64, add C:\TDM-GCC-64\bin to PATH environment variable).

I used the installer https://sourceforge.net/projects/tdm-gcc/files/TDM-GCC%20Installer/tdm64-gcc-5.1.0-2.exe/download

After installation of TDM-GCC-64, edit C:\MinGW\msys\1.0\etc\fstab, to look like:

	# /etc/fstab -- mount table configuration for MSYS.
	# Please refer to /etc/fstab.sample for explanatory annotation.
	
	# MSYS-Portable needs this "magic" comment:
	# MSYSROOT=C:/MinGW/msys/1.0
	
	# Win32_Path				Mount_Point
	#-------------------------------------	-----------
	#C:/MinGW				/mingw
	C:/TDM-GCC-64				/mingw


3. LAMMPS (14May16) from http://lammps.sandia.gov/download.html (place in C:\lammps-14May16)

4. MATLAB R2015b (Windows 64-bit) - pre-installed on my machine at C:\MATLAB

5. Gnumex 2.06 from http://sourceforge.net/projects/gnumex/files/ (place in C:\Gnumex)



B. Compile LAMMPS

1. Unset read-only permissions on C:\lammps-14May16\

2. Run MSYS as Administrator. In Windows explorer, navigate to C:\MinGW\msys\1.0, right-click msys.bat, then Run as administrator. 
This opens a command line window. Make sure that PATH is set correctly. On the command line, 

	$ g++ -v

should return

	Using built-in specs.
	COLLECT_GCC=C:\TDM-GCC-64\bin\g++.exe
	COLLECT_LTO_WRAPPER=C:/TDM-GCC-64/bin/../libexec/gcc/x86_64-w64-mingw32/5.1.0/lto-wrapper.exe
	Target: x86_64-w64-mingw32
	Configured with: ../../../src/gcc-5.1.0/configure --build=x86_64-w64-mingw32 --enable-targets=all --enable-languages=ada,c,c++,fortran,lto,objc,obj-c++ --enable-libgomp --enable-lto --enable-graphite
	--enable-cxx-flags=-DWINPTHREAD_STATIC --disable-build-with-cxx --disable-build-poststage1-with-cxx --enable-libstdcxx-debug --enable-threads=posix --enable-version-specific-runtime-libs --enable-full
	y-dynamic-string --enable-libstdcxx-threads --enable-libstdcxx-time --with-gnu-ld --disable-werror --disable-nls --disable-win32-registry --prefix=/mingw64tdm --with-local-prefix=/mingw64tdm --with-pk
	gversion=tdm64-1 --with-bugurl=http://tdm-gcc.tdragon.net/bugs
	Thread model: posix
	gcc version 5.1.0 (tdm64-1)

If not, add C:\TDM-GCC-64\bin\ to the PATH environment variable. Restart MSYS as administrator.

3. Compile libmeam.a. On MSYS command line,

    cd /c/lammps-14May16/lib/meam
    make -f Makefile.gfortran
   (ignore the warnings)

4. Compile libmpi_stubs.a. On MSYS command line,

    cd /c/lammps-14May16/src/STUBS
    make
   (ignore the warnings)

5. Fix the Makefile for compiling the LAMMPS executable and library. Using a text editor, 
   open C:\lammps-14May16\src\MAKE\OPTIONS\Makefile.g++_serial. In the "compiler/linker settings", add -lpsapi after LIB =, i.e.
	LINK =		g++
	LINKFLAGS =	-g -O
	LIB =  		-lpsapi
	SIZE =		size
   Save edited file and exit text editor.

6. Compile LAMMPS executable and static library. On MSYS command line,

    cd /c/lammps-14May16/src
    make clean-all
    make yes-meam
    make g++_serial
    make mode=lib g++_serial

    (If make complains about write permissions on some file or directory, 
     unset the Read-only flag for those files/directories, then re-run make)

7. Test the LAMMPS executable
    cd /c/lammps-14May16/examples/meam
    ../../src/lmp_serial_w64 < in.meam


C. Configure MATLAB with Gnumex

1. Run MATLAB

2. Create work directory for LAMMPS-TDM-GCC-64. On the MATLAB prompt, 
    >> mkdir LAMMPS-TDM-GCC-64

3. Setup Gnumex. On the MATLAB prompt, 
    Open C:\Gnumex\gnumex.m
    Run gnumex.m (Add C:\Gnumex to path)

        Use the following settings on the Gnumex GUI:

        MinGW root directory, navigate to C:\TDM-GCC-64
        Cygwin root directory, (empty)
        Path to g95.exe, (empty)
        Path to gfortran.exe, C:\TDM-GCC-64\bin 
        Path to Gnumex utilities, navigate to C:\Gnumex
        Environment / linking type, select MinGW
        Language for compilation, select C / C++
        Optimization level, select -O3
        Generate mex or engine exe?, select Mex
        Add stub, select No
        Path for libraries and .def files, navigate to the LAMMPS-TDM-GCC-64 directory created above
        Mex options file to create, navigate to the LAMMPS-TDM-GCC-64 directory created above

    Click 'Make options file', wait
        (If Gnumex warns about not being able to write files to some MATLAB directories,
         follow the workarounds)

    Exit Gnumex GUI


4. Copy the following files to the LAMMPS-TDM-GCC-64 directory created above

    C:\lammps-14May16\lib\meam\libmeam.a
    C:\lammps-14May16\src\STUBS\libmpi_stubs.a
    C:\lammps-14May16\src\liblammps.a

    C:\lammps-14May16\src\STUBS\mpi.h
    C:\lammps-14May16\src\library.h

    lammps_*.c gateway functions (from Kip Barret)
    lammps_MPCv3.m (from Kip Barret)

    lammps_setup_TDM-GCC-64.m (attached; from Kip Barrett, modified)
    test_run_lammps_MPC.m (attached; from Kip Barrett, modified)

    library.meam (attached)
    Al-example.parameter.meam (attached)


5. In MATLAB, change directory to the LAMMPS-TDM-GCC-64 directory created above
   >> mex -v setup
      (Answer 'n' (No) to "Would you like mex to locate installed compilers [y]/n?"
      (Answer 'gcc' to "Select a compiler:"
      (Verify that "Location: C:\TDM-GCC-64\bin")
      (Answer 'y' to "Are these correct [y]/n?")

   >> lammps_setup_TDM-GCC-64
	(ignore lots of warnings)


6. Test the *.mexw64

   >> test_run_lammps_MPC


The following should display:

	Return values are:

	 - SingleElement: temp  E0  box  alpha  rose_a  rose_E  E1  a1  E1box_volume  E1box_b_a  E1box_c_a  E1box_c_b  E1box_b_a_angle  E1box_c_a_angle  E1box_c_b_angle  E1box_ratios  E1box_angles  E2  a2  box2  E2box_volume  E2box_b_a  E2box_c_a  E2box_c_b  E2box_b_a_angle  E2box_c_a_angle  E2box_c_b_angle  E2box_ratios  E2box_angles  E3  a3  box3  E3box_volume  E3box_b_a  E3box_c_a  E3box_c_b  E3box_b_a_angle  E3box_c_a_angle  E3box_c_b_angle  E3box_ratios  E3box_angles 
 
	- Alloy: temp  Substitution 

	ans = 

    	SingleElement: [1x1 struct]
            	Alloy: [1x1 struct]

You can then use the workspace browser of MATLAB to examine 'ans'