Installation procedure of solvers for Winmostar Ver. 9 (Cygwin)

 Overview

For Winmostar's MD, Solid menu to launch solvers and post processing, it is assumed that various packages are installed and executable on Cygwin.
Packages that depend on the solvers are as follows.

Gromacs : Cygwin, Gromacs, Acpype, AmberTools, ERmod, Packmol
LAMMPS : Cygwin, Acpype, AmberTools, Packmol (LAMMPS Installation is instructed here)
Amber : Cygwin, AmberTools, Packmol
MODYLAS : Cygwin, MODYLAS, Acpype, AmberTools, Packmol
Quantum ESPRESSO : Cygwin, Phonopy, BoltzTraP, Packmol (Quantum ESPRESSO Installation is instructed here)
OpenMX : Cygwin, OpenMX, Packmol

These softwares are distributed under GNU GPL, BSD (for Phonopy) and MIT licenses (for Packmol) so they are available for free.

Theses programs are confirmed to run on Windows 10.
Please understand that calculation results are not guaranteed.

 1. Cygwin


Download setup-x86.exe from http://www.cygwin.com/.
※The latest version is 2.891. (12 April 2018)
Follow the wizard of setup.exe and install it.
The packages which need to be installed are "All default" and the following packages.

  Archive - libbz2-devel 1.0.6-3
  Archive - unzip 6.0-17
  Devel - autoconf 13-1
  Devel - cmake 3.6.2-1
  Devel - flex 2.6.4-2
  Devel - gcc-fortran 6.4.0-5
  Devel - gcc-g++ 6.4.0-5
  Devel - make 4.2.1-2
  Devel - pkg-config 0.29.1-1
  Devel - subversion 1.9.7-2
  Graphics - gnuplot 5.2.2-1
  Graphics - ImageMagick 6.9.9.11-3
  Graphics - ghostscript 9.23-1
  Interpreters - m4 1.4.18-1
  Libs - libboost-devel 1.64.0-1
  Libs - libfftw3-devel 3.3.6-pl1-1
  Libs - libfreetype-devel 2.6.5-1
  Libs - libmpfr4 3.1.6-1p1
  Libs - libnetcdf-devel 4.6.1-1
  Libs - libopenmpi-devel 1.10.7-1
  Libs - libpng-devel 1.6.34-1
  Libs - zlib-devel 1.2.11-1
  Math - bc 1.06.95-2s
  Math - liblapack-devel 3.7.1-1
  Net - openssh 7.7p1-1
  Python - python-h5py 2.5.0-1
  Python - python2-cython 0.25.2-1
  Python - python2-devel 2.7.14-1
  Python - python2-numpy 1.11.2-1
  Python - python2-pip 9.0.1-1
  Python - python2-yaml 3.12-1
  Science - openbabel 2.3.2-6
  Shells - tcsh 6.20.00-1
  Utils - dos2unix 7.4.0-1
  Utils - patchutils 0.3.4-1
  Web - wget 1.19.1-2


Package: _/libfontconfig-common
fontconfig_dtd.sh exit code 2

Above message might be shown after installation.
igore it and continue for now.
We recomment to edit /etc/profile.d/lang.sh so that
export LANG=C

You need to install grace, cygwin package has problems, so install it manually.
Download grace-5.1.25.tar.gz from ftp://plasma-gate.weizmann.ac.il/pub/grace/src/grace5/.
Launch Cygwin's terminal and compile it as shown below.

$ tar xvfz grace-5.1.25.tar.gz
$ cd grace-5.1.25
$ ./configure
$ make
$ make install

Add
export PATH=$PATH:/usr/local/grace/bin
to /etc/profile.d/winmostar.sh

 2. Gromacs


Download gromacs-5.0.7.tar.gz from http://www.gromacs.org/Downloads.
※ 5.1 or later have a problem for gmx rdf. So use 5.0.7 instead.
Launch cygwin terminal and compile as follows. (Set -DGMX_SIMD=AVX_256 for cmake to enable AVX.)

$ tar xvfz gromacs-5.0.7.tar.gz
$ cd gromacs-5.0.7
$ mkdir build
$ cd build
$ cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=OFF -DGMX_USE_RDTSCP=OFF -DGMX_SIMD=SSE2 -DGMX_DOUBLE=OFF
$ make
$ make install
$ cd ..
$ mkdir build_d
$ cd build_d
$ cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=OFF -DGMX_USE_RDTSCP=OFF -DGMX_SIMD=SSE2 -DGMX_DOUBLE=ON
$ make
$ make install

It is installed in /usr/local/gromacs.

Add
source /usr/local/gromacs/bin/GMXRC
to /etc/profile.d/winmostar.sh

 3. AmberTools


Download AmberTools18.tar.bz2 from http://ambermd.org/GetAmber.php#ambertools" target="_blank.
Complie it as follows.

$ tar xvfj AmberTools18.tar.bz2
$ mv amber18 /usr/local/
$ export AMBERHOME=/usr/local/amber18
$ cd $AMBERHOME
$ echo y | ./configure -cygwin -noX11 -nosse --skip-python gnu
$ sed -i 's/LDFLAGS=/LDFLAGS=-Wl,--allow-multiple-definition/' AmberTools/src/cpptraj/config.h
$ source amber.sh
$ make install AMBERBUILDFLAGS="-Wl,--allow-multiple-definition -DWITHOUT_BACKTRACE"

Add
source /usr/local/amber18/amber.sh
to /etc/profile.d/winmostar.sh

 4. Acpype


Get Acpype as follows.

$ svn checkout http://svn.code.sf.net/p/ccpn/code/branches/stable/ccpn/python/acpype/ acpype -r 10101

"/usr/bin/env python" failes when current directory is under C:\cygwin_wm , so changed the line as follow.

$ vi acpype/acpype.py
#!/usr/bin/env python

#!/usr/bin/python

Add option "-dr no" to antechamber.

$ vi acpype/acpype.py
if not os.path.exists(self.acExe):
 self.printError("no 'antechamber' executable!")
 return None
self.tleapExe = _getoutput('which tleap') or ''
self.sleapExe = _getoutput('which sleap') or ''

if not os.path.exists(self.acExe):
 self.printError("no 'antechamber' executable!")
 return None
self.acExe += ' -dr no '
self.tleapExe = _getoutput('which tleap') or ''
self.sleapExe = _getoutput('which sleap') or ''

$ mv acpype /usr/local

Add
export PATH=$PATH:/usr/local/acpype
to /etc/profile.d/winmostar.sh

 5. ERmod


Download ermod-0.3.4.tar.gz from http://sourceforge.net/projects/ermod/files/?source=navbar
Compile as follows.

$ tar zxvf ermod-0.3.4.tar.gz
$ cd ermod-0.3.4/vmdplugins
$ make
$ cp compile/*.so libexec/
$ cd ..
$ ./configure --prefix=/usr/local/ermod --disable-mpi --enable-openmp
$ export LANG=C
$ make
$ make install

See ERmod wiki page for details.

 6. MODYLAS


You need agreement to MODYLAS License to use MODYLAS.

Get MODYLAS_1.0.4.tar_1.gz from http://www.modylas.org/.
Compile as follows.

$ tar -zxvf MODYLAS_1.0.4.tar_1.gz
$ cd MODYLAS_1.0.4/source
$ export FCFLAGS="-DMPIPARA -cpp -O3 -DCOMM_CUBE -DFJMPIDIR -DSYNC_COM -DONEPROC_AXIS" $ ./configure --with-kind-fortran-compiler=INTEL --prefix=/usr/local/MODYLAS_1.0.4
$ cd src
$ vi parse_f.f
Replace line 363
9000 format(‘ERROR:…’, i)
to
9000 format(‘ERROR:…’, i8)

$ make
$ make install

Add
export PATH=$PATH:/usr/local/MODYLAS_1.0.4/bin
to /etc/profile.d/winmostar.sh

MODYLAS website for details.

You need other programs to use full function of MODYLAS.
Please contact Winmostar support.

 7. OpenMX


Get openmx3.8(openmx3.8.tar.gz) and patch(patch3.8.4.tar.gz on 05/Mar./2018) from http://www.openmx-square.org/download.html.

Compile as follows.

$ tar xvfz openmx3.8.tar.gz
$ cd openmx3.8/source
$ cp ../../patch3.8.4.tar.gz .
$ tar xvfz patch3.8.4.tar.gz
$ touch TRAN_Main_Analysis.c
$ touch TRAN_Main_Analysis_NC.c
$ vi makefile
Change CC, FC, CPPFLAGS, LIB as follows.
CC=gcc -fopenmp -O3 -I/usr/include -Dkcomp -Dnosse
FC=gfortran -O3 -I/usr/include -Dkcomp
CPPFLAGS=-DNDEBUG
LIB=-static /usr/lib/libfftw3.dll.a -llapack -lblas -lgfortran /usr/lib/libmpi_mpifh.dll.a /usr/lib/libmpi.dll.a -lquadmath

$ vi openmx_common.h
#define fp_bsize 200000

$ make
$ make install
$ gcc bandgnu13.c -lm -o ../work/bandgnu13.exe
$ make DosMain
$ cp -r ../../openmx3.8 /usr/local

Get fermisurfer_1.7.1.zip from https://ja.osdn.net/projects/fermisurfer/releases/
Unpack and install as follows.
$ unzip fermisurfer_1.7.1.zip
$ cp -r fermisurfer /usr/local/

Add
export PATH=$PATH:/usr/local/openmx3.8/work:/usr/local/fermisurfer/bin
export OPENMX_DATA_PATH=/usr/local/openmx3.8/DFT_DATA13
to /etc/profile.d/winmostar.sh

See OpenMX website and FermiSurfer website for details.

 8. Phonopy


Get phonopy-1.12.6.53.tar.gz from https://pypi.python.org/pypi/phonopy/1.12.6.53.
Compile as follows.

$ tar xvfz phonopy-1.12.6.53.tar.gz
$ cd phonopy-1.12.6.53
$ python setup.py install

 9. MDTraj


Get mdtraj-1.9.0.tar.gz from https://github.com/mdtraj/mdtraj/releases/tag/1.9.0.
Get mdtraj-1.9.0.patch.
Compile as follows.

$ pip2 install ase matplotlib pandas
$ tar xvfz mdtraj-1.9.0.tar.gz
$ cd mdtraj-1.9.0
$ patch -u -p1 -d mdtraj < ../mdtraj-1.9.0.patch
$ python2 setup.py install

 10. BoltzTraP


Get BoltzTraP.tar.bz2(v1.2.5) from https://www.imc.tuwien.ac.at/forschungsbereich_theoretische_chemie/forschungsgruppen/prof_dr_gkh_madsen_theoretical_materials_chemistry/boltztrap/.
Compile as follows.

$ tar xvfj BoltzTraP.tar.bz2
$ cd boltztrap-1.2.5/src/
$ vi x_trans
set log = :log

set log = log
$ rm BoltzTraP
$ make
$ cd ../..
$ mv boltztrap-1.2.5/ /usr/local/

Add
export PATH=$PATH:/usr/local/boltztrap-1.2.5/src
export PATH=$PATH:/usr/local/boltztrap-1.2.5/util
to /etc/profile.d/winmostar.sh

 11. Packmol

Get Packmol 18.166 (packmol-18.166.zip) from https://github.com/mcubeg/packmol/releases.
Compile as follows.

$ unzip packmol-18.166.zip
$ cd packmol-18.166
$ ./configure `which gfortran`
$ vi Makefile
FLAGS= -O3 --fast-math

FLAGS= -O3 --fast-math -m32
$ make
$ cd ..
$ mv packmol-18.166 /usr/local/

Add
export PATH=$PATH:/usr/local/packmol-18.166
to /etc/profile.d/winmostar.sh

 Citation

1. SOUSA DA SILVA, A. W. & VRANKEN, W. F. ACPYPE - AnteChamber PYthon Parser interfacE.
BMC Research Notes 2012, 5:367 doi:10.1186/1756-0500-5-367 http://www.biomedcentral.com/1756-0500/5/367

2. Antechamber
J. Wang, W. Wang, P.A. Kollman and D.A. Case. "Automatic atom type and bond type perception in molecular mechanical calculations".
Journal of Molecular Graphics and Modelling, 25, 247-260 (2006).
J. Wang, R.M. Wolf, J.W. Caldwell, P.A. Kollman and D.A. Case. "Development and testing of a general AMBER force field".
Journal of Computational Chemistry, 25, 1157-1174 (2004).



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