Molden has a powerful Z-matrix editor which give full control over the geometry and allows you to build molecules from scratch, including polypeptides.ĬCL:G: MOLDEN in Windows 7. Molden also features an stand alone forcefield program ambfor, which can optimise geometries with the combined Amber (protein) and GAFF (small molecules) force fields.Ītom typing can be done automatically and interactively from within Molden, as well as firing optimisation jobs. It can calculate and display the true or Multipole Derived Electrostatic Potential and atomic charges can be fitted to the Electrostatic Potential calculated on a Connolly surface. Molden also can animate reaction paths and molecular vibrations. It can write a variety of graphics instructions postscript, XWindows, VRML, povray, OpenGL, tekronix4014, hpgl, hp2392 and Figure.īoth Xwindows and OpenGL versions of Molden are also capable of importing and displaying of chemx, PDB, and a variety of mopac/ampac files and lots of other formats. Molden supports contour plots, 3-d grid plots with hidden lines and a combination of both. Either the spherically averaged atomic density or the oriented ground state atomic density can be subtracted for a number of standard basis sets. Molden is capable of displaying Molecular Orbitals, the electron density and the Molecular minus Atomic density. Molden reads all the required information from the GAMESS / GAUSSIAN outputfile. License: Freeware Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format. The directories for the corresponding library and header files can be found by using dpkg -L Īnd other flags can be extracted from the ~abinit/doc/build/config-template.Ratings: 25 votes Please vote: OS: Linux, Windows, Mac. These libraries are available via apt ( libfftw3-devand libxml2-dev). More specialized libraries might be harder to detect.įor example, the following section was added to the config file to detect customized FFT and XML libraries. Take a look at the template file ~abinit/doc/build/config-template.ac9.įor example, the setting of LINALG_LIBS in this template file is givenīy the line #LINALG_LIBS="-L/usr/local/lib -llapack -lblas". When fine tuning variables and flags for a particular linux distribution, it is advised to The directory was extracted via dpkg -L liblapack-dev and dpkg -L libblas-dev. The LINALG_LIBS variable was explicitly set for this linux distrubution. One uses ‘-‘ when typing a flag but ‘_’ inside the config file, e.g.
# MPI settings with_mpi = "yes" enable_mpi_io = "yes" # linear algebra settings with_linalg_flavor = "netlib" LINALG_LIBS = "-L/usr/lib/x86_64-linux-gnu -llapack -lblas" # mandatory libraries with_libxc = "yes" with_hdf5 = "yes" with_netcdf = "yes" with_netcdf_fortran = "yes" Note that it is also possible to generate these libraries via the ABINIT fallbacks: LIBXC, a library containing exchange-correlation potentials, from the libxc-dev package. These libraries are available via the libhdf5-dev, libnetcdf-dev and libnetcdff-dev packages from apt.įor parallel IO, the libpnetcdf-dev is required. HDF5, NetCDF and NetCDF-Fortran, libraries to write/read binary files in netcdf4 format. mkl from Intel (or you might try the libmkl-full-dev package).MPICH from apt ( libmpich-dev package) or ĭepending on your distribution, you might need to manually add the mpi-default-dev package,Ī fallback (see next point) is available inside ABINIT (basic version of lapack),īut you might want to install a math library yourself, especially for parallel computations:.Open MPI from apt ( libopenmpi-dev package) or.
To use but more optimized for intel architecture.Ī MPI library installed (If you want to benefit from parallelism recommended). This is a commercial compiler, slightly more complicated
Ubuntu or similar Ubuntu-based distributions
Then we discuss how to compile the source code.Ī possible list of prerequisites (tested for Ubuntu 19.10) is: The prerequisites are first discussed qualitatively, because the installation mayĭepend on the linux distribution. YAML-based test suite Python tools and API Zero-point renormalization of the band gap and temperature-dependent band gaps Tutorial on polarization and finite electric fields Calculation of *U* and J using Cococcioni's approach