I was using SIESTA, and just learning the program in general, however, was having trouble finding a suitable way to automatically generate FDF files, I understand this can be done manually, and have been doing that, but I wanted an automatic solution.
I heard about wxDragon, however the website is offline (If anyone has macOS Binaries that would be amazing) but are there any other tools?
You can use the sisl code to convert and manage fdf files.
Say reading the xyz file and converting this to the appropriate fdf file can be done with this command-line utility:
sgeom input.xyz output.fdf
sgeom POSCAR output.fdf
The input.xyz contains the lattice information in case it has been generated by sisl or ASE.
Note, I am the author of sisl.
You can use OpenBabel to convert between several formats:
abinit -- ABINIT Output Format [Read-only]
acesin -- ACES input format [Write-only]
acesout -- ACES output format [Read-only]
acr -- ACR format [Read-only]
adf -- ADF cartesian input format [Write-only]
adfband -- ADF Band output format [Read-only]
adfdftb -- ADF DFTB output format [Read-only]
adfout -- ADF output format [Read-only]
alc -- Alchemy format
aoforce -- Turbomole AOFORCE output format [Read-only]
arc -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
ascii -- ASCII format [Write-only]
axsf -- XCrySDen Structure Format [Read-only]
bgf -- MSI BGF format
box -- Dock 3.5 Box format
bs -- Ball and Stick format
c09out -- Crystal 09 output format [Read-only]
c3d1 -- Chem3D Cartesian 1 format
c3d2 -- Chem3D Cartesian 2 format
cac -- CAChe MolStruct format [Write-only]
caccrt -- Cacao Cartesian format
cache -- CAChe MolStruct format [Write-only]
cacint -- Cacao Internal format [Write-only]
can -- Canonical SMILES format
car -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
castep -- CASTEP format [Read-only]
ccc -- CCC format [Read-only]
cdjson -- ChemDoodle JSON
cdx -- ChemDraw binary format [Read-only]
cdxml -- ChemDraw CDXML format
cht -- Chemtool format [Write-only]
cif -- Crystallographic Information File
ck -- ChemKin format
cml -- Chemical Markup Language
cmlr -- CML Reaction format
cof -- Culgi object file format
com -- Gaussian Input [Write-only]
confabreport -- Confab report format [Write-only]
CONFIG -- DL-POLY CONFIG
CONTCAR -- VASP format
CONTFF -- MDFF format
copy -- Copy raw text [Write-only]
crk2d -- Chemical Resource Kit diagram(2D)
crk3d -- Chemical Resource Kit 3D format
csr -- Accelrys/MSI Quanta CSR format [Write-only]
cssr -- CSD CSSR format [Write-only]
ct -- ChemDraw Connection Table format
cub -- Gaussian cube format
cube -- Gaussian cube format
dallog -- DALTON output format [Read-only]
dalmol -- DALTON input format
dat -- Generic Output file format [Read-only]
dmol -- DMol3 coordinates format
dx -- OpenDX cube format for APBS
ent -- Protein Data Bank format
exyz -- Extended XYZ cartesian coordinates format
fa -- FASTA format
fasta -- FASTA format
fch -- Gaussian formatted checkpoint file format [Read-only]
fchk -- Gaussian formatted checkpoint file format [Read-only]
fck -- Gaussian formatted checkpoint file format [Read-only]
feat -- Feature format
fh -- Fenske-Hall Z-Matrix format [Write-only]
fhiaims -- FHIaims XYZ format
fix -- SMILES FIX format [Write-only]
fps -- FPS text fingerprint format (Dalke) [Write-only]
fpt -- Fingerprint format [Write-only]
fract -- Free Form Fractional format
fs -- Fastsearch format
fsa -- FASTA format
g03 -- Gaussian Output [Read-only]
g09 -- Gaussian Output [Read-only]
g16 -- Gaussian Output [Read-only]
g92 -- Gaussian Output [Read-only]
g94 -- Gaussian Output [Read-only]
g98 -- Gaussian Output [Read-only]
gal -- Gaussian Output [Read-only]
gam -- GAMESS Output [Read-only]
gamess -- GAMESS Output [Read-only]
gamin -- GAMESS Input
gamout -- GAMESS Output [Read-only]
gau -- Gaussian Input [Write-only]
gjc -- Gaussian Input [Write-only]
gjf -- Gaussian Input [Write-only]
got -- GULP format [Read-only]
gpr -- Ghemical format
gr96 -- GROMOS96 format [Write-only]
gro -- GRO format
gukin -- GAMESS-UK Input
gukout -- GAMESS-UK Output
gzmat -- Gaussian Z-Matrix Input
hin -- HyperChem HIN format
HISTORY -- DL-POLY HISTORY [Read-only]
inchi -- InChI format
inchikey -- InChIKey [Write-only]
inp -- GAMESS Input
ins -- ShelX format [Read-only]
jin -- Jaguar input format
jout -- Jaguar output format [Read-only]
k -- Compare molecules using InChI [Write-only]
lmpdat -- The LAMMPS data format [Write-only]
log -- Generic Output file format [Read-only]
lpmd -- LPMD format
mcdl -- MCDL format
mcif -- Macromolecular Crystallographic Info
MDFF -- MDFF format
mdl -- MDL MOL format
ml2 -- Sybyl Mol2 format
mmcif -- Macromolecular Crystallographic Info
mmd -- MacroModel format
mmod -- MacroModel format
mna -- Multilevel Neighborhoods of Atoms (MNA) [Write-only]
mol -- MDL MOL format
mol2 -- Sybyl Mol2 format
mold -- Molden format
molden -- Molden format
molf -- Molden format
molreport -- Open Babel molecule report [Write-only]
moo -- MOPAC Output format [Read-only]
mop -- MOPAC Cartesian format
mopcrt -- MOPAC Cartesian format
mopin -- MOPAC Internal
mopout -- MOPAC Output format [Read-only]
mp -- Molpro input format [Write-only]
mpc -- MOPAC Cartesian format
mpd -- MolPrint2D format [Write-only]
mpo -- Molpro output format [Read-only]
mpqc -- MPQC output format [Read-only]
mpqcin -- MPQC simplified input format [Write-only]
mrv -- Chemical Markup Language
msi -- Accelrys/MSI Cerius II MSI format [Read-only]
msms -- M.F. Sanner's MSMS input format [Write-only]
nul -- Outputs nothing [Write-only]
nw -- NWChem input format [Write-only]
nwo -- NWChem output format [Read-only]
orca -- ORCA output format [Read-only]
orcainp -- ORCA input format [Write-only]
out -- Generic Output file format [Read-only]
outmol -- DMol3 coordinates format
output -- Generic Output file format [Read-only]
paint -- Painter format [Write-only]
pc -- PubChem format [Read-only]
pcjson -- PubChem JSON
pcm -- PCModel Format
pdb -- Protein Data Bank format
pdbqt -- AutoDock PDBQT format
png -- PNG 2D depiction
pointcloud -- Point cloud on VDW surface [Write-only]
pos -- POS cartesian coordinates format [Read-only]
POSCAR -- VASP format
POSFF -- MDFF format
pov -- POV-Ray input format [Write-only]
pqr -- PQR format
pqs -- Parallel Quantum Solutions format
prep -- Amber Prep format [Read-only]
pwscf -- PWscf format [Read-only]
qcin -- Q-Chem input format [Write-only]
qcout -- Q-Chem output format [Read-only]
report -- Open Babel report format [Write-only]
res -- ShelX format [Read-only]
rinchi -- RInChI [Write-only]
rsmi -- Reaction SMILES format
rxn -- MDL RXN format
sd -- MDL MOL format
sdf -- MDL MOL format
siesta -- SIESTA format [Read-only]
smi -- SMILES format
smiles -- SMILES format
smy -- SMILES format using Smiley parser [Read-only]
stl -- STL 3D-printing format [Write-only]
svg -- SVG 2D depiction [Write-only]
sy2 -- Sybyl Mol2 format
t41 -- ADF TAPE41 format [Read-only]
tdd -- Thermo format
text -- Read and write raw text
therm -- Thermo format
tmol -- TurboMole Coordinate format
txt -- Title format
txyz -- Tinker XYZ format
unixyz -- UniChem XYZ format
VASP -- VASP format
vmol -- ViewMol format
wln -- Wiswesser Line Notation [Read-only]
xed -- XED format [Write-only]
xml -- General XML format [Read-only]
xsf -- XCrySDen Structure Format [Read-only]
xyz -- XYZ cartesian coordinates format
yob -- YASARA.org YOB format
zin -- ZINDO input format [Write-only]
Many software use it in the background to make their "own" conversions. You can download it from here or just installed from your Linux repository.
Another option is c2x which supports both Siesta and Vasp, amongst others, and has Mac binaries for download. [Declaration of interest: I wrote c2x.]
c2x --fdf POSCAR out.fdf
etc. Converting from xyz is trickier, due to different conventions about if/where to put the unit cell parameter, required by Siesta, in an xyz file. C2x attempts to support the common conventions.
I use SIESTA regularly so I'll tell you the way I do it. You can use sisl as @nickpapior proposed, so I will give you a different alternative. Using the program gdis, with it can open multiple molecular coordinate formats, including xyz, mol, pdb, etc. Then, in the top left corner, you have the option of saving the molecule in SIESTA format. This is nice when you have a molecule with many atoms. Then what I do is to delete all the presets gdis puts in the fdf file except for SystemLabel, NumberOfAtoms, NumberOfSpecies, block ChemicalSpeciesLabel, block AtomicCoordinatesAndAtomicSpecies. Then at the end I add the line include defaults.fdf. defaults.fdf is a file with all the parameters I use. Usually, within the same project that file doesn't change much from simulation to simulation. That's not a 100 % automatic solution but is pretty close. If you are in Ubuntu or Debian-based system you can install it easily from the command line with apt.
One little warning, if you are creating a .fdf file from a .pdb in that format molecules are enumerated, for example, C1, C2, C3, ... Then, before creating the fdf you have to select all atoms of the same species and relabel them. That's easy to do inside the program in editor mode.
Inside the program, you can select and configure some settings for the fdf but I still recommend you have your own defaults.
