Programs and Utilities

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Fortran Programs
Name Remark
aar.f ADF output extraction
allign.f Remove rotational motion from a set of geometries (for vibrational function calculation, see surfaces.f and peswf.f
analcfp.f Analyzes wavefunction from the lanthanide program (crystal field theory), see also CFP.doc
analfinp.f Identifies amide groups in FILE.X and amide modes in F.INP
aveg.f Averages geometries in FILE.X
bder.f Numerical calculation of polarizability derivatives
bderq.f Numerical calculation of polarizability derivatives in normal modes
boltzman.f Vibrations from ensemble of Gaussian outputs
bumat.f symmetry-adapted vibrational coordinates, from Quantum chemistry program exchange
bumatc6.f bmat.f, for redundant internal coordinates
bumatd.f bmat.f, for redundant internal coordinates, diagonal only
bumatw.f A variation of bumatd.f
cctf.f Compares S-vectors (vibrations) in two molecules
cctn.f Cartesian coordinate transfer of force field and intensity tensors cctn.doc
cctnbig.f as cctn.f, but for extra large molecules, force field matrix is compressed
cff.f Makes input for the lanthanide program (crystal field theory)
cfp.f Makes coefficients of fractional parentage (crystal field theory)
ch3.f vibrational spectra of toluene and similar molecules with a free rotating group
ch3n.f ch3 for two rotating groups
chopg.f chop Gaussian output
chopg1.f chops off Gaussian TDDFT output, unnecessary for RNSOS
chopk.f chops Gaussian output into individual jobs
cicond.f reduces ciss_a file, for Grimme's tdft program
comparemo.f compare MOs in similar chromophores
contact.f selects contact molecules, for cluster/crystall modelling
contactc.f selects contact molecules, for cluster/crystall modelling
convg.f extracts Gaussian normal mode cubic and quartic constants into CQQ.TXT.SCR and DQQ,TXT,SCR
coord2.f a variant of coord.f
corcoef.f calculates correlation coefficient for two sets of data, correlate Nth column in file1 with Mth column of file2
corcoemf.f Correlate all columns in a file with each other
correcttdc.f Adds transition dipole coupling correction to force field
cscale.f force field perturbational scaling
cticad5.f extracts FF from cadpac output (obsolete)
cubcut.f cut through Gaussian orbital .cub file
cubcut2.f cut through Gaussian orbital .cub file
dar2.f extracts Dalton output, force field and Raman tensors
dare.f dar2.f for Dalton2
dc_psi.f dc.f for arbitrary system size, cf. dc.doc and dodc.doc
dcanal.f CD for a row of twisted dipoles
dcroa.f CD-ROA for a row of twisted dipoles
distr.f distribution function from a set of data (e.g. torsion angles in MD)
distr2.f distribution function from a set of data (e.g. torsion angles in MD), 2D
divide.f divides Gaussian multi-output into separate files
dodc.f supplementary to dc.f, places the vibrational transition dipoles into molecules (dodc.doc)
dodcg.f supplementary to dc.f, places the electronic transition dipoles into molecules, form Gaussian output
dodcg1.f supplementary to dc.f, places the electronic transition dipoles into molecules, form Gaussian and Turbomole output
dodcg2.f supplementary to dc.f, places the electronic transition dipoles into molecules, form Gaussian and Turbomole output, other version
dodcgn.f supplementary to dc.f, places the electronic transition dipoles into molecules, form Gaussian and Turbomole output, the newest version
dusch.f Makes Duschinsky transformation and other matrices for Franck-Condon factors, see guvcde.doc
dynalook.f Looks at changes in a hydration shell, in FILE.X
dynamiM.f generation of spectra from MD trajectories (from autocorrelation functions), dynamiM.doc
eattt.f removes contributions of selected atoms from polarizability derivatives
findrydberg.f analyzes electronic transitions in Gaussian output, identifies Rydberg states
fitnma.f computes fitting coefficients for the amide group solvation model
fixper.f fixes periodic conditions in a coordinate scan output
flow.f MD flow monitoring (developing version)
fof.f Decomposition of Gaussian spherical harmonics
fpc.f fixed partial charge model of IR and VCD
fphase.f unifies phases of two vibrational S-vectors
fragmentdna.f Fragments peptides and nucleic acids, for tensor transfer
ft.f Polynomial fit
ftry.f original force field scaling program
ftry95.f original force field scaling program, other version
gadf.f extracts adf outputs - Exc. spectra
gahtables.f Extracts anharmonic spectral intensities from Gaussian output
gar.f extracts force field, atomic polar and axial tensors and polarizability derivatives from Gaussian 03 archive
gar_castep.f extracts vibrational files from CASTEP
gar_cfour.f extracts vibrational files from C4
gar_cp2k.f extracts vibrational files from CP2K
gar9.f extracts force field, atomic polar and axial tensors and polarizability derivatives from Gaussian 09 archive (Josef Kapitan's version)
gcm.f extracts vibrationally-resolved electronic band from Gaussian 09/16 output
gcomp.f a statistical analysis of a set of geometries gcomp.doc
genchar.f generates charges around a solute based on a MD solvatation
generate_cpf.f Generates coefficients of fractional parentage (crystal field theory)
get_tinker_pot.f generates M charges around a molecule of N atoms, get_tinker_potential.doc
getfpc.f extracts Mulliken charges from Gaussian output
gg.f get geometry from Gaussian output
ggbest.f gets lowest-energy geometry from Gaussian output
ggopt.f gets optimized geometry from Gaussian output
gjjconf.f extracts J-coupling constants from Gaussian output
gmopt.f optimized geometry from MOPAC output
gnmr.f extracts shielding from Gaussian output
gnmrconf.f extracts shielding from Gaussian output, gnmrconf.doc
gnmrpara.f extracts paramagnetic NMR parameters from Gaussian output
gnnj.f Derivatives of MCD Gnj tensor
goin.f makes inputs for the original scaling program
goverlap.f analyses a set of geometries
goverlap95.f analyses a set of geometries, another version
guvcd4.f extracts electronic excitations from Gaussian output, J. Sebek's version
guvcde.f extracts electronic excitations from gaussian and calculates CD/MCD by SOS method, see guvcde.doc
ham.f Makes script for WHAM Tinker calculation
hof.f Harmonic oscillator wavefunction
hydr.f empirical force field water correction, hydration_manual.doc
hypep.f empirical force field water correction
hypep_ttt.f empirical force field water correction
ict.f Tensor transfer (see cctn.f), but in internal coordinates
inco.f Cartesian-internal coordinate conversion
inputcage.f define a grid around a molecule for orbital etc. plotting
integral.f a 3D integration
intt.f Rewrites tensors into internal bond-based coordinates
iraich5.f 5-member ring coordinates
IRaichfourier.f 5-member ring coordinates
irroa.f induced resonance roa
irroaw.f induced resonance roa
joinroatab.f joins many .TAB files
jointab.f joins many .TAB files
jointabe.f joins many .TAB files, weighed by energies in EN.LST
kuknasodik.f analyses Na position around a DNA molecule (for MD)
kuknauhly.f analyses DNA torsional angles in MD
makea.f Exctracts Amber MD geometry
makebonds.f generate bonds for a molecule based on inter-atomic distances
makebondslong.f generate bonds for a molecule based on inter-atomic distances, loose criteria
makecc.f Making big FILE.X movie file from CASTEP output
makecrystal.f Takes geometry of a crystal cell, and propagates it, makecrystal.doc
makecrystalfc.f Takes geometry and force field of a crystal cell and makes the dynamic matrices
makecrystalff.f Takes geometry and force field of a crystal cell and makes the dynamic matrices
makef.f extracts Tinker MD geometries into FILE.X
makef2.f extracts Tinker MD geometries into FILE.X, atom interval accepted
makefc.f extracts CPMD geometries into FILE.X
mcdvdiv.f Devides gaussian output with numerical differentiation, for vibrationally resolved MCD
mcmtorsion.f geometry parameters from a list of geometries
molxyz.f internal-Cartesian coordiante transformation
mroa.f for simulation of rotationally resolved magnetic Raman optical activity (and vibrational circular dichroism) , for NO2
mroax.f for simulation of rotationally resolved magnetic Raman optical activity (and vibrational circular dichroism) , for X2 molecules
mulliken.f as getfptc.f, gets Mulliken charges
ndft.f Displays vibrational harmonic wafefunction/density
ndft_m4.f Displays vibrational anharmonic wafefunction/density
ndft_w.f fits nuclear charge density form a harmonic wavefunction
new1.f defines internal vibrational and symmetry-adapted vibrational coordinates; to obtain potential energy distribution, you need also bumat.f, goin.f, and ftry.f, see also PED.doc and intrinsic.zip.
new2.f defines scaling factors and atomic masses for vibrations
new3.f calculates vibrational frequencies in internal coordinates
new4.f calculates vibrational frequencies in Cartesian coordinates
new4c.f calculates vibrational frequencies in Cartesian coordinates, crystal version
new4big.f calculates vibrational frequencies in Cartesian coordinates, very large molecules (Davidson diagonalization)
new4ft.f IR and VCD spectra of large molecules by Fourier propagation (without diagonalization) ,21.5.2008
new4ft2.f IR and VCD spectra of large molecules by Fourier propagation (without diagonalization), other version , 2.5.2008
new4ftq.f IR and VCD spectra of large molecules by Fourier propagation (without diagonalization), parallel version 3.11.2008
new4ftr.f IR and VCD spectra of large molecules by Fourier propagation (without diagonalization), raman extension 15.4.2013
new4ftr5.f IR and VCD spectra of large molecules by Fourier propagation (without diagonalization), raman extension, dynamic allocation, 18.4.2013
new4fts.f IR and VCD spectra of large molecules by Fourier propagation (without diagonalization), 9.6.2008
new5.f produces IR and VCD spectra from dipole derivatives and S-matrix
new5psi.f produces IR and VCD spectra from dipole derivatives and S-matrix, for arbitrary system size
new6.f produces Raman and ROA spectra from polarizability derivatives and S-matrix
new6c.f produces Raman and ROA spectra from polarizability derivatives and S-matrix , crystal
new7.f inelestic neutron scattering
newa.f automatic vibrational spectra generation
numforce.f calculates force field (Hessian) from many gradients
orbcpl.f rotational strengths between orbitals
par.f extracts vibrational data (geometry, FF) from CPMD output
pedall.f approximate potential energy disctribution
perpes.f Completes 2D PES for Sigmaplot plotting
pessp.f Generation of spectra from peswf output
peswf.f vibrational function for anharmonic molecular motions peswf.doc
pmz.f Gaussian input generation, also for numerical differentiations pmz.doc
prepflex.f empirical FF correction
prephyd1.f "
prephyd2.f "
prephyd3.f "
prephyd4.f "
prephyd5.f "
prephyd6.f "
prephydraflex.f
prepmd2.f spectra-lrestrained MD, prepareation script
prepnumf.f prepares inputs for a numerical differentiation (obsolete)
prepq.f makes script driving optimization in normal modes of many files
qgrad.f optimization in normal mode coordinates QGRADoptions.doc, runopt script, quick start qgrad_start.tgz
rcd.f rotational CD
rdf.f radial distribution function for MD simulations, runopt script,,
rdf3d.f 3-D solvent probability distribution from MD simulations rdf3d.doc; see also pvs.doc for parallel variable selection of MD clusters
readnmr.f extract NMR parameters from Gaussian output
redim.f string substitutions if a list of files
rewritebasis.f rewrites Gaussian-Turbomole basis formats
RNSOS.tgz program for Sum Over State Calculations, SOS.doc
rtime.f looks at FILE.X snapshots and analyzes interaction of solvent with a solute
rotdip.f comparemo.f output manipulation
rtt.f extracts Turbomole output
rwbc.f replace water in Gaussian input by charges
rxyzt.f converts Turbomole coord into FILE.X
scub.f FT smoothing of cub file
seroa.f SEROA, seroa-man.doc,
S4.tgz anharmonic vibrational energies and properties S4.doc S4-suplement.doc
slowft.f slow FT
sortconf.f an analysis of multiple conformers in Gaussian output
sortCQQ.f sorting cubic constants
sortDQQ.f sorting quartic constants
specav2d.f spectra averaging 2D
specave.f spectra averaging
specav1n2.f spectra averaging in a range
specomp.f optical spectra comparison and fit, specomp.doc
ssd.f supporting program for ch3.f, normal mode phase correction during the scan
ssdn.f supporting program for ch3.f, normal mode phase correction during the scan ,2D
stretch.f stretch a molecule according a normal mode displacement
surfaces.f PES smoothing, to peswf.f
tabprnf.f generates XY spectrum from intensities in .TAB files
tgrad.f Optimization of large molecules using fragments (developing), tgrad.doc
tinkerinp.f makes Gaussian input form Tinker geometries
tinkertomcm.f geometry conversion
tinkertorsion.f Tinker MD coordinate statistics
Tinker with Helical Periodic Boundary Conditions Tinker 6.2 modified source code
trcd.f transforms AH constants, mass substitutions (two S-matrices)
turbo.f extracts electronic transitions from Turbomole output
turbog.f extracts electronic transitions from Turbomole output
uworks.f beyond BO, developing, uworks.doc
v3atm.f defines polarizabilities in internal molecualr frame
wham.f calculates the potential of mean forces (PMF) using the weighted histogram analysis method (WHAM) in Tinker, see also ham.f, tscan.f, dynamic.f, gethist.f, wrhist.f, and WHAM.doc
wr2.f making a formatted number list
wr3.f another making a formatted number list, increment other than one
xcharge.f find a charge for peptide in FILE.X
xinp.f makes Gaussian input from a .x (mcm format) file
xshell.f selects a solvent shell around a molecule xshell.doc
xtorsion.f calculates internal coordinates for a set of geometries

Pascal (Delphi) Programs
Name Remark
density.zip orbital and density visualization
mcm95.zip molecular graphics
magnet.zip liquid chromatography simualtion (MD)
monitor.zip disk space monitor
play.zip vibrational normal mode displacement visualization
sc95.zip spectra viewer SC95.doc
tabprn95.zip spectra generation from intensity tables