Programs and Utilities
No Support, No Guarantee!!
| 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, see makecrystal.doc |
| contacts.f | selects contact molecules, for cluster/crystall modelling, pair interactions only, see makecrystal.doc |
| contacts.f | selects contact molecules, for cluster/crystall modelling, a version of contact, see makecrystal.doc |
| 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 |
| cpropag.f | propagates a one-dimensional periodic structure, see makecrystal.doc |
| 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, see also irroa.doc |
| 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, see also contactc.f contacts.f contactp.f, makecrystalff.f, cpropag.g and x00.f |
| 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, makecrystal.doc |
| 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 |
| specompnl.f | optical spectra comparison and fit, specompnl.doc |
| specompG.f | optical spectra comparison and fit, free energy specompG.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 |
| x00.f | makes tensors of elementary cell,makecrystal.doc |
| 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 |