Programs and Utilities

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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, 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 |

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 |

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 |