├── AUTHORS ├── Build_Centos.sh ├── Build_Ubuntu.sh ├── Build_micromamba.sh ├── CITATION.cff ├── ChangeLog.md ├── Makefile.am ├── Makefile.in ├── NEWS ├── README.md ├── aclocal.m4 ├── automekin.yml ├── configure.ac ├── docs ├── Makefile.am ├── Makefile.in ├── README.md └── tutorial.pdf ├── examples ├── Bz.xyz ├── FA.dat ├── FA.xyz ├── FA_2level.dat ├── FA_HL.dat ├── FA_biasH2.dat ├── FA_biasH2O.dat ├── FA_bxde.dat ├── FA_bxde_qcore.dat ├── FA_ck.dat ├── FA_external.dat ├── FA_programopt.dat ├── FA_qcore.dat ├── FA_singletraj.dat ├── FAthermo.dat ├── Makefile.am ├── Makefile.in ├── N2.xyz ├── assoc.dat ├── assoc_qcore.dat ├── cat.xyz ├── co.xyz ├── diels.xyz ├── diels_bias.dat ├── qcore_template ├── qcore_template_wb97xd3 ├── rdiels.xyz ├── rdiels_bias.dat ├── ttors.dat ├── ttors.xyz └── vdW.dat ├── install-sh ├── license.txt ├── logo.png ├── missing ├── modules ├── 2021 ├── Makefile.am └── Makefile.in ├── notebooks ├── AutoMeKin.ipynb ├── AutoMeKin2.ipynb └── amk_tools.ipynb ├── scripts ├── AMK_parameters.py ├── DVV.py ├── DVV_hl.py ├── FormulaPROD.sh ├── HLscripts │ ├── FINAL.sh │ ├── IDENTIFYPROD.sh │ ├── IRC.sh │ ├── IRC_ANALYSIS.sh │ ├── KMC.sh │ ├── LOCATE_BARRIERLESS.sh │ ├── MIN.sh │ ├── Makefile.am │ ├── Makefile.in │ ├── PLOT_RELEVANT.sh │ ├── PRODs.sh │ ├── REMOVE_TS.sh │ ├── RXN_NETWORK.sh │ ├── RXN_NETWORK1.sh │ ├── SORT.sh │ ├── TS.sh │ ├── TWEAK_RXNET.sh │ ├── compare_frags.sh │ ├── get_G_g09.sh │ ├── get_NM_g09.sh │ ├── get_NM_g09_molden.sh │ ├── get_ZPE_g09.sh │ ├── get_energy_g09_CCSDT.sh │ ├── get_energy_g09_DFT.sh │ ├── get_energy_g09_HF.sh │ ├── get_energy_g09_MP2.sh │ ├── get_freq_g09.sh │ ├── get_geom_g09.sh │ ├── get_geom_irc_g09.sh │ ├── get_minfminr_g09.sh │ ├── hlcalcs.sh │ ├── linked_paths.py │ ├── linked_paths.sh │ ├── makerxyz.sh │ ├── nfrag.sh │ ├── reduce_RXNet.py │ ├── runIRC.sh │ ├── runMIN.sh │ └── runTS.sh ├── Heuristics.py ├── Integrators.py ├── Langevin.py ├── LocateTs.py ├── MOPAC_DEV │ ├── Makefile.am │ ├── Makefile.in │ └── mopac ├── Makefile.am ├── Makefile.in ├── abort.sh ├── amk.sh ├── amk_frag.sh ├── amk_parallel.sh ├── bond_order.py ├── bots.py ├── bxde.py ├── check_ts_structure.sh ├── check_vdw_atoms.py ├── chemical_formula.sh ├── com.sh ├── conf_isomer_ts.sh ├── createMat.py ├── cyclic_graph.py ├── deg.sh ├── deg_form.sh ├── diff.sh ├── diffGT.sh ├── emax_from_temp.py ├── entos.py ├── final.sh ├── format.sh ├── format_rxnet.sh ├── get_NM_mopac.sh ├── get_freq_mopac.sh ├── get_geom_mopac.sh ├── get_geom_thermo_mopac.sh ├── get_minn.sh ├── get_minx.sh ├── get_ts_properties.sh ├── getminfminr.sh ├── identifyprod.sh ├── initialqv_mopac_samp1.sh ├── initialqv_mopac_samp2.sh ├── irc.sh ├── irc_analysis.sh ├── kinetics.sh ├── kmc.sh ├── llcalcs.sh ├── locate_barrierless.sh ├── mdiss.py ├── mdiss.sh ├── min.sh ├── minandprod.sh ├── modeanalysis.py ├── mopacamk.py ├── neb_barrless.py ├── ntraj.sh ├── nx.sh ├── plot_relevant.sh ├── redo_screening.sh ├── reduce.sh ├── reduce2.sh ├── reduce3.sh ├── remove_ts.sh ├── runAS.sh ├── runGP.sh ├── run_test.sh ├── runbarless.sh ├── runirc.sh ├── runmin.sh ├── rxn.py ├── rxn_network.sh ├── rxn_network1.sh ├── screening.sh ├── screening_assoc.sh ├── sel_mol.sh ├── select.sh ├── select_assoc.sh ├── simplifyRXN.sh ├── snapshots_mopac.sh ├── sort.sh ├── sort_assoc.sh ├── symm.sh ├── tag_prod.py ├── thermochem.py ├── tors.sh ├── track.py ├── track_view.sh ├── tsll_view.sh ├── tweak_rxnet.sh └── utils.sh ├── share ├── MD ├── Makefile.am ├── Makefile.in ├── amk_build ├── atsymb ├── diagram_template0 ├── diagram_template1 ├── dynamics_template ├── elements ├── elements2 ├── freq_template1 ├── freq_template2 ├── g09_test.dat ├── grad ├── grad_hl ├── header.pdf ├── hl_input_template ├── hl_input_template_notemp ├── hl_input_template_qm ├── opt ├── optTS ├── opt_frozen ├── opt_thermo ├── optfreq ├── optmin_hl ├── optts_hl ├── path_template ├── pop_template.gnu ├── prod_hl ├── scan_tors ├── sp_template ├── thermo_template ├── ts_templatefast └── ts_templateslow └── src ├── HL ├── Makefile.am ├── Makefile.in └── diag.f ├── Makefile.am ├── Makefile.in ├── atsymb.f90 ├── bbfs.f90 ├── constants.f90 ├── constants_rrkm.f90 ├── intern.f90 ├── kmc.f90 ├── kmcEND.f90 ├── nm.f90 ├── omegas.f90 ├── rotate.f90 ├── rrkm.f ├── sprint.f ├── sprint2.f ├── symm.f ├── symm0.f ├── termo.f90 └── tst.f90 /AUTHORS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/AUTHORS -------------------------------------------------------------------------------- /Build_Centos.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/Build_Centos.sh -------------------------------------------------------------------------------- /Build_Ubuntu.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/Build_Ubuntu.sh -------------------------------------------------------------------------------- /Build_micromamba.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/Build_micromamba.sh -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/CITATION.cff -------------------------------------------------------------------------------- /ChangeLog.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/ChangeLog.md -------------------------------------------------------------------------------- /Makefile.am: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/Makefile.am -------------------------------------------------------------------------------- /Makefile.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/Makefile.in -------------------------------------------------------------------------------- /NEWS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/NEWS -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/README.md -------------------------------------------------------------------------------- /aclocal.m4: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/aclocal.m4 -------------------------------------------------------------------------------- /automekin.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/automekin.yml -------------------------------------------------------------------------------- /configure.ac: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/configure.ac -------------------------------------------------------------------------------- /docs/Makefile.am: -------------------------------------------------------------------------------- 1 | docdir= $(prefix)/doc 2 | dist_doc_DATA = tutorial.pdf 3 | 4 | -------------------------------------------------------------------------------- /docs/Makefile.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/docs/Makefile.in -------------------------------------------------------------------------------- /docs/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/docs/README.md -------------------------------------------------------------------------------- /docs/tutorial.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/docs/tutorial.pdf -------------------------------------------------------------------------------- /examples/Bz.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/Bz.xyz -------------------------------------------------------------------------------- /examples/FA.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/FA.dat -------------------------------------------------------------------------------- /examples/FA.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/FA.xyz -------------------------------------------------------------------------------- /examples/FA_2level.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/FA_2level.dat -------------------------------------------------------------------------------- /examples/FA_HL.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/FA_HL.dat -------------------------------------------------------------------------------- /examples/FA_biasH2.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/FA_biasH2.dat -------------------------------------------------------------------------------- /examples/FA_biasH2O.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/FA_biasH2O.dat -------------------------------------------------------------------------------- /examples/FA_bxde.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/FA_bxde.dat -------------------------------------------------------------------------------- /examples/FA_bxde_qcore.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/FA_bxde_qcore.dat -------------------------------------------------------------------------------- /examples/FA_ck.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/FA_ck.dat -------------------------------------------------------------------------------- /examples/FA_external.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/FA_external.dat -------------------------------------------------------------------------------- /examples/FA_programopt.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/FA_programopt.dat -------------------------------------------------------------------------------- /examples/FA_qcore.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/FA_qcore.dat -------------------------------------------------------------------------------- /examples/FA_singletraj.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/FA_singletraj.dat -------------------------------------------------------------------------------- /examples/FAthermo.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/FAthermo.dat -------------------------------------------------------------------------------- /examples/Makefile.am: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/Makefile.am -------------------------------------------------------------------------------- /examples/Makefile.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/Makefile.in -------------------------------------------------------------------------------- /examples/N2.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/N2.xyz -------------------------------------------------------------------------------- /examples/assoc.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/assoc.dat -------------------------------------------------------------------------------- /examples/assoc_qcore.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/assoc_qcore.dat -------------------------------------------------------------------------------- /examples/cat.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/cat.xyz -------------------------------------------------------------------------------- /examples/co.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/co.xyz -------------------------------------------------------------------------------- /examples/diels.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/diels.xyz -------------------------------------------------------------------------------- /examples/diels_bias.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/diels_bias.dat -------------------------------------------------------------------------------- /examples/qcore_template: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/qcore_template -------------------------------------------------------------------------------- /examples/qcore_template_wb97xd3: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/qcore_template_wb97xd3 -------------------------------------------------------------------------------- /examples/rdiels.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/rdiels.xyz -------------------------------------------------------------------------------- /examples/rdiels_bias.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/rdiels_bias.dat -------------------------------------------------------------------------------- /examples/ttors.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/ttors.dat -------------------------------------------------------------------------------- /examples/ttors.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/ttors.xyz -------------------------------------------------------------------------------- /examples/vdW.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/examples/vdW.dat -------------------------------------------------------------------------------- /install-sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/install-sh -------------------------------------------------------------------------------- /license.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/license.txt -------------------------------------------------------------------------------- /logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/logo.png -------------------------------------------------------------------------------- /missing: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/missing -------------------------------------------------------------------------------- /modules/2021: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/modules/2021 -------------------------------------------------------------------------------- /modules/Makefile.am: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/modules/Makefile.am -------------------------------------------------------------------------------- /modules/Makefile.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/modules/Makefile.in -------------------------------------------------------------------------------- /notebooks/AutoMeKin.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/notebooks/AutoMeKin.ipynb -------------------------------------------------------------------------------- /notebooks/AutoMeKin2.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/notebooks/AutoMeKin2.ipynb -------------------------------------------------------------------------------- /notebooks/amk_tools.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/notebooks/amk_tools.ipynb -------------------------------------------------------------------------------- /scripts/AMK_parameters.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/AMK_parameters.py -------------------------------------------------------------------------------- /scripts/DVV.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/DVV.py -------------------------------------------------------------------------------- /scripts/DVV_hl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/DVV_hl.py -------------------------------------------------------------------------------- /scripts/FormulaPROD.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/FormulaPROD.sh -------------------------------------------------------------------------------- /scripts/HLscripts/FINAL.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/FINAL.sh -------------------------------------------------------------------------------- /scripts/HLscripts/IDENTIFYPROD.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/IDENTIFYPROD.sh -------------------------------------------------------------------------------- /scripts/HLscripts/IRC.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/IRC.sh -------------------------------------------------------------------------------- /scripts/HLscripts/IRC_ANALYSIS.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/IRC_ANALYSIS.sh -------------------------------------------------------------------------------- /scripts/HLscripts/KMC.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/KMC.sh -------------------------------------------------------------------------------- /scripts/HLscripts/LOCATE_BARRIERLESS.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/LOCATE_BARRIERLESS.sh -------------------------------------------------------------------------------- /scripts/HLscripts/MIN.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/MIN.sh -------------------------------------------------------------------------------- /scripts/HLscripts/Makefile.am: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/Makefile.am -------------------------------------------------------------------------------- /scripts/HLscripts/Makefile.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/Makefile.in -------------------------------------------------------------------------------- /scripts/HLscripts/PLOT_RELEVANT.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/PLOT_RELEVANT.sh -------------------------------------------------------------------------------- /scripts/HLscripts/PRODs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/PRODs.sh -------------------------------------------------------------------------------- /scripts/HLscripts/REMOVE_TS.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/REMOVE_TS.sh -------------------------------------------------------------------------------- /scripts/HLscripts/RXN_NETWORK.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/RXN_NETWORK.sh -------------------------------------------------------------------------------- /scripts/HLscripts/RXN_NETWORK1.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/RXN_NETWORK1.sh -------------------------------------------------------------------------------- /scripts/HLscripts/SORT.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/SORT.sh -------------------------------------------------------------------------------- /scripts/HLscripts/TS.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/TS.sh -------------------------------------------------------------------------------- /scripts/HLscripts/TWEAK_RXNET.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/TWEAK_RXNET.sh -------------------------------------------------------------------------------- /scripts/HLscripts/compare_frags.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/compare_frags.sh -------------------------------------------------------------------------------- /scripts/HLscripts/get_G_g09.sh: -------------------------------------------------------------------------------- 1 | awk '/Thermal correction to Gibbs Free Energy/{print $7;exit}' $1 2 | -------------------------------------------------------------------------------- /scripts/HLscripts/get_NM_g09.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/get_NM_g09.sh -------------------------------------------------------------------------------- /scripts/HLscripts/get_NM_g09_molden.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/get_NM_g09_molden.sh -------------------------------------------------------------------------------- /scripts/HLscripts/get_ZPE_g09.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/get_ZPE_g09.sh -------------------------------------------------------------------------------- /scripts/HLscripts/get_energy_g09_CCSDT.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/get_energy_g09_CCSDT.sh -------------------------------------------------------------------------------- /scripts/HLscripts/get_energy_g09_DFT.sh: -------------------------------------------------------------------------------- 1 | file=$1 2 | nc=$2 3 | awk '/sp ca/{++fl};/SCF Done/{if(fl=='$nc'-1) e=$5};END{print e}' $file 4 | 5 | -------------------------------------------------------------------------------- /scripts/HLscripts/get_energy_g09_HF.sh: -------------------------------------------------------------------------------- 1 | file=$1 2 | nc=$2 3 | awk '/sp ca/{++fl};/SCF Done/{if(fl=='$nc'-1 && $3 ~ /HF/) e=$5};END{print e}' $file 4 | 5 | -------------------------------------------------------------------------------- /scripts/HLscripts/get_energy_g09_MP2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/get_energy_g09_MP2.sh -------------------------------------------------------------------------------- /scripts/HLscripts/get_freq_g09.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/get_freq_g09.sh -------------------------------------------------------------------------------- /scripts/HLscripts/get_geom_g09.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/get_geom_g09.sh -------------------------------------------------------------------------------- /scripts/HLscripts/get_geom_irc_g09.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/get_geom_irc_g09.sh -------------------------------------------------------------------------------- /scripts/HLscripts/get_minfminr_g09.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/get_minfminr_g09.sh -------------------------------------------------------------------------------- /scripts/HLscripts/hlcalcs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/hlcalcs.sh -------------------------------------------------------------------------------- /scripts/HLscripts/linked_paths.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/linked_paths.py -------------------------------------------------------------------------------- /scripts/HLscripts/linked_paths.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/linked_paths.sh -------------------------------------------------------------------------------- /scripts/HLscripts/makerxyz.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/makerxyz.sh -------------------------------------------------------------------------------- /scripts/HLscripts/nfrag.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/nfrag.sh -------------------------------------------------------------------------------- /scripts/HLscripts/reduce_RXNet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/reduce_RXNet.py -------------------------------------------------------------------------------- /scripts/HLscripts/runIRC.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/runIRC.sh -------------------------------------------------------------------------------- /scripts/HLscripts/runMIN.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/runMIN.sh -------------------------------------------------------------------------------- /scripts/HLscripts/runTS.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/HLscripts/runTS.sh -------------------------------------------------------------------------------- /scripts/Heuristics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/Heuristics.py -------------------------------------------------------------------------------- /scripts/Integrators.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/Integrators.py -------------------------------------------------------------------------------- /scripts/Langevin.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/Langevin.py -------------------------------------------------------------------------------- /scripts/LocateTs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/LocateTs.py -------------------------------------------------------------------------------- /scripts/MOPAC_DEV/Makefile.am: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/MOPAC_DEV/Makefile.am -------------------------------------------------------------------------------- /scripts/MOPAC_DEV/Makefile.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/MOPAC_DEV/Makefile.in -------------------------------------------------------------------------------- /scripts/MOPAC_DEV/mopac: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/MOPAC_DEV/mopac -------------------------------------------------------------------------------- /scripts/Makefile.am: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/Makefile.am -------------------------------------------------------------------------------- /scripts/Makefile.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/Makefile.in -------------------------------------------------------------------------------- /scripts/abort.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/abort.sh -------------------------------------------------------------------------------- /scripts/amk.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/amk.sh -------------------------------------------------------------------------------- /scripts/amk_frag.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/amk_frag.sh -------------------------------------------------------------------------------- /scripts/amk_parallel.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/amk_parallel.sh -------------------------------------------------------------------------------- /scripts/bond_order.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/bond_order.py -------------------------------------------------------------------------------- /scripts/bots.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/bots.py -------------------------------------------------------------------------------- /scripts/bxde.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/bxde.py -------------------------------------------------------------------------------- /scripts/check_ts_structure.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/check_ts_structure.sh -------------------------------------------------------------------------------- /scripts/check_vdw_atoms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/check_vdw_atoms.py -------------------------------------------------------------------------------- /scripts/chemical_formula.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/chemical_formula.sh -------------------------------------------------------------------------------- /scripts/com.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/com.sh -------------------------------------------------------------------------------- /scripts/conf_isomer_ts.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/conf_isomer_ts.sh -------------------------------------------------------------------------------- /scripts/createMat.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/createMat.py -------------------------------------------------------------------------------- /scripts/cyclic_graph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/cyclic_graph.py -------------------------------------------------------------------------------- /scripts/deg.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/deg.sh -------------------------------------------------------------------------------- /scripts/deg_form.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/deg_form.sh -------------------------------------------------------------------------------- /scripts/diff.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/diff.sh -------------------------------------------------------------------------------- /scripts/diffGT.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/diffGT.sh -------------------------------------------------------------------------------- /scripts/emax_from_temp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/emax_from_temp.py -------------------------------------------------------------------------------- /scripts/entos.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/entos.py -------------------------------------------------------------------------------- /scripts/final.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/final.sh -------------------------------------------------------------------------------- /scripts/format.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/format.sh -------------------------------------------------------------------------------- /scripts/format_rxnet.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/format_rxnet.sh -------------------------------------------------------------------------------- /scripts/get_NM_mopac.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/get_NM_mopac.sh -------------------------------------------------------------------------------- /scripts/get_freq_mopac.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/get_freq_mopac.sh -------------------------------------------------------------------------------- /scripts/get_geom_mopac.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/get_geom_mopac.sh -------------------------------------------------------------------------------- /scripts/get_geom_thermo_mopac.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/get_geom_thermo_mopac.sh -------------------------------------------------------------------------------- /scripts/get_minn.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/get_minn.sh -------------------------------------------------------------------------------- /scripts/get_minx.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/get_minx.sh -------------------------------------------------------------------------------- /scripts/get_ts_properties.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/get_ts_properties.sh -------------------------------------------------------------------------------- /scripts/getminfminr.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/getminfminr.sh -------------------------------------------------------------------------------- /scripts/identifyprod.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/identifyprod.sh -------------------------------------------------------------------------------- /scripts/initialqv_mopac_samp1.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/initialqv_mopac_samp1.sh -------------------------------------------------------------------------------- /scripts/initialqv_mopac_samp2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/initialqv_mopac_samp2.sh -------------------------------------------------------------------------------- /scripts/irc.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/irc.sh -------------------------------------------------------------------------------- /scripts/irc_analysis.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/irc_analysis.sh -------------------------------------------------------------------------------- /scripts/kinetics.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/kinetics.sh -------------------------------------------------------------------------------- /scripts/kmc.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/kmc.sh -------------------------------------------------------------------------------- /scripts/llcalcs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/llcalcs.sh -------------------------------------------------------------------------------- /scripts/locate_barrierless.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/locate_barrierless.sh -------------------------------------------------------------------------------- /scripts/mdiss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/mdiss.py -------------------------------------------------------------------------------- /scripts/mdiss.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/mdiss.sh -------------------------------------------------------------------------------- /scripts/min.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/min.sh -------------------------------------------------------------------------------- /scripts/minandprod.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/minandprod.sh -------------------------------------------------------------------------------- /scripts/modeanalysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/modeanalysis.py -------------------------------------------------------------------------------- /scripts/mopacamk.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/mopacamk.py -------------------------------------------------------------------------------- /scripts/neb_barrless.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/neb_barrless.py -------------------------------------------------------------------------------- /scripts/ntraj.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/ntraj.sh -------------------------------------------------------------------------------- /scripts/nx.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/nx.sh -------------------------------------------------------------------------------- /scripts/plot_relevant.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/plot_relevant.sh -------------------------------------------------------------------------------- /scripts/redo_screening.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/redo_screening.sh -------------------------------------------------------------------------------- /scripts/reduce.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/reduce.sh -------------------------------------------------------------------------------- /scripts/reduce2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/reduce2.sh -------------------------------------------------------------------------------- /scripts/reduce3.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/reduce3.sh -------------------------------------------------------------------------------- /scripts/remove_ts.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/remove_ts.sh -------------------------------------------------------------------------------- /scripts/runAS.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/runAS.sh -------------------------------------------------------------------------------- /scripts/runGP.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/runGP.sh -------------------------------------------------------------------------------- /scripts/run_test.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/run_test.sh -------------------------------------------------------------------------------- /scripts/runbarless.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/runbarless.sh -------------------------------------------------------------------------------- /scripts/runirc.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/runirc.sh -------------------------------------------------------------------------------- /scripts/runmin.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/runmin.sh -------------------------------------------------------------------------------- /scripts/rxn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/rxn.py -------------------------------------------------------------------------------- /scripts/rxn_network.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/rxn_network.sh -------------------------------------------------------------------------------- /scripts/rxn_network1.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/rxn_network1.sh -------------------------------------------------------------------------------- /scripts/screening.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/screening.sh -------------------------------------------------------------------------------- /scripts/screening_assoc.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/screening_assoc.sh -------------------------------------------------------------------------------- /scripts/sel_mol.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/sel_mol.sh -------------------------------------------------------------------------------- /scripts/select.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/select.sh -------------------------------------------------------------------------------- /scripts/select_assoc.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/select_assoc.sh -------------------------------------------------------------------------------- /scripts/simplifyRXN.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/simplifyRXN.sh -------------------------------------------------------------------------------- /scripts/snapshots_mopac.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/snapshots_mopac.sh -------------------------------------------------------------------------------- /scripts/sort.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/sort.sh -------------------------------------------------------------------------------- /scripts/sort_assoc.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/sort_assoc.sh -------------------------------------------------------------------------------- /scripts/symm.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/symm.sh -------------------------------------------------------------------------------- /scripts/tag_prod.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/tag_prod.py -------------------------------------------------------------------------------- /scripts/thermochem.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/thermochem.py -------------------------------------------------------------------------------- /scripts/tors.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/tors.sh -------------------------------------------------------------------------------- /scripts/track.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/track.py -------------------------------------------------------------------------------- /scripts/track_view.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/track_view.sh -------------------------------------------------------------------------------- /scripts/tsll_view.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/tsll_view.sh -------------------------------------------------------------------------------- /scripts/tweak_rxnet.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/tweak_rxnet.sh -------------------------------------------------------------------------------- /scripts/utils.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/scripts/utils.sh -------------------------------------------------------------------------------- /share/MD: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/MD -------------------------------------------------------------------------------- /share/Makefile.am: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/Makefile.am -------------------------------------------------------------------------------- /share/Makefile.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/Makefile.in -------------------------------------------------------------------------------- /share/amk_build: -------------------------------------------------------------------------------- 1 | 1142 2 | -------------------------------------------------------------------------------- /share/atsymb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/atsymb -------------------------------------------------------------------------------- /share/diagram_template0: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/diagram_template0 -------------------------------------------------------------------------------- /share/diagram_template1: -------------------------------------------------------------------------------- 1 | plot NaN 2 | pause -1 3 | 4 | -------------------------------------------------------------------------------- /share/dynamics_template: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/dynamics_template -------------------------------------------------------------------------------- /share/elements: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/elements -------------------------------------------------------------------------------- /share/elements2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/elements2 -------------------------------------------------------------------------------- /share/freq_template1: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/freq_template1 -------------------------------------------------------------------------------- /share/freq_template2: -------------------------------------------------------------------------------- 1 | 2 | method oldgeo force 3 | title 4 | freq calc 5 | -------------------------------------------------------------------------------- /share/g09_test.dat: -------------------------------------------------------------------------------- 1 | %KJob L301 2 | # 3 | 4 | title 5 | 6 | 0 2 7 | h 8 | 9 | 10 | -------------------------------------------------------------------------------- /share/grad: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/grad -------------------------------------------------------------------------------- /share/grad_hl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/grad_hl -------------------------------------------------------------------------------- /share/header.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/header.pdf -------------------------------------------------------------------------------- /share/hl_input_template: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/hl_input_template -------------------------------------------------------------------------------- /share/hl_input_template_notemp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/hl_input_template_notemp -------------------------------------------------------------------------------- /share/hl_input_template_qm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/hl_input_template_qm -------------------------------------------------------------------------------- /share/opt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/opt -------------------------------------------------------------------------------- /share/optTS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/optTS -------------------------------------------------------------------------------- /share/opt_frozen: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/opt_frozen -------------------------------------------------------------------------------- /share/opt_thermo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/opt_thermo -------------------------------------------------------------------------------- /share/optfreq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/optfreq -------------------------------------------------------------------------------- /share/optmin_hl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/optmin_hl -------------------------------------------------------------------------------- /share/optts_hl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/optts_hl -------------------------------------------------------------------------------- /share/path_template: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/path_template -------------------------------------------------------------------------------- /share/pop_template.gnu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/pop_template.gnu -------------------------------------------------------------------------------- /share/prod_hl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/prod_hl -------------------------------------------------------------------------------- /share/scan_tors: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/scan_tors -------------------------------------------------------------------------------- /share/sp_template: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/sp_template -------------------------------------------------------------------------------- /share/thermo_template: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/thermo_template -------------------------------------------------------------------------------- /share/ts_templatefast: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/ts_templatefast -------------------------------------------------------------------------------- /share/ts_templateslow: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/share/ts_templateslow -------------------------------------------------------------------------------- /src/HL/Makefile.am: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/src/HL/Makefile.am -------------------------------------------------------------------------------- /src/HL/Makefile.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/src/HL/Makefile.in -------------------------------------------------------------------------------- /src/HL/diag.f: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/src/HL/diag.f -------------------------------------------------------------------------------- /src/Makefile.am: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/src/Makefile.am -------------------------------------------------------------------------------- /src/Makefile.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/src/Makefile.in -------------------------------------------------------------------------------- /src/atsymb.f90: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/src/atsymb.f90 -------------------------------------------------------------------------------- /src/bbfs.f90: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/src/bbfs.f90 -------------------------------------------------------------------------------- /src/constants.f90: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/src/constants.f90 -------------------------------------------------------------------------------- /src/constants_rrkm.f90: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/src/constants_rrkm.f90 -------------------------------------------------------------------------------- /src/intern.f90: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/src/intern.f90 -------------------------------------------------------------------------------- /src/kmc.f90: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/src/kmc.f90 -------------------------------------------------------------------------------- /src/kmcEND.f90: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/src/kmcEND.f90 -------------------------------------------------------------------------------- /src/nm.f90: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/src/nm.f90 -------------------------------------------------------------------------------- /src/omegas.f90: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/src/omegas.f90 -------------------------------------------------------------------------------- /src/rotate.f90: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/src/rotate.f90 -------------------------------------------------------------------------------- /src/rrkm.f: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/src/rrkm.f -------------------------------------------------------------------------------- /src/sprint.f: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/src/sprint.f -------------------------------------------------------------------------------- /src/sprint2.f: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/src/sprint2.f -------------------------------------------------------------------------------- /src/symm.f: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/src/symm.f -------------------------------------------------------------------------------- /src/symm0.f: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/src/symm0.f -------------------------------------------------------------------------------- /src/termo.f90: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/src/termo.f90 -------------------------------------------------------------------------------- /src/tst.f90: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emartineznunez/AutoMeKin/HEAD/src/tst.f90 --------------------------------------------------------------------------------