### BCC2 Methodology Input Example Source: https://manual.q-chem.com/latest/Ch6.S6.SS7.html Example input file for running a BCC2 calculation in Q-Chem. ```text $molecule 1 2 F H 1 1.001 $end $rem UNRESTRICTED TRUE JOBTYPE SP EXCHANGE HF GEN_SCFMAN_FINAL TRUE DO_BCC2 3 run BCC2 SCF_ALGORITHM DIIS SCF_GUESS GWH BASIS sto-3g AUX_BASIS rimp2-vdz SCF_CONVERGENCE 8 THRESH 14 PURECART 1111 INTEGRAL_SYMMETRY FALSE $end ``` -------------------------------- ### Example .qchemrc File Source: https://manual.q-chem.com/latest/sect_customization.html A practical example of overriding default $rem settings for DIIS subspace size, convergence threshold, and SCF cycles. ```text $rem DIIS_SUBSPACE_SIZE 5 Modify max DIIS subspace size THRESH 10 10**(-10) threshold MAX_SCF_CYCLES 100 More than the default of 50 $end ``` -------------------------------- ### Example $svp Input Section Source: https://manual.q-chem.com/latest/subsec_SS%28V%29PE.html A concrete example of an $svp input section defining cavity and dielectric parameters. ```text $svp RHOISO=0.001, DIELST=78.39, NPTLEB=110 $end ``` -------------------------------- ### OVOCV OO-DFT Analysis Input Example Source: https://manual.q-chem.com/latest/sect_ovocv-analysis.html Example input for performing OVOCV analysis on a charge transfer system, including initial data generation and subsequent excitation analysis. ```Q-Chem $molecule 0 1 N 0.000000000 0.000000000 -2.149985070 H -0.469826010 -0.813762490 -2.534400940 H -0.469826010 0.813762490 -2.534400940 H 0.939652030 0.000000000 -2.534400940 F 0.000000000 0.000000000 15.850014930 F 0.000000000 0.000000000 17.275484090 $end $comment IMOM we use for TRIPLET EXCITATIONS or MIXED-SPIN configurations $end $rem thresh 14 scf_convergence 8 method hf basis def2-TZVP scf_algorithm diis_gdm sym_ignore true #make sure symmetry is off symmetry false XC_GRID 50000194 unrestricted true ovocv_analysis 1 save_ovocv_init_data 1 $end @@@ $rem unrestricted true thresh 14 scf_convergence 6 method hf basis def2-TZVP mom_method imom mom_start 1 scf_guess read scf_max_cycles 500 sym_ignore true symmetry false XC_GRID 50000194 make_cube_files true plots 1 ovocv_analysis 1 load_ovocv_init_data 1 ovocv_quadrature 9 ovocv_thresh 15000 ovocv_excite_analysis 1 ovocv_excite_type 1 save_ovocv 0 $end $molecule read $end $occupied 1 2 3 4 5 6 7 8 9 10 11 12 13 15 1 2 3 4 5 6 7 8 9 10 11 12 13 14 $end $plots grid_points 50 50 50 $end ``` -------------------------------- ### Interactive Input for input-Q-Chem-t-rex.sh Source: https://manual.q-chem.com/latest/sect_Romberg.html Example session for generating finite-field input files. ```text Components: x=1 y=2 z=3 all_beta=4 all_alpha=5 4 File name eth- Number of field amplitudes 5 Smallest field amplitude F_0 0.0004 a (F_k=a^k F_0) 2.0 Number of files created 101 ``` -------------------------------- ### User-Defined Basis Set Input Example Source: https://manual.q-chem.com/latest/Ch8.S4.SS3.html Example of a complete Q-Chem input file defining a non-standard basis set with PURECART settings. ```text $molecule 0 1 O H O oh H O oh 2 hoh oh = 1.2 hoh = 110.0 $end $rem EXCHANGE hf BASIS gen user-defined general basis BASIS2 sto-3g sto-3g orbitals as initial guess PURECART 112 Cartesian d functions, pure f and g $end $basis H 0 S 2 1.00 1.30976 0.430129 0.233136 0.678914 **** O 0 S 2 1.00 49.9810 0.430129 8.89659 0.678914 SP 2 1.00 1.94524 0.049472 0.511541 0.49336 0.963782 0.612820 D 1 1.00 0.39000 1.000000 F 1 1.00 4.10000 1.000000 G 1 1.00 3.35000 1.000000 **** $end ``` -------------------------------- ### Batch Job Input File Example Source: https://manual.q-chem.com/latest/Ch3.S5.SS1.html Demonstrates a sequence of three jobs: a geometry optimization, a frequency calculation using the previous geometry and MOs, and a higher-level single-point energy calculation. ```Q-Chem $comment Optimize H-H at HF/6-31G* $end $molecule 0 1 H H 1 r r = 1.1 $end $rem JOBTYPE opt Optimize the bond length METHOD hf BASIS 6-31G* $end @@@ $comment Now calculate the frequency of H-H at the same level of theory. $end $molecule read $end $rem JOBTYPE freq Calculate vibrational frequency METHOD hf BASIS 6-31G* SCF_GUESS read Read the MOs from disk $end @@@ $comment Now a single point calculation at at MP2/6-311G(d,p)//HF/6-31G* $end $molecule read $end $rem METHOD mp2 BASIS 6-311G(d,p) $end ``` -------------------------------- ### ALMO-MSDFT diabatization configuration Source: https://manual.q-chem.com/latest/subsec_frag_diabat.html Example of an ALMO-MSDFT calculation setup for an ethylene dimer system. ```Q-Chem C 0.000000 0.000000 0.000000 C 1.332000 0.000000 0.000000 H -0.574301 0.000000 -0.928785 H -0.574301 0.000000 0.928785 H 1.906301 0.000000 0.928785 H 1.906301 0.000000 -0.928785 -- 0 1 C -0.000000 4.000000 0.000000 C 1.332000 4.000000 -0.000000 H -0.574301 4.000000 0.928785 H -0.574301 4.000000 -0.928785 H 1.906301 4.000000 -0.928785 H 1.906301 4.000000 0.928785 $end $rem METHOD PBE0 BASIS 6-31+G(D) UNRESTRICTED TRUE THRESH 14 SCF_CONVERGENCE 8 SCFMI_MODE 1 FRGM_METHOD STOLL FRAG_DIABAT_METHOD ALMO_MSDFT INTEGRAL_SYMMETRY FALSE POINT_GROUP_SYMMETRY FALSE $end $almo_coupling 1 2 0 1 -- 0 1 1 2 $end ``` -------------------------------- ### Q-Chem input for energy and gradient calculations with occ-RI-K Source: https://manual.q-chem.com/latest/subsec_occrik.html Example input file demonstrating the configuration for energy and gradient calculations using the occ-RI-K method. Ensure RI_J is set to false as recommended. ```text $molecule 0 1 C 0.0000000 0.3057430 5.7138876 C 0.0000000 -0.5442831 4.4256275 C 0.0000000 0.3675825 3.1787857 C 0.0000000 -0.4853210 1.8908707 C 0.0000000 0.4264823 0.6439435 C 0.0000000 -0.4264823 -0.6439435 C 0.0000000 0.4853210 -1.8908707 C 0.0000000 -0.3675825 -3.1787857 C 0.0000000 0.5442831 -4.4256275 C 0.0000000 -0.3057430 -5.7138876 H 0.8973039 0.9418895 5.7433715 H -0.8973039 0.9418895 5.7433715 H -0.8965960 -1.1827891 4.4155828 H 0.8965960 -1.1827891 4.4155828 H 0.8966512 1.0057416 3.1940146 H -0.8966512 1.0057416 3.1940146 H -0.8966512 -1.1234851 1.8761493 H 0.8966512 -1.1234851 1.8761493 H 0.8966507 1.0646443 0.6587590 H -0.8966507 1.0646443 0.6587590 H -0.8966507 -1.0646443 -0.6587590 H 0.8966507 -1.0646443 -0.6587590 H 0.8966512 1.1234851 -1.8761493 H -0.8966512 1.1234851 -1.8761493 H -0.8966512 -1.0057416 -3.1940146 H 0.8966512 -1.0057416 -3.1940146 H 0.8965960 1.1827891 -4.4155828 H -0.8965960 1.1827891 -4.4155828 H 0.8973039 -0.9418895 -5.7433715 H 0.0000000 0.3580832 -6.5913113 H -0.8973039 -0.9418895 -5.7433715 H 0.0000000 -0.3580832 6.5913113 $end $rem JOBTYPE force EXCHANGE HF BASIS cc-pVTZ AUX_BASIS cc-pVTZ-JK OCC_RI_K 1 RI_K_GRAD 1 INCFOCK 0 PURECART 1111 $end ``` -------------------------------- ### SQC/MM simulation input Source: https://manual.q-chem.com/latest/sect_MMND.html Example input for an SQC/MM nonadiabatic dynamics simulation starting on the S2 state with Wigner-sampled initial conditions. ```Q-Chem $molecule 0 1 C -1.10077021 -0.38619733 0.05617695 C 0.09675762 -1.08610723 -0.30779113 C 1.28662554 -0.41739388 -0.28021086 O 1.41824439 0.84326764 0.06159343 O -1.12106364 0.80448471 0.39946439 H 0.49060260 1.16255871 0.27980893 H 0.06099112 -2.12846061 -0.60005353 H 2.23038546 -0.89206633 -0.54524306 H -2.05177379 -0.94757617 0.02607669 $end $rem JOBTYPE freq METHOD pbe0 BASIS 6-31g* $end @@@ $molecule read $end $rem JOBTYPE aimd METHOD pbe0 BASIS 6-31g* CIS_N_ROOTS 4 CIS_SINGLETS true CIS_TRIPLETS false AIMD_METHOD qcmd !initiates quasi-classical nonadiabatic dynamics QCMD_METHOD sqc TIME_STEP 10 !in atomic units AIMD_STEPS 340 QCMD_INITSTATE 2 !start on S2 QCMD_INITNUC wigner !sample from a Wigner distribution SQC_GAMADJUST true AIMD_TEMP 0 RPA 0 $end ``` -------------------------------- ### Ehrenfest simulation input Source: https://manual.q-chem.com/latest/sect_MMND.html Example input for an Ehrenfest nonadiabatic dynamics simulation starting on the S5 state with Boltzmann-sampled initial conditions. ```Q-Chem $molecule 0 1 Na 0.00000000 0.00000000 0.93444743 H 0.00000000 0.00000000 -0.93444743 $end $rem JOBTYPE freq METHOD hflyp BASIS 6-31g* $end @@@ $molecule read $end $rem JOBTYPE aimd METHOD hflyp BASIS 6-31g* CIS_N_ROOTS 6 CIS_SINGLETS true CIS_TRIPLETS false AIMD_METHOD qcmd !initiates quasi-classical nonadiabatic dynamics QCMD_METHOD ehrenfest TIME_STEP 10 !in atomic units AIMD_STEPS 340 QCMD_INITSTATE 5 !start on S5 QCMD_INITNUC boltzmann !sample from a Boltzmann distribution AIMD_TEMP 300 RPA 0 $end ``` -------------------------------- ### Triplet Excited State Geometry Optimization in Single-Precision Source: https://manual.q-chem.com/latest/sec_SP_EOM_CC.html Example of a geometry optimization for a triplet excited state of a uracil-water complex using a single-precision setup. ```Q-Chem $molecule 0 1 N 0.034130 -.986909 0.000000 N -1.173397 .981920 0.000000 C -1.218805 -.408164 0.000000 C -0.007302 1.702153 0.000000 C 1.196200 1.107045 0.000000 C 1.289085 -.345905 0.000000 O 2.310232 -.996874 0.000000 O -2.257041 -1.026495 0.000000 H 0.049329 -1.997961 0.000000 H -2.070598 1.437050 0.000000 H -0.125651 2.776484 0.000000 H 2.111671 1.674079 0.000000 O 1.747914 -1.338382 -3.040233 H 2.180817 -1.817552 -2.333676 H 0.813180 -1.472188 -2.883392 $end $rem JOB_TYPE = opt METHOD = ccsd BASIS = cc-pvdz CC_STATE_TO_OPT = [1,1] MEM_TOTAL = 30000 EE_TRIPLETS = [1] CC_SP_T_CONV = 4 CC_SP_E_CONV = 6 CC_SINGLE_PREC = 1 EOM_SINGLE_PREC = 1 CC_SP_DM = 1 CC_EOM_PROP = 1 EOM_ARESP_SINGLE_PREC = 1 $end ``` -------------------------------- ### Basic QM/MM Optimization Input Source: https://manual.q-chem.com/latest/sect_CHARMM.html Example input file for a QM/MM optimization of a water dimer using the Q-Chem/Charmm interface. ```Q-Chem $molecule 0 1 O -0.91126 1.09227 1.02007 H -1.75684 1.51867 1.28260 H -0.55929 1.74495 0.36940 $end $rem METHOD hf ! HF Exchange BASIS cc-pvdz ! Correlation Consistent Basis QM_MM true ! Turn on QM/MM calculation JOBTYPE force ! Need this for QM/MM optimizations $end $external_charges 1.20426 -0.64330 0.79922 -0.83400 1.01723 -1.36906 1.39217 0.41700 0.43830 -0.06644 0.91277 0.41700 $end ``` -------------------------------- ### SMD Model with User-Defined Solvent Configuration Source: https://manual.q-chem.com/latest/ex_SMx-User-Solvent.html Example input file demonstrating the use of the $smx section to define custom solvent parameters for the SMD model. ```Q-Chem $comment User-defined specification of pentane. (Result should be equivalent to SOLVENT = PENTANE) $end $molecule 0 1 C -0.361658 -0.986967 0.222366 C -1.331098 0.144597 -0.108363 O -0.592574 1.354183 0.036738 C 0.798089 1.070899 0.136509 C 0.964682 -0.396154 -0.256319 H -0.625676 -1.925862 -0.267011 H -0.333229 -1.158101 1.302753 H -1.697529 0.068518 -1.140448 H -2.193412 0.181620 0.562129 H 1.130199 1.238399 1.169839 H 1.348524 1.754318 -0.514697 H 1.050613 -0.489646 -1.343151 H 1.843065 -0.855802 0.199659 $end $rem METHOD b3lyp BASIS 6-31G* SOLVENT_METHOD smd $end $smx solvent other epsilon 1.840 SolN 1.357 SolA 0.000 ! could be omitted SolB 0.000 ! could be omitted SolG 22.300 SolC 0.000 ! could be omitted SolH 0.000 ! could be omitted $end ``` -------------------------------- ### CAP-AIMD Simulation Input Source: https://manual.q-chem.com/latest/ex_CAP_HF_energy_decomp.html Example input for an Ab Initio Molecular Dynamics (AIMD) simulation using a CAP. This setup includes velocity initialization and specific AIMD control parameters in the $rem section. ```Q-Chem $molecule READ $end $velocity 3.6095e-05 4.1623e-06 2.3754e-05 -9.7386e-04 -1.4552e-05 -1.2310e-03 -2.8737e-04 1.2165e-04 2.9068e-04 3.3619e-05 -1.3939e-04 1.0849e-04 6.4312e-04 2.0187e-04 -4.2066e-04 -2.1196e-04 1.3012e-03 -2.1364e-04 $end $rem ¯JOBTYPE¯¯AIMD ¯METHOD¯¯¯HF ¯BASIS¯¯¯GENERAL ¯GEN_SCFMAN¯¯TRUE ¯SKIP_OLD_SCFMAN¯TRUE ¯SCF_CONVERGENCE¯8 ¯MAX_SCF_CYCLES¯¯3000 integral_symmetry FALSE point_group_symmetry False ¯SCF_GUESS¯¯READ ¯COMPLEX_CCMAN¯¯TRUE ¯UNRESTRICTED¯¯TRUE ¯MOM_START¯¯1 ¯MOM_METHOD¯¯MOM ¯TIME_STEP¯¯2 ¯AIMD_STEPS¯¯200 ¯FOCK_EXTRAP_ORDER 0 ¯FOCK_EXTRAP_POINTS 0 ¯AIMD_MOMENTS¯¯1 ¯AIMD_PRINT¯¯2¯! Print Mulliken charges and dipole moments at each step ¯CS_STRICT¯¯TRUE $end $complex_ccman ¯CS_HF ¯¯¯1 ¯CAP_TYPE ¯¯1 ¯CAP_ETA ¯¯230 ¯CAP_X ¯¯¯4360 ¯CAP_Y ¯¯¯2680 ¯CAP_Z ¯¯¯4360 $end $basis H¯0 cc-pvtz **** C 0 S 8 1.00 8236.0000000 0.0005310 1235.0000000 0.0041080 280.8000000 0.0210870 79.2700000 0.0818530 25.5900000 0.2348170 8.9970000 0.4344010 3.3190000 0.3461290 0.3643000 -0.0089830 S 8 1.00 8236.0000000 -0.0001130 1235.0000000 -0.0008780 280.8000000 -0.0045400 79.2700000 -0.0181330 25.5900000 -0.0557600 8.9970000 -0.1268950 3.3190000 -0.1703520 0.3643000 0.5986840 S 1 1.00 11.8760000 1.0000000 S 1 1.00 4.2920000 1.0000000 S 1 1.00 0.9059000 1.0000000 S 1 1.00 0.1285000 1.0000000 P 3 1.00 18.7100000 0.0140310 4.1330000 0.0868660 1.2000000 0.2902160 P 1 1.00 33.1900000 1.0000000 P 1 1.00 8.7780000 1.0000000 P 1 1.00 0.3827000 1.0000000 P 1 1.00 0.1209000 1.0000000 D 1 1.00 14.8390000 1.0000000 D 1 1.00 1.0970000 1.0000000 D 1 1.00 0.3180000 1.0000000 F 1 1.00 0.7610000 1.0000000 P¯1¯¯1.00 ¯¯0.06045¯1.00 P¯1¯¯1.00 ¯¯0.030225¯1.00 P¯1¯¯1.00 ¯¯0.0151125¯1.00 **** $end ``` -------------------------------- ### Example of $plots input deck Source: https://manual.q-chem.com/latest/sect_plot.mo.html This input deck demonstrates evaluating the HOMO and LUMO of H2 on a 1x1x15 grid along the bond axis. ```Q-Chem $molecule 0 1 H 0.0 0.0 0.35 H 0.0 0.0 -0.35 $end $rem METHOD hf BASIS 6-31g** IANLTY 200 $end $plots Plot the HOMO and the LUMO on a line 1 0.0 0.0 1 0.0 0.0 15 -3.0 3.0 2 0 0 0 1 2 $end ``` -------------------------------- ### OVOCV OO-DFT Analysis for LMCT in Fe(H2O)6 3+ Source: https://manual.q-chem.com/latest/sect_ovocv-analysis.html This example demonstrates a multi-step workflow for OVOCV analysis, starting with initial data generation, followed by a fragment-based SCF guess, and concluding with excitation analysis. ```Q-Chem $molecule +3 6 -- +3 6 Fe -0.5022247054 1.2927779200 0.0001938411 -- 0 1 H 2.1134166395 2.0808631740 -0.0009010689 H -0.5027205697 -1.3235141738 -0.7847973080 H -3.1183219511 2.0796505928 -0.0004236834 H 0.2840444564 1.2933014045 2.6166394903 H -0.5027751731 3.9101762183 0.7846214605 O 1.5358193871 1.2947592260 -0.0014374082 H 2.1156949943 0.5103151332 -0.0009786075 O -0.5019595039 3.3312830798 -0.0005116891 H -0.5019009551 3.9098531329 -0.7858415694 O -0.5013746615 1.2930914301 2.0381118720 H -1.2864874118 1.2932385232 2.6170717164 O -2.5401948736 1.2938974534 0.0009627059 H -3.1195714968 0.5090879007 0.0019042859 O -0.5018840213 -0.7448372467 0.0005186723 H -0.5008290080 -1.3235744599 0.7857827770 O -0.5020354665 1.2915906981 -2.0378380237 H 0.2835925140 1.2915440728 -2.6160740707 H -1.2869601935 1.2917959205 -2.6170203924 $end $rem jobtype sp method wb97x-v basis def2-tzvp scf_max_cycles 1000 scf_algorithm gdm sym_ignore true symmetry false thresh 14 scf_convergence 7 unrestricted true ovocv_analysis 1 save_ovocv_init_data 1 $end ``` ```Q-Chem $molecule +3 6 -- +2 5 Fe -0.5022247054 1.2927779200 0.0001938411 -- +1 2 H 2.1134166395 2.0808631740 -0.0009010689 H -0.5027205697 -1.3235141738 -0.7847973080 H -3.1183219511 2.0796505928 -0.0004236834 H 0.2840444564 1.2933014045 2.6166394903 H -0.5027751731 3.9101762183 0.7846214605 O 1.5358193871 1.2947592260 -0.0014374082 H 2.1156949943 0.5103151332 -0.0009786075 O -0.5019595039 3.3312830798 -0.0005116891 H -0.5019009551 3.9098531329 -0.7858415694 O -0.5013746615 1.2930914301 2.0381118720 H -1.2864874118 1.2932385232 2.6170717164 O -2.5401948736 1.2938974534 0.0009627059 H -3.1195714968 0.5090879007 0.0019042859 O -0.5018840213 -0.7448372467 0.0005186723 H -0.5008290080 -1.3235744599 0.7857827770 O -0.5020354665 1.2915906981 -2.0378380237 H 0.2835925140 1.2915440728 -2.6160740707 H -1.2869601935 1.2917959205 -2.6170203924 $end $rem jobtype sp scf_guess fragmo FRGM_METHOD STOLL SCF_PRINT_FRGM TRUE method wb97x-v basis def2-tzvp scf_max_cycles 1000 scf_algorithm gdm sym_ignore true symmetry false thresh 14 scf_convergence 7 unrestricted true $end $rem_frgm SCF_CONVERGENCE 5 SCF_ALGORITHM DIIS_GDM THRESH 14 $end ``` ```Q-Chem $molecule read $end $rem jobtype sp method wb97x-v basis def2-tzvp scf_guess read mom_method imom mom_start 1 sym_ignore true symmetry false thresh 14 scf_convergence 7 scf_max_cycles 2000 unrestricted true make_cube_files true plots 1 ovocv_analysis 1 load_ovocv_init_data 1 ovocv_quadrature 9 ovocv_thresh 20000 ovocv_excite_analysis 1 ovocv_excite_type 2 save_ovocv 0 $end $plots grid_points 50 50 50 $end ``` -------------------------------- ### Cartesian Coordinate Examples Source: https://manual.q-chem.com/latest/sect_molinput_coords.html Examples of defining H2O geometry using atomic numbers or atomic symbols. ```text $molecule 0 1 8 0.000000 0.000000 -0.212195 1 1.370265 0.000000 0.848778 1 -1.370265 0.000000 0.848778 $end ``` ```text $molecule 0 1 O 0.000000 0.000000 -0.212195 H 1.370265 0.000000 0.848778 H -1.370265 0.000000 0.848778 $end ``` -------------------------------- ### Q-Chem Input File for Romberg Calculation Source: https://manual.q-chem.com/latest/sect_Romberg.html Example input file for ethylene using B3LYP with required high-precision and symmetry settings. ```text $molecule 0 1 C 0.00000000 0.00000000 -0.66880000 H 0.94859916 0.00000000 -1.19917145 H -0.94859916 0.00000000 -1.19917145 C -0.00000000 0.00000000 0.66880000 H -0.54409413 0.77704694 1.19917145 H 0.54409413 -0.77704694 1.19917145 $end $rem BASIS = sto-3g EXCHANGE = B3lyp SCF_CONVERGENCE = 13 ! tight convergence for finite field calculations SCF_MAX_CYCLES = 200 CC_PRINT_PREC = 16 ! decimal points of total energies INTEGRAL_SYMMETRY = false ! all symmetries need to be turned off $end ``` -------------------------------- ### Basis Set Projection Input Example Source: https://manual.q-chem.com/latest/sect_projection.html Demonstrates using BASIS2 to provide an initial guess for a calculation with a general basis set. ```Q-Chem $molecule 0 1 O H 1 r H 1 r 2 a r 0.9 a 104.0 $end $rem METHOD mp2 BASIS general BASIS2 sto-3g $end $basis O 0 S 3 1.000000 3.22037000E+02 5.92394000E-02 4.84308000E+01 3.51500000E-01 1.04206000E+01 7.07658000E-01 SP 2 1.000000 7.40294000E+00 -4.04453000E-01 2.44586000E-01 1.57620000E+00 1.22156000E+00 8.53955000E-01 SP 1 1.000000 3.73684000E-01 1.00000000E+00 1.00000000E+00 SP 1 1.000000 8.45000000E-02 1.00000000E+00 1.00000000E+00 **** H 0 S 2 1.000000 5.44717800E+00 1.56285000E-01 8.24547000E-01 9.04691000E-01 S 1 1.000000 1.83192000E-01 1.00000000E+00 **** $end ``` -------------------------------- ### Generating density and spin-density cube files Source: https://manual.q-chem.com/latest/sec_cubefiles.html Example input for generating cube files for ground and excited-state densities, including spin densities, for the HOO radical. ```Q-Chem $molecule 0 2 H 1.004123 -0.180454 0.000000 O -0.246002 0.596152 0.000000 O -1.312366 -0.230256 0.000000 $end $rem PLOT_SPIN_DENSITY true MAKE_CUBE_FILES true SCF_CONVERGENCE 8 METHOD b3lyp BASIS 6-31+G* CIS_N_ROOTS 1 $end $plots grid information and request to plot 2 densities 20 -5.0 5.0 20 -5.0 5.0 20 -5.0 5.0 0 2 0 0 0 1 $end ``` -------------------------------- ### Example PE-HF calculation input Source: https://manual.q-chem.com/latest/subsec_PE_job_control.html Example configuration for a PE-HF calculation involving 4-Nitroaniline and six water molecules. ```text $comment The potential file \texttt{gen\_scfman\_pe\_potfile.pot} can be found in the samples folder. $end ``` -------------------------------- ### Z-matrix Parameterized and Explicit Examples Source: https://manual.q-chem.com/latest/sect_molinput_coords.html Examples showing the use of parameters versus explicit values in Z-matrix definitions. ```text $molecule 0 1 O1 O2 O1 oo H1 O1 ho O2 hoo H2 O2 ho O1 hoo H1 hooh oo = 1.5 oh = 1.0 hoo = 120.0 hooh = 180.0 $end ``` ```text $molecule 0 1 O1 O2 O1 1.5 H1 O1 1.0 O2 120.0 H2 O2 1.0 O1 120.0 H1 180.0 $end ``` -------------------------------- ### Simulating the IR spectrum of water using QCT-MD Source: https://manual.q-chem.com/latest/subsec_QCT.html Example input for a QCT-MD simulation of water, using AIMD_INIT_VELOC set to quasiclassical to trigger quasi-classical initial conditions. ```Q-Chem $molecule 0 1 O 0.000000 0.000000 0.520401 H -1.475015 0.000000 -0.557186 H 1.475015 0.000000 -0.557186 $end $rem JOBTYPE freq INPUT_BOHR true METHOD hf BASIS 3-21g $end @@@ $molecule read $end $rem JOBTYPE aimd INPUT_BOHR true METHOD hf BASIS 3-21g SCF_CONVERGENCE 6 TIME_STEP 20 ! (in atomic units) AIMD_STEPS 1250 ! 600 fs total simulation time AIMD_TEMP 12 AIMD_PRINT 2 FOCK_EXTRAP_ORDER 6 ! Use a 6th-order extrapolation FOCK_EXTRAP_POINTS 12 ! of the previous 12 Fock matrices AIMD_MOMENTS 1 AIMD_NUCL_SAMPLE_RATE 5 AIMD_NUCL_VACF_POINTS 1000 AIMD_INIT_VELOC quasiclassical AIMD_QCT_WHICH_TRAJECTORY 1 ! Loop over several values to get ! the correct Boltzmann distribution. $end ``` -------------------------------- ### Q-Chem Input for ωB97M-V/SNK Energy Calculation Source: https://manual.q-chem.com/latest/sect_snk.html Example input file demonstrating the configuration of SNK parameters alongside standard job settings. ```text $molecule 0 1 O 0.0000000000 0.0000000000 0.21981483259 H 0.0000000000 1.4194772274 -0.87926122007 H 0.0000000000 -1.4194772274 -0.87926122007 $end $rem input_bohr = true jobtype = sp method = wB97M-V basis = cc-pvtz scf_convergence = 8 snk 1 snk_batch_size 256 snk_thresh_b 12 snk_thresh_e 10 snk_thresh_k 7 snk_thresh_fp32_m 5 $end ``` -------------------------------- ### Example $molecule Section with Custom MM Parameters Source: https://manual.q-chem.com/latest/Ch11.S3.SS2.html Demonstrates how to reference user-defined MM atom types (using negative indices) within the $molecule section. ```text $molecule 0 1 O -0.790909 1.149780 0.907453 -1 2 3 0 0 H -1.628044 1.245320 1.376372 -2 1 0 0 0 H -0.669346 1.913705 0.331002 -2 1 0 0 0 $end ```