### Example geom.inp Configuration Source: https://zhjun-sci.com/abcluster/doc/geom-input.html A comprehensive example of a geom.inp file containing all available configuration options for cluster optimization. ```text 1lm_dir mol # Save the local minima to this folder. 2num_calcs 1000 # Total number of calculations. 3do_coarse_opt yes # no: Do NOT the coarse optimization. 4min_energy_gap 1.E-4 # When two energies differ smaller than 5 # this value, they are treated as identical. 6 # A negative number means do not remove 7 # energetically degenerated ones. 8max_geom_iters 3000 # The maximum number of iterations for local optimization. 9 # If it is less or equal than zero, then the number is unlimited. 10 11components 12 water.xyz 1000 13 box 0 0 0 30 30 30 14 **** 15 xylitol.xyz 1000 16 fix 0 0 0 15 15 15 17 nH nH 18 **** 19end 20 21charmm # Parameters and PSF. 22 test/par_all35_ethers.prm 23 test/ether.psf 24end 25 26xtb # charge, uhf, gfn, (solvent) 27 0 0 2 28end 29 30savegjf 31 %chk=gsh-$index$.chk 32 %mem=10GB 33 %nproc=24 34 $hash$MP2/cc-pVTZ Opt Freq Output=wfn 35 $blank$ 36 GSH generated from ABCluster, energy = $energy$ 37 $blank$ 38 0 1 39 >>>> 40 gsh-$index$.wfn 41end 42 43commands 44 $charmm$ 45end ``` -------------------------------- ### Example lj38.inp File Content Source: https://zhjun-sci.com/abcluster/doc/abcinp.html The generated input file structure for an atom simulation. ```text 138 # number of atoms 2lj38i.xyz # initial guess file ; * - random guess 3LennardJones # force field types 4lj38.par # force field parameters 530 # population size 6300 # maximal generations 75 # scout limit 85.00000000 # amplitude 9lj38 # save optimized configuration to .xyz and .gjf 1030 # number of LMs to be saved ``` -------------------------------- ### Standard rigidmol input file Source: https://zhjun-sci.com/abcluster/doc/_sources/eg-rigidgpu.rst.txt Example input file for a rigidmol global optimization task. ```bash h2o6.cluster # cluster file name 20 # population size 20 # maximal generations 3 # scout limit 4.0 # amplitude h2o6 # save optimized configuration 30 # number of LMs to be saved ``` -------------------------------- ### View naclh2o10.out results Source: https://zhjun-sci.com/abcluster/doc/_sources/skill.rst.txt Example output showing the energy ranking of calculated local minima. ```bash -- Result Report -- Results are energy-increasingly reordered. Structures of energies within 1.000E-04 are treated as degenerate. All minima are saved to "naclh2o10". ------------------------------------------------------------------- # index Energy NaiveRMSD ------------------------------------------------------------------- 0 410 -78.90900677 0.00000000 1 1315 -73.85642855 11.13424019 ... omitted ... 33 859 -62.49102429 9.53495472 ``` -------------------------------- ### Optimization Result Summary Source: https://zhjun-sci.com/abcluster/doc/_sources/eg-geom-xtb.rst.txt Example output showing the energy-ordered results of the optimization process. ```bash -- Result Report -- Results are energy-increasingly reordered. Structures of energies within 1.000E-04 are treated as degenerate. All minima are saved to "co6te8". ------------------------------------------------------------------- # index Energy NaiveRMSD ------------------------------------------------------------------- 0 954 -255485.30137014 0.00000000 1 1649 -13270.21996894 9.77918423 2 708 -379.80860329 8.25823482 ... omitted ... 108 929 -51.90294094 9.92663264 109 29 -51.86444358 8.63886023 110 66 -51.86429930 9.29717029 111 199 -51.84758402 9.00426358 112 1213 -51.84370999 9.19951625 ``` -------------------------------- ### Example aip-cycles.txt Content Source: https://zhjun-sci.com/abcluster/doc/_sources/geom-bonding.rst.txt Lists the atom indices forming cycles within the molecule. ```bash 38 40 46 48 52 58 60 62 68 74 80 89 99 50 45 42 67 70 76 85 78 72 ``` -------------------------------- ### Example XYZ file for Co6Te8 core Source: https://zhjun-sci.com/abcluster/doc/_sources/eg-geom-xtb.rst.txt The global minimum structure file used as the core for the optimization. ```bash 14 -51.86444358 Co 5.18912366 4.53807660 5.15436968 Co 4.63921329 6.73032694 4.33024999 Co 5.57653575 4.28771551 2.73430585 Co 3.73287281 2.69503667 3.34312049 Co 3.09922668 5.44745620 2.69377997 Co 2.32298551 4.63312799 4.83935341 Te 3.65939955 5.91817891 6.45016152 Te 5.16439545 6.53843136 1.92985727 Te 1.55874524 3.57414579 2.71643092 Te 3.68082433 2.75955616 5.79296888 Te 5.94894157 2.39529023 4.27916498 Te 2.22874466 7.03012888 4.38569672 Te 3.80790879 3.72603676 1.12877717 Te 6.88875884 5.89174763 3.98837449 ``` -------------------------------- ### ABCluster Input Configuration Source: https://zhjun-sci.com/abcluster/doc/skill.html Example input file defining the cluster components, optimization parameters, and xTB settings. ```text 1lm_dir naclh2o10 # Save the local minima to this folder. 2num_calcs 2000 # Total number of calculations. 3do_coarse_opt yes # Coarse pre-optimization (recommended). 4min_energy_gap 1.E-4 # Energies closer than this are treated as identical. 5max_geom_iters 3000 # Max iterations for each local optimization. 6 7components 8 h2o.xyz 10 9 random 0 0 0 8 8 8 10 **** 11 na.xyz 1 12 random 0 0 0 8 8 8 13 **** 14 cl.xyz 1 15 random 0 0 0 8 8 8 16 **** 17end 18 19xtb 20 0 0 1 # charge, unpaired electrons, GFN type (1 = GFN1-xTB) 21end 22 23commands 24 $xTB$ 25end ``` -------------------------------- ### View topgen Output Source: https://zhjun-sci.com/abcluster/doc/_sources/eg-pincer.rst.txt Example output generated by the topgen command. ```bash Analyze topology for the molecule from "pincer.xyz" ... done. Exporting results to "pincer" + .gjf: GJF file with bonding information. -cycles.txt: Containing cycle texts that can be used for ABCluster:geom calculation. -bonding.xyz: XYZ file with bonding information for ABCluster:geom calculation. -rigid.xyz: XYZ file with bonding information for ABCluster:rigidmol calculation. .psf: PSF file with topology informaition for ABCluster:geom/NAMD calculations. In "pincer-rigid.xyz" and "pincer.psf": "X" means unknown atomic type. Total charge: 1.8360 ``` -------------------------------- ### Example XYZ Structure File Source: https://zhjun-sci.com/abcluster/doc/_sources/eg-geom-cp2k.rst.txt A sample XYZ file format representing a graphene oxide model structure. ```bash 124 -829.3320055707 C 0.6432795582 1.4146381445 12.9802103805 C 1.8638405295 0.7068348736 13.1358213883 C 3.0803261454 1.4117958723 13.2926182146 C 4.2826452613 0.7049969815 13.4870725811 C 5.4908939226 1.4183747968 13.6173292256 C 6.6945610217 0.7086518738 13.7044774152 C 7.9024899763 1.4278111301 13.7202904813 C 9.1068015792 0.7190504163 13.6370502922 C 10.3144403340 1.4355578787 13.5249758495 C 11.5141472647 0.7292051997 13.3245409163 C 12.7285238514 1.4409268334 13.1735625500 C 13.9454351317 0.7326485987 12.9974247960 C 15.1770415433 1.4301435475 12.9268878534 C 16.4093490282 0.7204721712 12.9136194279 C 0.6527631899 2.8319555916 13.0403244189 C 1.8691198475 3.5247382130 13.2528534491 C 3.0871709142 2.8287137498 13.3671638582 C 4.2802068410 3.5288023773 13.6746472393 C 5.4929582858 2.8314678050 13.7365915100 C 6.6924957067 3.5357798292 13.9782707015 C 7.9043631825 2.8383988195 13.8719868403 C 9.1216246522 3.5404615840 13.9597571598 C 10.3210695315 2.8454166260 13.6974578387 C 11.5429395786 3.5450362446 13.6591436703 C 12.7356297186 2.8503322354 13.3275571037 C 13.9651113637 3.5501152720 13.2375295895 C 15.1851408619 2.8472003599 13.0203390970 C 16.4208344084 3.5359621542 13.0533771591 C 0.6441811503 5.6279654088 13.3965857081 C 1.8728741720 4.9242285617 13.4881166107 C 3.0318853880 5.5796320552 13.9222434798 C 4.2649866705 4.9134821550 14.0198081831 C 5.4335432648 5.5637056006 14.4877076867 C 6.6808855036 4.9105244991 14.3827642479 C 7.9080442650 5.5594291871 14.6773251573 ``` -------------------------------- ### Example Generated Cluster File Source: https://zhjun-sci.com/abcluster/doc/_sources/eg-h2o6.rst.txt An example of a cluster file generated by rigidmol containing rigid coordinates for each molecule. ```bash 1 tip4p.xyz 6 Water hexamer 3.5 7.0 -0.2 1.3 2.9 0.6 4.0 0.9 3.1 4.3 3.2 3.8 -1.8 4.4 1.0 0.8 0.2 0.6 4.2 3.4 3.9 1.9 0.2 3.2 3.6 4.7 2.9 3.6 1.7 1.7 5.1 5.2 -0.6 1.6 2.8 3.5 ``` -------------------------------- ### Extracting CHARMM Parameters Source: https://zhjun-sci.com/abcluster/doc/_sources/eg-nhch32co.rst.txt Example of raw parameter entries found in the par_all36_cgenff.prm file. ```bash CG2O5 0.0 -0.0900 2.00 ! adm, acetone, 11/08 CG2O6 0.0 -0.0700 2.00 ! UREA, CO3 (carbonate) from acetate heat of solvation CG2O7 0.0 -0.0580 1.5630 ! carbon dioxide, JES ``` -------------------------------- ### Optimization Output Summary Source: https://zhjun-sci.com/abcluster/doc/_sources/eg-isomerxtb.rst.txt Example output showing the energy ranking of found isomers after the optimization process. ```bash Reordered from low to high energy: =============================================================== # Energy Match-RMSD =============================================================== 10 -31.82883469 0.00000000 31 -31.82879105 0.09780278 49 -31.81744864 1.87717016 19 -31.81703116 1.06064506 14 -31.81614914 1.74735890 26 -31.81613549 1.74618650 2 -31.81468986 1.66046500 20 -31.81414834 1.55327721 21 -31.81373995 1.50768747 45 -31.81256386 1.72172715 32 -31.81242730 1.88329240 29 -31.81053323 1.85723016 23 -31.80945836 1.81423700 22 -31.80737746 1.23237316 40 -31.80544331 2.00421183 6 -31.80494744 1.14790243 28 -31.80483576 1.65162493 42 -31.80296347 1.19522877 27 -31.80092339 1.24375689 11 -31.80090745 1.24153852 39 -31.79799814 1.29473162 34 -31.79521218 1.86632054 46 -31.79422879 1.53204441 1 -31.79411906 1.58712360 7 -31.78526106 1.61499059 8 -31.76968806 2.06136973 33 -31.76852420 2.03850515 =============================================================== ``` -------------------------------- ### Define isomer input file Source: https://zhjun-sci.com/abcluster/doc/eg-isomergs.html Example input file for isomer to find the global minimum of Al3O4+. ```text 1al3o4 # Result file name 2Al 3 O 4 # Symbols 3cube 3 3 3 # Structure types 440 # Maximal number of calculations 5>>>> 6xyz2gaussian optfile $inp$ > $xxx$.gjf 7g16 < $xxx$.gjf > $xxx$.log 2>/dev/null 8gaussian2xyz $xxx$.log > $out$ 9>>>> ``` -------------------------------- ### Single GPU Performance Input Configuration Source: https://zhjun-sci.com/abcluster/doc/eg-rigidgpu.html Example input file for performing a single energy calculation on a cluster using GPU acceleration. ```text 1mol.cluster # cluster file name 21 # population size 31 # maximal generations 43 # scout limit 510.00000000 # amplitude 6mol # save optimized configuration 730 # number of LMs to be saved ``` -------------------------------- ### Configure au20.inp for D2d symmetry Source: https://zhjun-sci.com/abcluster/doc/_sources/eg-pointgroup.rst.txt Example configuration file for generating Au20 clusters with D2d symmetry constraints. ```bash atom Au 20 pointgroup D2d ``` -------------------------------- ### Defining nndimethylurea.xyz Parameters Source: https://zhjun-sci.com/abcluster/doc/_sources/eg-nhch32co.rst.txt Example of an XYZ file structure with appended parameter data for molecular optimization. ```bash 14 dimethylurea C -3.40944156863935 1.48217854479510 0.18460221407169 O -2.83617751600667 2.55594436393475 0.29160616578062 N -4.77159876631838 1.40346427888521 0.01033470214576 H -5.17936611057651 2.32373985124644 -0.02398130498834 N -2.71942098770917 0.27746301048357 0.25258402399382 H -1.74237705636477 0.48553039432599 0.40014513551919 C -5.63042059274161 0.33540415616324 0.49938800446410 H -6.45368224181311 0.76470101295480 1.07232563209061 H -6.05781648140388 -0.26211048052894 -0.31127284718113 H -5.06868507307871 -0.32252499680997 1.16139152177693 C -2.93625253356738 -0.80249737836091 -0.70510480675735 H -2.73548051116983 -0.49573138113413 -1.73834868327471 H -2.27102803030176 -1.62710593941345 -0.45152402911762 H -3.95491690030879 -1.17972228654170 -0.65012968852358 all36_cgenff q epsilon (kJ/mol) sigma (AA) +0.60 0.2929 3.5636 # CG2O6 -0.58 -0.69 +0.34 -0.69 +0.34 +0.07 +0.09 +0.09 +0.09 +0.07 +0.09 +0.09 +0.09 ``` ```bash 14 dimethylurea C -3.40944156863935 1.48217854479510 0.18460221407169 O -2.83617751600667 2.55594436393475 0.29160616578062 N -4.77159876631838 1.40346427888521 0.01033470214576 H -5.17936611057651 2.32373985124644 -0.02398130498834 N -2.71942098770917 0.27746301048357 0.25258402399382 H -1.74237705636477 0.48553039432599 0.40014513551919 C -5.63042059274161 0.33540415616324 0.49938800446410 H -6.45368224181311 0.76470101295480 1.07232563209061 H -6.05781648140388 -0.26211048052894 -0.31127284718113 H -5.06868507307871 -0.32252499680997 1.16139152177693 C -2.93625253356738 -0.80249737836091 -0.70510480675735 H -2.73548051116983 -0.49573138113413 -1.73834868327471 H -2.27102803030176 -1.62710593941345 -0.45152402911762 H -3.95491690030879 -1.17972228654170 -0.65012968852358 all36_cgenff q epsilon (kJ/mol) sigma (AA) +0.60 0.2929 3.5636 # CG2O6 -0.58 0.5021 3.0291 # OG2D1 -0.69 0.8368 3.2963 # NG2S2 +0.34 0.1925 0.4000 # HGP1 -0.69 0.8368 3.2963 # NG2S2 +0.34 0.1925 0.4000 # HGP1 +0.07 0.3264 3.6527 # CG331 +0.09 0.1004 2.3876 # HGA3 +0.09 0.1004 2.3876 # HGA3 +0.09 0.1004 2.3876 # HGA3 +0.07 0.3264 3.6527 # CG331 +0.09 0.1004 2.3876 # HGA3 +0.09 0.1004 2.3876 # HGA3 +0.09 0.1004 2.3876 # HGA3 ``` -------------------------------- ### Configure Gaussian Interface for ABCluster Source: https://zhjun-sci.com/abcluster/doc/api.html Example configuration for integrating Gaussian with ABCluster using the required input and output file placeholders. ```bash 1>>>> 2xyz2gaussian optfile $inp$ > $xxx$.gjf 3g16 < $xxx$.gjf > $xxx$.log 2>/dev/null 4gaussian2xyz $xxx$.log > $out$ 5>>>> ``` -------------------------------- ### Basic EDA Input Configuration Source: https://zhjun-sci.com/abcluster/doc/_sources/eda.rst.txt Example input file for a standard EDA calculation, requiring the 'type U' setting in the scf block. ```bash basis def2-svp end scf charge 0 spin2p1 1 type U # For EDA calculations, this must be added explicitly. end grimmedisp type bj end eda type tso # You can also change it to: gks frag 0 1 1-5 # Define GeH3F. frag 0 1 6-8 # Define HCN. end task eda b3lyp end ``` -------------------------------- ### Example XYZ file for topgen Source: https://zhjun-sci.com/abcluster/doc/_sources/geom-bonding.rst.txt A standard XYZ format file representing an organic molecule, used as input for the topgen tool. ```bash 113 AIP(+1) N 10.45900000 -12.94900000 -8.94000000 H 10.14300000 -12.08200000 -9.34300000 H 11.09900000 -12.80100000 -8.17700000 H 9.66400000 -13.46100000 -8.55100000 C 11.12800000 -13.81000000 -9.92500000 H 10.48100000 -13.86000000 -10.80200000 C 11.21100000 -15.19900000 -9.28200000 O 11.48200000 -15.27400000 -8.08600000 C 12.52800000 -13.25600000 -10.32800000 H 13.18900000 -13.32500000 -9.46100000 C 12.50400000 -11.77400000 -10.78600000 H 11.61400000 -11.56800000 -11.38000000 H 13.33800000 -11.59800000 -11.46700000 C 13.18200000 -14.11500000 -11.43200000 H 14.17300000 -13.74000000 -11.68900000 H 12.58500000 -14.11600000 -12.34500000 H 13.32000000 -15.15200000 -11.12300000 N 10.86100000 -16.25800000 -10.02800000 H 10.63200000 -16.06600000 -10.99200000 C 12.65700000 -10.74000000 -9.65700000 H 12.73000000 -9.73500000 -10.07300000 H 13.57000000 -10.91400000 -9.08500000 H 11.82400000 -10.73000000 -8.95800000 C 10.63500000 -17.66700000 -9.63800000 H 10.42500000 -18.14800000 -10.59400000 C 9.32200000 -17.82400000 -8.85000000 O 8.44600000 -18.59600000 -9.23100000 C 11.85000000 -18.46100000 -9.07300000 H 12.67900000 -18.38800000 -9.77700000 H 11.58400000 -19.51900000 -9.05700000 C 12.34800000 -18.12800000 -7.66200000 O 11.63600000 -18.31400000 -6.68200000 N 9.15900000 -16.99400000 -7.82000000 H 9.97600000 -16.44000000 -7.57700000 N 13.57300000 -17.63100000 -7.53200000 H 14.15700000 -17.47000000 -8.33800000 H 13.90400000 -17.39300000 -6.61000000 C 7.91700000 -16.59300000 -7.18800000 H 7.17100000 -16.53900000 -7.98100000 C 8.12600000 -15.13200000 -6.75300000 O 8.58800000 -14.32500000 -7.56700000 C 7.45500000 -17.63700000 -6.13700000 H 8.13900000 -17.64100000 -5.28900000 H 7.47900000 -18.64500000 -6.55300000 S 5.76100000 -17.29100000 -5.53200000 N 7.75900000 -14.75500000 -5.52100000 H 7.33100000 -15.46600000 -4.94500000 C 7.84900000 -13.41900000 -4.90300000 H 7.63700000 -13.58400000 -3.84500000 C 4.79400000 -17.78100000 -6.98300000 O 5.31900000 -18.26600000 -7.98300000 C 6.75400000 -12.45200000 -5.39100000 O 6.36800000 -11.52400000 -4.68400000 C 9.26200000 -12.81100000 -4.98000000 H 9.52900000 -12.52000000 -5.99400000 H 10.01500000 -13.51100000 -4.61600000 H 9.32600000 -11.91300000 -4.36400000 N 6.23100000 -12.71300000 -6.58600000 H 6.63300000 -13.48600000 -7.10100000 C 5.06800000 -12.13300000 -7.22300000 H 4.39300000 -11.78600000 -6.43700000 C 4.34200000 -13.27600000 -7.94400000 O 4.98800000 -14.22300000 -8.40500000 C 5.45000000 -10.90600000 -8.08100000 H 5.68700000 -10.08200000 -7.40700000 H 4.57100000 -10.57200000 -8.63400000 C 6.59600000 -11.05600000 -9.08100000 N 3.00400000 -13.22600000 -7.97800000 H 2.56500000 -12.44000000 -7.52100000 C 6.46800000 -11.89100000 -10.21300000 H 5.57000000 -12.47000000 -10.37200000 C 7.77500000 -10.29500000 -8.91600000 H 7.88200000 -9.63800000 -8.06300000 C 2.08200000 -14.21600000 -8.54300000 H 1.10200000 -13.74300000 -8.47200000 C 7.49800000 -11.95200000 -11.17200000 H 7.38000000 -12.57800000 -12.04600000 C 8.79400000 -10.33800000 -9.88700000 H 9.66700000 -9.70800000 -9.77900000 C 2.02900000 -15.45100000 -7.63000000 O 1.11000000 -15.59700000 -6.82700000 C 2.36100000 -14.49400000 -10.05000000 H 3.31200000 -15.01000000 -10.17600000 H 2.50200000 -13.52900000 -10.53900000 C 8.65300000 -11.16400000 -11.01900000 H 9.41100000 -11.17300000 -11.78900000 C 1.27900000 -15.25700000 -10.85600000 H 1.58500000 -15.16900000 -11.90000000 N 3.04600000 -16.31000000 -7.73200000 H 3.78900000 -16.04200000 -8.36900000 C 1.22600000 -16.76700000 -10.57000000 H 0.61600000 -17.28000000 -11.31500000 H 0.78900000 -16.98800000 -9.59700000 H 2.22000000 -17.21500000 -10.60300000 C -0.11500000 -14.61600000 -10.76300000 H -0.55300000 -14.73700000 -9.77100000 H -0.80200000 -15.07400000 -11.47600000 ``` -------------------------------- ### Multiple GPU Performance Input Configuration Source: https://zhjun-sci.com/abcluster/doc/eg-rigidgpu.html Example input file modified to support multiple individuals in the population for multi-GPU utilization. ```text 1mol.cluster # cluster file name 232 # population size 32 # maximal generations 43 # scout limit 510.00000000 # amplitude 6mol # save optimized configuration 730 # number of LMs to be saved ``` -------------------------------- ### Define TIP4P Water with Virtual Sites Source: https://zhjun-sci.com/abcluster/doc/eg-nhch32co.html Example of a TIP4P water molecule structure including a virtual site labeled qLP. ```text 4 H2O O 0.00000000 0.00000000 0.21451132 qLP 0.00000000 0.00000000 0.06451132 H 0.00000000 0.75695033 -0.37137096 H 0.00000000 -0.75695033 -0.37137096 TIP4P q epsilon (kJ/mol) sigma (AA) 0.000 0.64852 3.1536 # OT -1.040 0.00000 0.0000 # LP +0.520 0.00000 0.0000 # HT +0.520 0.00000 0.0000 # HT ``` -------------------------------- ### Prepare au6.inp Input File Source: https://zhjun-sci.com/abcluster/doc/eg-isomergs.html Configuration file for the global optimization of Au6, specifying the result file name, symbols, structure type, and calculation commands. ```text 1au6 # Result file name 2Au 6 # Symbols 3plane 4 3 # Structure types 420 # Maximal number of calculations 5>>>> 6xyz2gaussian optfile $inp$ > $xxx$.gjf 7g16 < $xxx$.gjf > $xxx$.log 2>/dev/null 8gaussian2xyz $xxx$.log > $out$ 9>>>> ``` -------------------------------- ### Urea Topology Definition Source: https://zhjun-sci.com/abcluster/doc/_sources/eg-nhch32co.rst.txt Example of a urea residue definition from the CHARMM CGenFF topology file. ```bash RESI UREA 0.00 ! CH4N2O, Urea, adm GROUP ATOM N1 NG2S2 -0.69 ATOM H11 HGP1 0.34 ATOM H12 HGP1 0.34 ATOM C2 CG2O6 0.60 ATOM O2 OG2D1 -0.58 ATOM N3 NG2S2 -0.69 ATOM H31 HGP1 0.34 ATOM H32 HGP1 0.34 ``` -------------------------------- ### Run Conformation Search Source: https://zhjun-sci.com/abcluster/doc/_sources/eg-aip.rst.txt Command to execute the conformation search using the prepared input file. ```bash $ geom aip.inp > aip.out ``` -------------------------------- ### Optimization Result Report Source: https://zhjun-sci.com/abcluster/doc/_sources/eg-geom-charmm.rst.txt Example output showing the energy-ordered results of the global optimization process. ```text -- Result Report -- Results are energy-increasingly reordered. Structures of energies within 1.000E-04 are treated as degenerate. All minima are saved to "deca-ala-packing". ------------------------------------------------------------------- # index Energy NaiveRMSD ------------------------------------------------------------------- 0 19 -4146.88610026 0.00000000 1 5 -4136.05019723 14.82412036 2 0 -4121.59161174 14.58105056 3 3 -4046.70846315 18.63580831 4 14 -4043.04825505 15.53391890 5 16 -4012.00784464 16.42782901 6 1 -4010.99019118 17.58161163 ``` -------------------------------- ### View optimization results Source: https://zhjun-sci.com/abcluster/doc/_sources/eg-geom-xtb.rst.txt Sample output showing the result report of the optimization. ```bash -- Result Report -- Results are energy-increasingly reordered. Structures of energies within 1.000E-04 are treated as degenerate. All minima are saved to "naclh2o10". ------------------------------------------------------------------- # index Energy NaiveRMSD ------------------------------------------------------------------- 0 410 -78.90900677 0.00000000 1 1315 -73.85642855 11.13424019 2 270 -72.33437367 8.23789070 3 471 -71.89726049 2.84818350 4 595 -71.66037145 0.96099577 5 1138 -71.33515351 1.70326738 6 656 -71.30962706 6.91732743 7 309 -70.21312469 8.33181645 8 1007 -69.27883414 4.11576652 9 424 -68.96145859 1.36910299 10 777 -68.61390125 9.25461485 ... omitted ... 28 966 -63.05453856 10.34934592 29 863 -62.49368470 9.79444040 30 1883 -62.49337541 9.23302757 31 648 -62.49194643 9.39246214 32 1811 -62.49123647 9.68901769 33 859 -62.49102429 9.53495472 ``` -------------------------------- ### Define Rigid Components in geom.inp Source: https://zhjun-sci.com/abcluster/doc/geom-bonding.html Example of a component block where molecules are placed without assigned flexibility. ```text 1components aip-bonding.xyz 1 fix 0 0 0 0 0 0 **** water.xyz 100 random -5 -5 -5 5 5 5 **** end ``` -------------------------------- ### Configure Electric Field Optimization Input (ef-8.inp) Source: https://zhjun-sci.com/abcluster/doc/_sources/eg-electricfield.rst.txt Input configuration for optimization under an electric field, mirroring the vacuum configuration. ```bash ef-8.cluster # cluster file name 30 # population size 50 # maximal generations 3 # scout limit 10.00000000 # amplitude ef-8 # save optimized configuration 30 # number of LMs to be saved ``` -------------------------------- ### MB-EDA Output Summary Source: https://zhjun-sci.com/abcluster/doc/eda.html Example output table showing the energy decomposition components for the cluster calculation. ```text 1Table 5. Summary (kcal/mol). 2--------------------------------------------------------------------------------------------------------------------------------- 3 Interactions delE_el delE_xc delE_pl delE_ct delE_bsse delE_disp delE_tot 4--------------------------------------------------------------------------------------------------------------------------------- 5 SUM of 2-body -3.51853640E+02 1.04231044E+02 -5.50310217E+01 -9.70290703E+01 4.35696096E+01 -1.98079059E+01 -3.75920984E+02 6 SUM of 3-body 1.72107484E-09 1.45358519E+00 2.82254671E+01 2.81735373E+01 -1.24450163E+01 1.01531078E-02 4.54177264E+01 7 SUM of 4-body -4.14670076E-09 1.70212282E-02 -2.25462767E+00 -5.15894065E+00 1.89758583E+00 2.28017787E-05 -5.49893846E+00 8 Remain 7.51748885E-09 -8.58522126E-04 6.43113307E-02 4.30266615E-01 -1.22896862E-01 5.97720460E-07 3.70823167E-01 9--------------------------------------------------------------------------------------------------------------------------------- 10 SUM -3.51853640E+02 1.05700792E+02 -2.89958710E+01 -7.35842070E+01 3.28992822E+01 -1.97977294E+01 -3.35631373E+02 11--------------------------------------------------------------------------------------------------------------------------------- ``` -------------------------------- ### Input Configuration for Li5F5 Optimization Source: https://zhjun-sci.com/abcluster/doc/_sources/eg-isomerxtb.rst.txt Input file setup for the ionic cluster Li5F5, specifying the result name, atomic composition, and structure sampling parameters. ```bash li5f5 # Result file name Li 5 F 5 # Symbols cube 4 4 4 # Structure types 50 # Maximal number of calculations >>>> ./runxTB.sh $inp$ $out$ $xxx$ >>>> ``` -------------------------------- ### EDA Calculation Output Results Source: https://zhjun-sci.com/abcluster/doc/eda.html Example output showing the energy decomposition components for the GeH3F-NCH complex. ```text 1WITH BSSE correction: 2Electrostatic interaction energy: -4.98 kcal/mol 3Exchange-correlation interaction energy: 4.22 kcal/mol 4Polarization interaction energy: -0.62 kcal/mol 5Charge transfer interaction energy: -1.31 kcal/mol 6Grimme's dispersion interaction: -1.58 kcal/mol 7---------------------------------------------------------------- 8Total interaction energy: -4.27 kcal/mol ```