ABCluster

https://zhjun-sci.com/abcluster/doc/
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ABCluster is a black-box program designed for the global optimization of chemical clusters using the...
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### 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
```
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