Added xTB Standalone Support

Aditya Wibawa Sakti 2 years ago
parent d4be395790
commit 58a1f9020d
  1. 4
      README.md
  2. BIN
      README.pdf
  3. 19
      bin/cmmde.py
  4. 86
      cmmde_gui/test/naftalena/cmmd.engrad
  5. BIN
      cmmde_gui/test/naftalena/cmmd.gbw
  6. 8
      cmmde_gui/test/naftalena/cmmd.in
  7. 1844
      cmmde_gui/test/naftalena/cmmd.opt
  8. 2798
      cmmde_gui/test/naftalena/cmmd.out
  9. BIN
      cmmde_gui/test/naftalena/cmmd.xtbrestart
  10. 20
      cmmde_gui/test/naftalena/cmmd.xyz
  11. 6
      cmmde_gui/test/naftalena/cmmd_property.txt
  12. 120
      cmmde_gui/test/naftalena/cmmd_trj.xyz
  13. 1
      cmmde_gui/test/naftalena/geom.smi
  14. 20
      cmmde_gui/test/naftalena/geom.xyz
  15. 10
      cmmde_gui/test/naftalena/run.sh
  16. 8
      cmmde_gui/test/naftalena/run_babel.sh
  17. 1
      cmmde_gui/test/naftalena/slurm-2850.out
  18. 0
      cmmde_gui/test/naftalena/slurm-2851.out
  19. 0
      examples/xtb/.xtboptok
  20. 75
      examples/xtb/charges
  21. 6
      examples/xtb/cmmd.in
  22. 77
      examples/xtb/geom.xyz
  23. 8
      examples/xtb/run.sh
  24. 2
      examples/xtb/slurm-2858.out
  25. 100
      examples/xtb/wbo
  26. 1768
      examples/xtb/xtb.out
  27. 385
      examples/xtb/xtbopt.log
  28. 77
      examples/xtb/xtbopt.xyz
  29. BIN
      examples/xtb/xtbrestart
  30. 7700
      examples/xtb/xtbscan.log
  31. 160
      examples/xtb/xtbtopo.mol
  32. BIN
      lib/__pycache__/cmmde_xtb.cpython-39.pyc
  33. 59
      lib/cmmde_xtb.py

@ -9,7 +9,8 @@ This software is developed for decreasing the barrier in using popular open-sour
4. [DOCK6](https://dock.compbio.ucsf.edu/DOCK_6/index.htm) 4. [DOCK6](https://dock.compbio.ucsf.edu/DOCK_6/index.htm)
5. [DCDFTBMD](http://www.chem.waseda.ac.jp/dcdftbmd/?lang=en) 5. [DCDFTBMD](http://www.chem.waseda.ac.jp/dcdftbmd/?lang=en)
6. [Quantum Espresso](https://www.quantum-espresso.org/) 6. [Quantum Espresso](https://www.quantum-espresso.org/)
7. [xTB via Orca](https://github.com/grimme-lab/xtb) 7. [xTB](https://github.com/grimme-lab/xtb)
8. [Open Babel](http://openbabel.org/wiki/Main_Page)
## About CMMDE ## About CMMDE
CMMDE is a set of tools based on Python for running computational jobs, as well as analyzing, visualizing, and post-processing the results in free/libre and open source applications for computational molecular & material design. CMMDE is a set of tools based on Python for running computational jobs, as well as analyzing, visualizing, and post-processing the results in free/libre and open source applications for computational molecular & material design.
@ -47,3 +48,4 @@ cd CMMDE
chmod +x install.sh chmod +x install.sh
./install.sh ./install.sh
``` ```

Binary file not shown.

@ -9,6 +9,7 @@ from cmmde_mdpro import proprep, ligprep
from cmmde_dftb import poscar2gen, vasp2gen, dftb from cmmde_dftb import poscar2gen, vasp2gen, dftb
from cmmde_qe import qe from cmmde_qe import qe
from cmmde_nw import nwchem from cmmde_nw import nwchem
from cmmde_xtb import xtb
import time import time
@ -113,6 +114,20 @@ parser.add_argument('-nlig','--nligands',type=int,help='Jumlah ligan yang akan d
parser.add_argument('-solvent','--solvent',type=str,default='none',help='Pelarut yang digunakan dalam perhitungan.') parser.add_argument('-solvent','--solvent',type=str,default='none',help='Pelarut yang digunakan dalam perhitungan.')
# Input untuk simulasi MD sistem protein # Input untuk simulasi MD sistem protein
parser.add_argument('-protein','--protein',type=str,help='Struktur protein dalam format pdb') parser.add_argument('-protein','--protein',type=str,help='Struktur protein dalam format pdb')
# Input untuk perkiraan jalur reaksi menggunakan xTB
parser.add_argument('-nrun','--nrun',type=int,default=1,help='Jumlah banyaknya sampling path yang dilakukan. Default: 1.')
parser.add_argument('-npoint','--npoint',type=int,default=25,help='Jumlah banyaknya titik untuk interpolasi jalur reaksi. Default: 25.')
parser.add_argument('-anopt','--anopt',type=int,default=10,help='Jumlah maksimum step optimasi geometri yang dilakukan. Default: 10.')
parser.add_argument('-kpush','--kpush',type=float,default=0.003,help='Faktor skala untuk variasi nilai RMSD. Default: 0.003 atomic unit.')
parser.add_argument('-kpull','--kpull',type=float,default=-0.015,help='Tetapan pegas untuk menarik posisi atom. Default: -0.015 atomic unit.')
parser.add_argument('-ppull','--ppull',type=float,default=0.05,help='Kekuatan tarikan pegas teroptimasi. Default: 0.05 atomic unit.')
parser.add_argument('-alp','--alp',type=float,default=1.2,help='Lebar potensial Gaussian dalam satuan Angstrom. Default: 1.2 Angstrom.')
# Scanning geometri menggunkaan xTB standalone
parser.add_argument('-dist','--distance',type=str,default='None',help='Jarak antara dua buah atom dalam format: Serial1,Serial2,Jarak. Contoh: 4,1,1.5.')
parser.add_argument('-ang','--angle',type=str,default='None',help='Sudut antara tiga buah atom dalam format: Serial1,Serial2,Serial3,Sudut. Contoh: 4,1,3,180.')
parser.add_argument('-dih','--dihedral',type=str, default='None',help='Sudut dihedral antara empat buah atom dalam format: Serial1,Serial2,Serial4,Dihedral. Contoh: 4,1,3,2,120.')
parser.add_argument('-scanmode','--scanmode',type=str,default='None',help='Mode scan geometri yang diinginkan. Pilihan: concerted, sequential.')
parser.add_argument('-scan','--scan',type=str,default='None',help='Rentang Scanning dalam format: Titik1,Titik2,JumlahTitik. Contoh:2.5,1.0,100.')
# Input untuk perhitungan NEB # Input untuk perhitungan NEB
parser.add_argument('-produk','--produk',type=str,help='Struktur produk yang digunakan dalam interpolasi NEB dalam format koordinat Cartesian.') parser.add_argument('-produk','--produk',type=str,help='Struktur produk yang digunakan dalam interpolasi NEB dalam format koordinat Cartesian.')
parser.add_argument('-trans','--transitionstate',type=str,help='Struktur perkiraan keadaan transisi yang digunakan dalam format koordinat Cartesian.') parser.add_argument('-trans','--transitionstate',type=str,help='Struktur perkiraan keadaan transisi yang digunakan dalam format koordinat Cartesian.')
@ -382,3 +397,7 @@ if opt.job == 'proprep' and opt.software == 'gmx':
proprep(opt.protein) proprep(opt.protein)
if opt.job == 'ligprep' and opt.software == 'gmx': if opt.job == 'ligprep' and opt.software == 'gmx':
ligprep(opt.ligand,opt.charge) ligprep(opt.ligand,opt.charge)
# Program XTB Standalone
if opt.software == 'xtb':
xtb(opt.job,geom,opt.nproc,opt.produk,opt.temp,opt.nrun,opt.npoint,opt.anopt,opt.kpush,opt.kpull,opt.ppull,opt.alp,opt.distance,opt.angle,opt.dihedral,opt.scanmode,opt.iter,opt.scan)

@ -0,0 +1,86 @@
#
# Number of atoms
#
18
#
# The current total energy in Eh
#
-25.474385516520
#
# The current gradient in Eh/bohr
#
-0.000136215505
-0.000372377899
0.000001125693
-0.000132249935
0.000376634673
0.000002669203
0.000357078532
-0.000224212188
0.000007912916
-0.000003964442
0.000017074061
-0.000008976009
-0.000353164526
-0.000221756001
0.000006723727
0.000135880120
0.000372858276
0.000002848800
0.000131832079
-0.000373743978
0.000001854847
-0.000350246704
0.000220407573
0.000009477425
0.000002173643
-0.000012418889
-0.000013471275
0.000348731937
0.000220360870
0.000011264482
-0.000020605813
-0.000175411648
0.000006625481
-0.000021212117
0.000174448040
0.000000948031
0.000114956161
0.000060577107
-0.000013873284
-0.000115141875
0.000061148015
-0.000002672329
0.000020795481
0.000175133815
0.000005963698
0.000021199049
-0.000175385467
-0.000000735846
-0.000115264276
-0.000061390100
-0.000010707029
0.000115418193
-0.000061946260
-0.000006978532
#
# The atomic numbers and current coordinates in Bohr
#
6 4.5571258 -1.3287702 -0.0053890
6 4.5586789 1.3246830 -0.0046449
6 2.3301840 2.6290412 -0.0054059
6 -0.0043626 1.3419232 -0.0066633
6 -2.3374022 2.6317647 -0.0063895
6 -4.5674083 1.3299860 -0.0071734
6 -4.5689557 -1.3234642 -0.0086870
6 -2.3404501 -2.6278162 -0.0090882
6 -0.0059212 -1.3406585 -0.0078041
6 2.3271077 -2.6305315 -0.0071662
1 6.3357317 -2.3312669 -0.0045097
1 6.3384594 2.3250895 -0.0035117
1 2.3219079 4.6720601 -0.0051436
1 -2.3267515 4.6747709 -0.0055138
1 -6.3460252 2.3324659 -0.0065981
1 -6.3487246 -2.3238910 -0.0095580
1 -2.3321575 -4.6708323 -0.0104583
1 2.3164424 -4.6735365 -0.0081448

Binary file not shown.

@ -0,0 +1,8 @@
#CMMDE generated Orca input file
!XTB2 opt
%pal
nprocs 1
end
*xyzfile 0 1 geom.xyz

File diff suppressed because it is too large Load Diff

File diff suppressed because it is too large Load Diff

@ -0,0 +1,20 @@
18
Coordinates from ORCA-job cmmd
C 2.41152713335072 -0.70315491965030 -0.00285175640619
C 2.41234899929286 0.70099206550767 -0.00245799823640
C 1.23308025141841 1.39122869364744 -0.00286066883031
C -0.00230860377905 0.71011519433099 -0.00352606339333
C -1.23689996102567 1.39266987428458 -0.00338118661967
C -2.41696837199262 0.70379830277779 -0.00379601125133
C -2.41778724238201 -0.70034709816064 -0.00459698849307
C -1.23851286123808 -1.39058044924232 -0.00480925033694
C -0.00313334505810 -0.70944594331312 -0.00412973845697
C 1.23145236016325 -1.39201734055467 -0.00379216955028
H 3.35272482327401 -1.23365329886495 -0.00238641187896
H 3.35416825449150 1.23038438861012 -0.00185831172794
H 1.22870075528791 2.47234771346020 -0.00272186442839
H -1.23126388682849 2.47378219283471 -0.00291778014193
H -3.35817188229753 1.23428779710778 -0.00349157352384
H -3.35960034895426 -1.22975017185378 -0.00505785398497
H -1.23412458879329 -2.47169798545112 -0.00553432039391
H 1.22580851507043 -2.47312901547039 -0.00431005234558

@ -0,0 +1,6 @@
-------------------------------------------------------------
----------------------- !PROPERTIES! ------------------------
-------------------------------------------------------------
# -------------------------------------------------------------
----------------------- !GEOMETRIES! ------------------------
# -------------------------------------------------------------

@ -0,0 +1,120 @@
18
Coordinates from ORCA-job cmmd E -25.471091538490
C 2.431150 -0.696950 -0.009500
C 2.431520 0.694960 -0.003620
C 1.222970 1.392930 0.006450
C -0.002180 0.707060 0.004490
C -1.226640 1.394340 -0.001370
C -2.436240 0.697810 -0.010170
C -2.437350 -0.694110 -0.005370
C -1.229030 -1.392640 0.003820
C -0.003150 -0.707300 0.004240
C 1.221920 -1.394170 -0.001390
H 3.371650 -1.241270 -0.021400
H 3.372300 1.239120 -0.009030
H 1.243380 2.480380 0.012260
H -1.246110 2.481860 -0.004220
H -3.376340 1.243070 -0.022020
H -3.378530 -1.237370 -0.011250
H -1.250140 -2.480170 0.007200
H 1.241860 -2.481720 -0.003600
18
Coordinates from ORCA-job cmmd E -25.473780379000
C 2.414135 -0.699086 -0.006775
C 2.414821 0.696963 -0.003313
C 1.226571 1.391929 0.001600
C -0.002248 0.710122 0.000415
C -1.230322 1.393304 -0.002910
C -2.419482 0.699799 -0.007574
C -2.420363 -0.696257 -0.005261
C -1.232213 -1.391384 -0.000676
C -0.003141 -0.709920 -0.000088
C 1.225136 -1.392847 -0.003148
H 3.349911 -1.238622 -0.012404
H 3.351074 1.235770 -0.004726
H 1.245529 2.472464 0.005901
H -1.248272 2.473872 -0.003264
H -3.355040 1.239745 -0.013198
H -3.356808 -1.234683 -0.007451
H -1.251490 -2.471930 0.001927
H 1.243243 -2.473410 -0.003535
18
Coordinates from ORCA-job cmmd E -25.474250159220
C 2.409372 -0.701688 -0.004234
C 2.410206 0.699518 -0.002826
C 1.231309 1.391746 -0.001635
C -0.002290 0.711390 -0.002322
C -1.235103 1.393136 -0.003468
C -2.414829 0.702338 -0.005136
C -2.415627 -0.698874 -0.004917
C -1.236757 -1.391091 -0.003651
C -0.003136 -0.710880 -0.002942
C 1.229694 -1.392523 -0.003833
H 3.346481 -1.238191 -0.005706
H 3.347900 1.234992 -0.002411
H 1.242874 2.471682 0.000280
H -1.245553 2.473090 -0.002787
H -3.351855 1.238953 -0.006690
H -3.353384 -1.234256 -0.005517
H -1.248416 -2.471034 -0.002835
H 1.240154 -2.472478 -0.003851
18
Coordinates from ORCA-job cmmd E -25.474340578150
C 2.410431 -0.702683 -0.003226
C 2.411276 0.700516 -0.002585
C 1.232875 1.391504 -0.002623
C -0.002301 0.711012 -0.003220
C -1.236680 1.392919 -0.003459
C -2.415892 0.703325 -0.004167
C -2.416694 -0.699877 -0.004722
C -1.238297 -1.390844 -0.004565
C -0.003135 -0.710403 -0.003846
C 1.231233 -1.392275 -0.003864
H 3.349295 -1.237016 -0.003303
H 3.350750 1.233761 -0.001892
H 1.237573 2.472109 -0.001927
H -1.240194 2.473532 -0.002746
H -3.354723 1.237695 -0.004374
H -3.356190 -1.233098 -0.005103
H -1.243024 -2.471455 -0.004763
H 1.234735 -2.472892 -0.004095
18
Coordinates from ORCA-job cmmd E -25.474383190250
C 2.411713 -0.703268 -0.002655
C 2.412543 0.701105 -0.002420
C 1.233412 1.391150 -0.003072
C -0.002309 0.710208 -0.003696
C -1.237229 1.392591 -0.003385
C -2.417159 0.703909 -0.003610
C -2.417976 -0.700463 -0.004573
C -1.238836 -1.390499 -0.004997
C -0.003134 -0.709532 -0.004306
C 1.231774 -1.391934 -0.003807
H 3.352543 -1.234568 -0.001942
H 3.353998 1.231293 -0.001736
H 1.230048 2.472315 -0.003163
H -1.232613 2.473751 -0.002858
H -3.357996 1.235197 -0.003066
H -3.359423 -1.230666 -0.004969
H -1.235459 -2.471664 -0.005897
H 1.227145 -2.473095 -0.004328
18
Coordinates from ORCA-job cmmd E -25.474385516520
C 2.411527 -0.703155 -0.002852
C 2.412349 0.700992 -0.002458
C 1.233080 1.391229 -0.002861
C -0.002309 0.710115 -0.003526
C -1.236900 1.392670 -0.003381
C -2.416968 0.703798 -0.003796
C -2.417787 -0.700347 -0.004597
C -1.238513 -1.390580 -0.004809
C -0.003133 -0.709446 -0.004130
C 1.231452 -1.392017 -0.003792
H 3.352725 -1.233653 -0.002386
H 3.354168 1.230384 -0.001858
H 1.228701 2.472348 -0.002722
H -1.231264 2.473782 -0.002918
H -3.358172 1.234288 -0.003492
H -3.359600 -1.229750 -0.005058
H -1.234125 -2.471698 -0.005534
H 1.225809 -2.473129 -0.004310

@ -0,0 +1,20 @@
18
C 2.43115 -0.69695 -0.00950
C 2.43152 0.69496 -0.00362
C 1.22297 1.39293 0.00645
C -0.00218 0.70706 0.00449
C -1.22664 1.39434 -0.00137
C -2.43624 0.69781 -0.01017
C -2.43735 -0.69411 -0.00537
C -1.22903 -1.39264 0.00382
C -0.00315 -0.70730 0.00424
C 1.22192 -1.39417 -0.00139
H 3.37165 -1.24127 -0.02140
H 3.37230 1.23912 -0.00903
H 1.24338 2.48038 0.01226
H -1.24611 2.48186 -0.00422
H -3.37634 1.24307 -0.02202
H -3.37853 -1.23737 -0.01125
H -1.25014 -2.48017 0.00720
H 1.24186 -2.48172 -0.00360

@ -0,0 +1,10 @@
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
export PATH=/home/adit/opt/openmpi411/bin:$PATH
export OMP_NUM_THREADS=1
cd $PWD
$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe

@ -0,0 +1,8 @@
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS=1
cd $PWD
obabel geom.smi -O geom.xyz --gen3d

@ -0,0 +1,75 @@
-0.57867945
0.12330482
0.12689908
-0.09189003
0.08606314
-0.15696977
-0.01388823
0.01115225
0.00725991
0.01061040
0.00796883
0.00977780
-0.00447685
-0.01491119
-0.02978050
-0.02722387
-0.02961502
-0.02761892
0.03078032
0.08954994
0.03647950
0.03209002
0.02999592
-0.02724929
-0.02062862
-0.02554303
-0.02640057
-0.02772187
0.03489772
0.03646840
0.03380933
0.05679178
0.03946764
-0.02790415
-0.02834971
-0.02765220
-0.02865682
-0.01768288
0.05257133
0.03096555
0.02916248
0.03055154
0.03160205
-0.02959759
-0.02898275
-0.02946099
-0.03004953
-0.02602992
0.03353371
0.02862262
0.03347012
0.02916001
0.02595951
-0.01279610
-0.02732544
-0.02718452
-0.02695659
-0.02838905
0.03344760
0.08045090
0.03603254
0.03336957
0.03126512
-0.01839450
-0.02601870
-0.02759267
-0.02508686
-0.02766943
0.06002743
0.03858748
0.03585673
0.03662897
0.03633717
0.03193736
0.04147099

@ -0,0 +1,6 @@
$constrain
distance: 1,2,1.4
$scan
1: 4,1.4,100
$opt
maxcycle = 500

@ -0,0 +1,77 @@
75
energy: -110.900309438622 gnorm: 0.000476956992 xtb: 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54)
Ni -0.09028575139017 1.05626187671734 -1.40032543609075
P 1.49056983760457 0.00041561932325 -0.06080734861365
P -1.88473572952286 0.44952590495561 -0.35657360892326
N 1.02895663754726 1.10400736251903 -2.77720506088002
C 2.06757557261967 1.53131952649438 -3.18332723538468
C 3.20793685329482 1.91016245394040 -3.71383131252978
H -0.51013199176335 2.41762662907648 -1.73948169654133
C -3.51117332555613 0.61090585073000 -1.16991673165597
C -2.28482439083287 1.13160979705768 1.28333774041920
C -1.78100685960876 -1.35263195601095 -0.10957907971678
C 2.85662712603741 -0.75298277428454 -1.01186348908046
C 2.37004782909582 1.26748158257792 0.91732581891963
C 1.22163933835054 -1.26721088726341 1.22955204358818
C 2.23611294310828 2.59198428016156 0.51446839099237
C 2.89210407218110 3.60088284049938 1.19664341916966
C 3.68709909080796 3.29179861337528 2.28763843778383
C 3.82478057673134 1.97338519818039 2.69371445059695
C 3.17151309837544 0.96192219412327 2.01384997306818
H 3.28143107168968 -0.06513097900611 2.33433815575264
H 1.60287002442042 2.81858175135566 -0.34113397822863
H 2.78179378359575 4.62688214100725 0.87807898927883
H 4.20041027836766 4.07658482925547 2.82394763782885
H 4.44690211307115 1.73213534987742 3.54382726731833
C -4.41780707703862 -0.43635046258215 -1.28238558017602
C -3.84282662678673 1.86577431268289 -1.67112725022672
C -5.07156018788371 2.07517825289305 -2.26692228552826
C -5.97569733379983 1.02999010192156 -2.37331277787025
C -5.64562541105991 -0.22272482616634 -1.88454526578186
H -6.34721712574224 -1.04000777143667 -1.97229732504198
H -6.93522518244381 1.18987079399179 -2.84283753349094
H -4.16572263799214 -1.41888048097359 -0.90684473008857
H -3.11729550802682 2.66591350603892 -1.59948724130073
H -5.32445897776495 3.05084943387193 -2.65502050062577
C 4.19796672119399 -0.44989219685872 -0.82055325381551
C 5.16181933681541 -1.04834211866540 -1.61404540024440
C 4.79764134181786 -1.94524709140491 -2.60367908435743
C 3.45964834415617 -2.24268710440340 -2.80677956920685
C 2.49538371804378 -1.64509548818317 -2.01906970679278
H 1.44756224403147 -1.85521516492714 -2.18960483257756
H 4.49385055979548 0.25951664071796 -0.06127042215255
H 6.20405019844662 -0.80634952945750 -1.46143334828109
H 5.55432083549136 -2.40433556709558 -3.22303023206267
H 3.17015253120889 -2.93191950654955 -3.58691902757284
C 1.54941786590029 -2.60558809517675 1.05249449028474
C 1.28161449683729 -3.52546519695007 2.05069631851422
C 0.67927476660959 -3.12294173146884 3.23003209287696
C 0.33363196622262 -1.79273997936407 3.40611758369776
C 0.59568878158429 -0.87292499468675 2.41012368080011
H 2.02484987416092 -2.93032547081008 0.13779136855479
H 1.54875192815885 -4.56248570896378 1.90653293584721
H 0.32309924442599 0.16499541765010 2.54842743138190
H 0.47788074411977 -3.84337294996186 4.00930642908633
H -0.14290634933955 -1.47124683004818 4.32129956276960
C -1.31354233409010 -2.05738187273839 -1.21701394805092
C -1.15489171233855 -3.42777969103667 -1.15968222538261
C -1.45842356284967 -4.10429711437290 0.01144255257322
C -1.91397712019808 -3.40704297168263 1.11734713253341
C -2.07244626427197 -2.03284591729032 1.06422605013934
H -2.41573750635778 -1.49382234758003 1.93539220362731
H -1.08223033452525 -1.50956277520308 -2.12676935625086
H -0.79387079603549 -3.97077055115684 -2.02162799520968
H -1.33419555922600 -5.17599787056505 0.06338389713932
H -2.14384991303661 -3.93551839085528 2.03115609898636
C -1.35819215570531 1.99049412728023 1.86302972644386
C -3.46986728464012 0.84230553429840 1.95160992020785
C -3.70162706052729 1.38254776766268 3.20335968435977
C -2.76275353766619 2.21831150118451 3.78864933277745
C -1.59338308776698 2.52985078159700 3.11481713469147
H -0.45818537410003 2.23854249975912 1.30963612473897
H -4.21044872897551 0.20572135920704 1.48659718233452
H -4.62013281685454 1.15487431915264 3.72510850741329
H -2.95026531152889 2.63568963605653 4.76718314629179
H -0.86750166367990 3.19336388913234 3.56233808792617
H 4.13491020860763 1.47706053173965 -3.38389423323127
H 3.23854663639978 2.62890015710831 -4.51145289774504

@ -0,0 +1,8 @@
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS=1
cd $PWD
$XTB_COMMAND geom.xyz --opt -P 1 --input cmmd.in > xtb.out

@ -0,0 +1,2 @@
Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
normal termination of xtb

@ -0,0 +1,100 @@
1 2 0.84427417681960937
1 3 0.79054695156333776
1 4 0.91050014913262567
4 5 2.1335590644235296
1 6 0.11715577177264859
4 6 0.13841703661835511
5 6 1.6804432704048216
1 7 0.78391322483904269
3 8 0.97452769342762380
3 9 0.98591175276913545
3 10 0.98428405532438334
2 11 0.97097558036165643
2 12 0.97498509779637432
2 13 0.96880259450802575
12 14 1.3950392659857127
14 15 1.4382793605945186
12 16 0.10631889769481488
15 16 1.4416895152604481
14 17 0.10664401419723352
16 17 1.4291106681640886
12 18 1.3822267328446536
15 18 0.10999393888525678
17 18 1.4520978929688519
18 19 0.96270762503211760
14 20 0.90133014490492303
15 21 0.96957259051428113
16 22 0.97115344595891195
17 23 0.96978386241794012
8 24 1.3976084404509375
8 25 1.3825343152842111
24 26 0.10695209639041489
25 26 1.4555424256733012
8 27 0.10509187731714731
26 27 1.4276805051278456
24 28 1.4379954327735769
25 28 0.11009038546715444
27 28 1.4424603163140739
28 29 0.96946448732005575
27 30 0.97092950340931250
24 31 0.96076133286455923
25 32 0.95117551636193143
26 33 0.96920078408195087
11 34 1.4039850716965288
34 35 1.4371019640772982
11 36 0.10706064745391139
35 36 1.4429081650968467
34 37 0.10756928517508429
36 37 1.4289988684091077
11 38 1.3812792955523077
35 38 0.10987135639781342
37 38 1.4525883552714445
38 39 0.94919160963214411
34 40 0.95974595262630180
35 41 0.97001878668153418
36 42 0.97127145842517770
37 43 0.96979724544516832
13 44 1.3991433208488071
44 45 1.4417770279197613
13 46 0.10575308391317718
45 46 1.4386791230972082
44 47 0.10645700693874831
46 47 1.4299002830056664
13 48 1.3842975140345617
45 48 0.10890211472537245
47 48 1.4515454732462778
44 49 0.95837523482445164
45 50 0.97010621517377227
48 51 0.95120864432494845
46 52 0.97132511927671961
47 53 0.97007989576857945
10 54 1.3734797165775376
54 55 1.4540279504710683
10 56 0.10569140605930637
55 56 1.4263978836083830
54 57 0.10899035636406065
56 57 1.4423834470269963
10 58 1.4008503766396299
55 58 0.10633059584897500
57 58 1.4360695348521759
58 59 0.96105011766049775
54 60 0.91893949238170913
55 61 0.96917064420323507
56 62 0.97107913691089875
57 63 0.96974368925387577
9 64 1.3947577450333175
9 65 1.3847104515198900
64 66 0.10686462092357815
65 66 1.4512825718670750
9 67 0.10549978097885677
66 67 1.4301684320922552
64 68 1.4393382236999117
65 68 0.10971072753988990
67 68 1.4409328944731128
64 69 0.94167141089008521
65 70 0.96176760373332681
66 71 0.96934666872791730
67 72 0.97096180316890246
68 73 0.96958517787758924
6 74 0.94604004578594048
6 75 0.94690357565326799

File diff suppressed because it is too large Load Diff

@ -0,0 +1,385 @@
75
energy: -110.830060472410 gnorm: 0.006867121227 xtb: 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54)
Ni 0.07828004258115 0.88176698075741 -1.27292490171584
P 1.41658897046105 -0.00815423870404 -0.22674609440180
P -1.75370402002944 0.38695531403016 -0.19852647634920
N 1.11997073999923 0.89070035178507 -2.75909987184904
C 2.11688771598067 1.36763191664985 -3.21479238031500
C 3.20528306453374 1.80084008834109 -3.80444390950997
H -0.57164479291145 2.03652530357041 -1.90137768268988
C -3.35845435298075 0.64635474428722 -1.03542418690317
C -2.19243438855029 1.09073533362599 1.42134676136879
C -1.73643934516688 -1.42343609476839 -0.02205761932305
C 2.85172723740929 -0.77425339320566 -1.06879598224948
C 2.23195843769830 1.30344608587640 0.75671088341566
C 1.16496460468105 -1.24684344491312 1.10722563836631
C 2.04422592396696 2.62268720612952 0.35474792689807
C 2.63794905081058 3.66098554471000 1.05056766618675
C 3.42915010674661 3.38826098546593 2.15346285604396
C 3.62563201948251 2.07639266183811 2.55669058126369
C 3.03214825495613 1.03698129481532 1.86480812220203
H 3.18668465479603 0.01586444084169 2.18601632604091
H 1.41987857361368 2.82950822358917 -0.51551820273783
H 2.48299770175118 4.68139500668453 0.73184514875860
H 3.89462789788255 4.19556523746005 2.69992463917142
H 4.24652912905226 1.86231849418918 3.41499591753639
C -4.23993944273253 -0.37987687884067 -1.34939500697384
C -3.70234735002262 1.96262265256325 -1.32919013769864
C -4.91503475347359 2.25065832739431 -1.92330661255332
C -5.79356610463662 1.22420362509672 -2.23432026364342
C -5.45295201712869 -0.08664301468533 -1.94931327658203
H -6.13472999147496 -0.88833211101628 -2.19431408057934
H -6.74104254400785 1.44624810784827 -2.70277339086330
H -3.98241259745376 -1.40707567831745 -1.13199658715609
H -2.99950713856983 2.75235223859341 -1.09683361259193
H -5.17652342725500 3.27381946650316 -2.14968099226155
C 4.17569503967047 -0.43641880458911 -0.82686176231464
C 5.19066937936604 -1.05646799380359 -1.53602384843430
C 4.89540274120135 -2.01221063263183 -2.49211028783261
C 3.57491857898230 -2.34483825314053 -2.74840913730311
C 2.56098452179118 -1.72517237164792 -2.04513520061548
H 1.52672289568962 -1.95960960970165 -2.26348648572550
H 4.42248617203211 0.31937873149065 -0.09532798521229
H 6.21873100082521 -0.78389936230347 -1.34351885618791
H 5.69151863866265 -2.48863314055992 -3.04552921224699
H 3.33819956208610 -3.07953524513890 -3.50454703299123
C 1.47689337315749 -2.59176544691373 0.95021745691776
C 1.22039999283915 -3.49339272025256 1.96776635571689
C 0.64674455259800 -3.06700165013062 3.15279757081629
C 0.32209234412317 -1.73018554018236 3.31424867448034
C 0.57334320884602 -0.83024709269756 2.29718428015192
H 1.93076772334176 -2.93862428007462 0.03292980900263
H 1.47401140434471 -4.53521350262274 1.83377644337266
H 0.32065500350584 0.21277068982223 2.43316164642899
H 0.45306283864223 -3.77276823998362 3.94729388370485
H -0.12868091916980 -1.38635527531638 4.23459552846494
C -1.26174690840946 -2.07658275562020 -1.15913057343848
C -1.16207043227602 -3.45304597215587 -1.18379671857411
C -1.52826873576389 -4.18561083547243 -0.06473201978332
C -1.98865636513911 -3.53906459593985 1.06943518790190
C -2.09499499274339 -2.15846835170847 1.09751995464376
H -2.43961113713448 -1.66041876856714 1.99188322432513
H -0.97686433220172 -1.47589599647251 -2.02289552304607
H -0.79674957115592 -3.95767187968036 -2.06668513593799
H -1.44700115699999 -5.26259194481782 -0.07505730369624
H -2.26346232988640 -4.11254949591789 1.94277197173444
C -1.33853065347459 2.03471210915444 1.97997124322068
C -3.37168657845386 0.75301719359603 2.07756503806357
C -3.66187084581579 1.32155045363103 3.30404499546965
C -2.79164421949066 2.23955107190894 3.87211821867475
C -1.63482934896360 2.60574745269624 3.20461190934469
H -0.44517611172893 2.32404778808029 1.43780941528181
H -4.06331879952536 0.05934381452684 1.61946662637305
H -4.57363282703248 1.05374109455854 3.81824082851337
H -3.02411540326560 2.67917576123052 4.83094701671728
H -0.96531984812549 3.33567865362709 3.63604896241517
H 4.15825787759621 1.35325061973152 -3.58701934369225
H 3.16633280753476 2.57817954580469 -4.54448101295823
75
energy: -110.830087249832 gnorm: 0.001002516499 xtb: 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54)
Ni 0.08087093892510 0.87968363882606 -1.26986858237174
P 1.41495042881319 -0.00732560342268 -0.22791055002180
P -1.75323303470689 0.38621303961495 -0.19794132689769
N 1.12134766063993 0.89095425961678 -2.75692890973092
C 2.11794769517175 1.36906214209431 -3.21207348906935
C 3.20599771108090 1.80394801183349 -3.80116095726323
H -0.56696256500640 2.03430237235604 -1.90106720479491
C -3.35769769443327 0.64607500860939 -1.03545571840882
C -2.19227685445517 1.09058991776290 1.42157917450572
C -1.73648055833779 -1.42411716634202 -0.02177883360685
C 2.85068833445457 -0.77384467471092 -1.06912496860389
C 2.23128445833459 1.30360422659832 0.75584270765450
C 1.16450715806863 -1.24613425087486 1.10645544037754
C 2.04370068750485 2.62291768973183 0.35413951610758
C 2.63758412187900 3.66107949968168 1.05003118026305
C 3.42887726124657 3.38821510797431 2.15281803731534
C 3.62533062653469 2.07628636491143 2.55584765799134
C 3.03171655178175 1.03697877073257 1.86383747048343
H 3.18629875012303 0.01583912148001 2.18496994226553
H 1.41931399367385 2.82985579825594 -0.51604671933375
H 2.48265677843030 4.68153562298693 0.73145559298666
H 3.89442584174173 4.19544955183682 2.69934141856314
H 4.24627015009333 1.86212312709122 3.41411792406251
C -4.23921791650793 -0.38001793150420 -1.34982972988107
C -3.70179473671398 1.96247862197253 -1.32860308918219
C -4.91451810561054 2.25070658422638 -1.92262376581397
C -5.79295103855038 1.22433466591770 -2.23415714142836
C -5.45227136942788 -0.08658816201951 -1.94961385285184
H -6.13398129277981 -0.88821221650140 -2.19503111548883
H -6.74035874930817 1.44649653455076 -2.70271476055784
H -3.98179371512748 -1.40727317321453 -1.13261871769832
H -2.99914819501793 2.75221173207505 -1.09568325705273
H -5.17607409102034 3.27393872263232 -2.14862819806836
C 4.17480415766588 -0.43633471462304 -0.82688808109373
C 5.18992857569569 -1.05658495418232 -1.53578173215428
C 4.89482348828616 -2.01242074854444 -2.49180446340079
C 3.57436210714486 -2.34493035097711 -2.74829712633955
C 2.56027903497675 -1.72502489487103 -2.04536847401634
H 1.52609404835481 -1.95953044085518 -2.26391244718725
H 4.42164357981086 0.31949771938210 -0.09541239281880
H 6.21801755369661 -0.78414471518421 -1.34313433156669
H 5.69102595907767 -2.48904472890658 -3.04496684503403
H 3.33778650792892 -3.07976976241613 -3.50434800800311
C 1.47652107568604 -2.59114084366309 0.94962238759708
C 1.22021819378746 -3.49275557751669 1.96729833676799
C 0.64677895821239 -3.06634992596931 3.15241731404745
C 0.32226953683210 -1.72951110239206 3.31386160056894
C 0.57335913879920 -0.82958256407363 2.29670879672332
H 1.93029177649885 -2.93812830348455 0.03233715209032
H 1.47372212520761 -4.53461857390906 1.83333839717772
H 0.32077049464310 0.21342552755688 2.43281341770385
H 0.45316059588456 -3.77209756072542 3.94697002311811
H -0.12836144027306 -1.38567032143438 4.23427972939900
C -1.26186258985429 -2.07711631502968 -1.15894191552458
C -1.16230692325861 -3.45355574377750 -1.18376497086562
C -1.52855328344314 -4.18616547790886 -0.06474317612158
C -1.98883738750253 -3.53967954974753 1.06951384167902
C -2.09509498550797 -2.15911977583602 1.09772045201673
H -2.43946322130758 -1.66106940186251 1.99217865294408
H -0.97693341889177 -1.47632725154881 -2.02264263821553
H -0.79706893037551 -3.95810374574158 -2.06672920456474
H -1.44741739771433 -5.26314265547151 -0.07517712942451
H -2.26364268267010 -4.11317350361198 1.94283092509944
C -1.33861187099485 2.03485988411253 1.98006695434269
C -3.37151424904105 0.75277961063234 2.07773617897203
C -3.66183333685472 1.32137282429718 3.30414226955539
C -2.79184581311701 2.23967144310311 3.87210727523592
C -1.63508549336458 2.60602810207988 3.20459729890291
H -0.44528712992458 2.32428596618532 1.43790729098289
H -4.06292540068158 0.05880546114126 1.61976101239551
H -4.57352944281423 1.05338750917421 3.81835827781249
H -3.02449386916838 2.67944652879665 4.83082120017131
H -0.96577192648904 3.33619994800265 3.63592677161693
H 4.15832191220540 1.35265975934880 -3.58859135385740
H 3.16566274144876 2.57741626568244 -4.54521644113188
75
energy: -110.830080116484 gnorm: 0.001207068916 xtb: 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54)
Ni 0.08069799816839 0.88129246222120 -1.26998207900788
P 1.41470435401286 -0.00683595445268 -0.22839486146492
P -1.75265038732021 0.38550734732035 -0.19724669893835
N 1.12105473449248 0.88931972050927 -2.75741238221329
C 2.11848608223673 1.36431658084658 -3.21405086046765
C 3.20486112677130 1.79777231920185 -3.80726079330538
H -0.56880352144376 2.03503557503883 -1.90118089920751
C -3.35687069370003 0.64579642704593 -1.03520775343398
C -2.19201414617938 1.09026191188565 1.42197559826302
C -1.73635301843218 -1.42480045664849 -0.02135060979509
C 2.85042944620243 -0.77389001172753 -1.06929891306423
C 2.23118639051177 1.30402539878029 0.75534728470106
C 1.16427562213467 -1.24569278545026 1.10606205092886
C 2.04359698069810 2.62337286966507 0.35371750707993
C 2.63747745700484 3.66148272467174 1.04964846696295
C 3.42882561006125 3.38850987924203 2.15234977189128
C 3.62531908830487 2.07653654968751 2.55524665658915
C 3.03163095638094 1.03730098002480 1.86325070775685
H 3.18623911904068 0.01612498111427 2.18424616676755
H 1.41926058315725 2.83042274073468 -0.51648208106470
H 2.48250853789488 4.68195701200268 0.73114467816124
H 3.89440208079555 4.19569757222050 2.69890077969447
H 4.24633991784611 1.86227653701544 3.41342292841267
C -4.23828864129313 -0.38016521729453 -1.35031727400422
C -3.70104126775273 1.96234514798759 -1.32768729260772
C -4.91369316719053 2.25082244272359 -1.92175010080200
C -5.79199533128801 1.22456305543054 -2.23403691438155
C -5.45126269426519 -0.08648620360884 -1.95015060296399
H -6.13290341149827 -0.88801507388681 -2.19607362107597
H -6.73936514709597 1.44692065786134 -2.70258483672194
H -3.98086842335801 -1.40752703349341 -1.13362757375483
H -2.99854651086936 2.75202464668968 -1.09413348601558
H -5.17534092519237 3.27416872386011 -2.14713468542640
C 4.17455467456240 -0.43661448745223 -0.82700419679385
C 5.18963459270498 -1.05713335319584 -1.53567621088234
C 4.89447996786360 -2.01306225520059 -2.49158779117379
C 3.57398653273945 -2.34534467830322 -2.74819676342728
C 2.55996479609953 -1.72512605312090 -2.04546699598672
H 1.52574407640167 -1.95942484241122 -2.26415633161398
H 4.42145048620461 0.31933476359331 -0.09568192440081
H 6.21773833546374 -0.78483458327588 -1.34293150575477
H 5.69066206223934 -2.48992185363703 -3.04457467764879
H 3.33735353925553 -3.08026550547441 -3.50416038648073
C 1.47605492088787 -2.59074373709928 0.94927005122768
C 1.21981540950807 -3.49227822606593 1.96701469642916
C 0.64663462063024 -3.06574663562631 3.15221253010970
C 0.32232597936422 -1.72885904249853 3.31362988035744
C 0.57334764477155 -0.82904740699928 2.29637121952655
H 1.92963166468298 -2.93785181697380 0.03193540302506
H 1.47319569330869 -4.53417413225650 1.83306539259440
H 0.32103228543035 0.21402372344907 2.43252640667513
H 0.45306945355945 -3.77142384378797 3.94683999549752
H -0.12801978359573 -1.38487497065852 4.23413858680746
C -1.26187940718656 -2.07765458629823 -1.15865799878014
C -1.16261612133873 -3.45410897168552 -1.18373088696457
C -1.52898105079629 -4.18683148070277 -0.06481232600193
C -1.98907752491159 -3.54045576460841 1.06958478371186
C -2.09508220750783 -2.15988493226746 1.09803384836481
H -2.43930629927002 -1.66189844090176 1.99258146167544
H -0.97682652832209 -1.47672938094554 -2.02225033628409
H -0.79747449504591 -3.95857312678156 -2.06678145269943
H -1.44802031504716 -5.26381658358434 -0.07541598917358
H -2.26392285123170 -4.11403259799099 1.94283086429420
C -1.33873241622402 2.03503216195789 1.98019207552724
C -3.37121177050394 0.75226807448060 2.07809094483168
C -3.66181480153162 1.32112159573135 3.30430443471344
C -2.79217914220501 2.23988550024048 3.87206210233715
C -1.63550335931197 2.60646801349809 3.20452199041764
H -0.44541873700552 2.32454218239874 1.43804161978063
H -4.06237744351510 0.05797750255578 1.62022456409791
H -4.57344279810203 1.05295004178044 3.81854021820902
H -3.02501454337339 2.67980858294154 4.83066007909351
H -0.96644683891241 3.33695626104486 3.63570814865892
H 4.16010047682554 1.35768608977863 -3.58441939594971
H 3.16568242368737 2.58432726914501 -4.53765440538835
75
energy: -110.830090540995 gnorm: 0.000911324646 xtb: 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54)
Ni 0.07980172447341 0.88106936184447 -1.27095005539555
P 1.41480163964620 -0.00703153269392 -0.22857666738011
P -1.75253849267543 0.38513636743248 -0.19697097812919
N 1.12210600867169 0.89044507557885 -2.75706954730203
C 2.11930744038237 1.36803506678003 -3.21148221647875
C 3.20648353575273 1.80393117005206 -3.80128954437832
H -0.57088249557834 2.03471211098674 -1.90117168478851
C -3.35664434766897 0.64561395157074 -1.03501587381049
C -2.19189489758932 1.09000614400666 1.42218565249331
C -1.73626711984054 -1.42517049216632 -0.02110135117805
C 2.85047773450149 -0.77410146438273 -1.06946158694307
C 2.23105750706209 1.30413433567852 0.75507004723382
C 1.16417805212218 -1.24568244571059 1.10598889186492
C 2.04344795832141 2.62352209332845 0.35347313596111
C 2.63734400229461 3.66163695002286 1.04938532975260
C 3.42875205438078 3.38865347172668 2.15203025208950
C 3.62528328516181 2.07666827744724 2.55487124217003
C 3.03155107420803 1.03744364817843 1.86291808853100
H 3.18620853016230 0.01626393429648 2.18386397579182
H 1.41913429476847 2.83069743257675 -0.51671938979798
H 2.48234815478505 4.68211681435996 0.73089564924317
H 3.89435343142175 4.19583417687340 2.69856563119120
H 4.24638177146091 1.86238304567047 3.41297913039268
C -4.23792399342429 -0.38029383573730 -1.35062651034495
C -3.70078159847767 1.96224481820506 -1.32710736957246
C -4.91333859242523 2.25087190113317 -1.92126177321142
C -5.79154773088452 1.22467424042221 -2.23403323777475
C -5.45080162431330 -0.08646300921522 -1.95056176996964
H -6.13236941719492 -0.88794048025891 -2.19684041528433
H -6.73887233127711 1.44715655962508 -2.70260347463662
H -3.98045223036564 -1.40772133112892 -1.13430709701300
H -2.99832807389719 2.75186193197285 -1.09320891896414
H -5.17500056889639 3.27428888216189 -2.14629734135823
C 4.17456641278134 -0.43686040595960 -0.82715713849852
C 5.18961122524792 -1.05754131160544 -1.53569480817693
C 4.89441171390590 -2.01353290069452 -2.49153231369881
C 3.57390122675135 -2.34568970188861 -2.74822438006737
C 2.55992780166371 -1.72531363761120 -2.04560187940698
H 1.52567457276091 -1.95945174869608 -2.26436279182472
H 4.42146628153303 0.31914167942308 -0.09588607613101
H 6.21771749534433 -0.78531837854704 -1.34288221571334
H 5.69057628820207 -2.49052312663450 -3.04441530428523
H 3.33721661607816 -3.08063922373366 -3.50414154763904
C 1.47580605030981 -2.59073480324945 0.94923646199711
C 1.21956358357819 -3.49215754589402 1.96704798478196
C 0.64652464196580 -3.06547237158783 3.15226394640241
C 0.32234467573158 -1.72854306576616 3.31361934795337
C 0.57334006476161 -0.82885920819150 2.29625900846976
H 1.92924302806692 -2.93792747543731 0.03186313043899
H 1.47284754230381 -4.53407588716904 1.83312892770691
H 0.32117939632257 0.21426472126852 2.43235676285679
H 0.45297146676330 -3.77106808706173 3.94695661527860
H -0.12784949607409 -1.38441983377053 4.23415041688339
C -1.26191758961343 -2.07799162186919 -1.15848794682121
C -1.16282189028415 -3.45445972064013 -1.18367605438811
C -1.52923598482945 -4.18723210113158 -0.06480391835097
C -1.98920738388090 -3.54089789946150 1.06966483501285
C -2.09502878664697 -2.16030679110124 1.09824528170072
H -2.43919005570217 -1.66235920707167 1.99283762759322
H -0.97680182444630 -1.47702029871044 -2.02202672880885
H -0.79775394773795 -3.95889442446984 -2.06677260390850
H -1.44839242820091 -5.26422620962573 -0.07549619782532
H -2.26408890665445 -4.11452117698624 1.94287009017710
C -1.33883216710316 2.03508731682728 1.98021151574903
C -3.37103706107927 0.75189230340145 2.07833608382620
C -3.66180776626739 1.32095661802116 3.30441230787677
C -2.79238463567688 2.24002712448863 3.87199828149766
C -1.63577288054921 2.60672846021230 3.20440752584637
H -0.44556655745351 2.32468487227072 1.43801697691082
H -4.06206383677560 0.05740594378565 1.62055916213666
H -4.57339794338578 1.05270440984939 3.81867141407816
H -3.02532902847481 2.68007880645894 4.83051068516129
H -0.96689201369058 3.33745468519148 3.63546370655770
H 4.15952112208772 1.35452532556150 -3.58808875133124
H 3.16599629338708 2.58219872717877 -4.54023766297062
75
energy: -110.830092138474 gnorm: 0.000528796768 xtb: 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54)
Ni 0.08024427094612 0.88030997583889 -1.27008783828989
P 1.41497771575524 -0.00714867347512 -0.22890953738001
P -1.75230087048645 0.38476234738698 -0.19668297223499
N 1.12155635089810 0.89187633675014 -2.75690744217788
C 2.11835491422073 1.37038386158506 -3.21126537312849
C 3.20663630914065 1.80577132901243 -3.79953027379204
H -0.56921926710232 2.03394294791625 -1.90183491699665
C -3.35640013119622 0.64531614208838 -1.03459197146712
C -2.19167612242653 1.08963352859401 1.42248337325409
C -1.73604449502242 -1.42558363427943 -0.02075677851768
C 2.85047996028356 -0.77427535070777 -1.06988803483311
C 2.23102732464868 1.30430346941366 0.75445684312796
C 1.16406330793213 -1.24550160196729 1.10581770386264
C 2.04316351219274 2.62364545972164 0.35287949503565
C 2.63702909124270 3.66182348883229 1.04877405332241
C 3.42859346061043 3.38893750703839 2.15135772444828
C 3.62530705962588 2.07698351868867 2.55418868716394
C 3.03165096172695 1.03769919423120 1.86224563663885
H 3.18634489391197 0.01653532424719 2.18323642540910
H 1.41864774727145 2.83075244737601 -0.51718486505865
H 2.48189467022388 4.68229152170525 0.73032030983572
H 3.89417555723984 4.19615973742794 2.69785870871670
H 4.24648962834332 1.86275192050331 3.41225400171069
C -4.23740995036257 -0.38050985253466 -1.35113551420133
C -3.70054884330393 1.96209283734594 -1.32592360820539
C -4.91291283309764 2.25097092043514 -1.92029499987943
C -5.79091340973570 1.22487334433715 -2.23398191038373
C -5.45011719190370 -0.08641658409241 -1.95128083984541
H -6.13148236137674 -0.88781769554061 -2.19835300335951
H -6.73808829548318 1.44756131814317 -2.70274209774079
H -3.97984794908461 -1.40804659010646 -1.13543502121794
H -2.99817464931393 2.75160439610536 -1.09141928768061
H -5.17453993591038 3.27450180657596 -2.14484095427247
C 4.17459164421984 -0.43722555348943 -0.82745854672754
C 5.18959173561079 -1.05826246679565 -1.53577053393631
C 4.89428678068484 -2.01436632827174 -2.49146766217159
C 3.57373060117103 -2.34628539689413 -2.74828490295612
C 2.55979809734218 -1.72558371015173 -2.04589305342032
H 1.52551876494858 -1.95953203465318 -2.26471231351834
H 4.42153855922872 0.31882863274711 -0.09624713527834
H 6.21772827156207 -0.78621161764932 -1.34288788131147
H 5.69041671558501 -2.49163095531779 -3.04415945671998
H 3.33697654182036 -3.08128169150514 -3.50412762067127
C 1.47536951888857 -2.59063178695704 0.94909652223569
C 1.21909695627136 -3.49190114380949 1.96703994192876
C 0.64633593374008 -3.06497322808563 3.15230736240645
C 0.32245421332866 -1.72796019700436 3.31360343438282
C 0.57351087324393 -0.82840451515219 2.29613616207207
H 1.92858893750176 -2.93798597905753 0.03167440832248
H 1.47213748084837 -4.53388045729795 1.83316640970535
H 0.32152025251750 0.21477047950136 2.43213950541296
H 0.45277013416650 -3.77045479265004 3.94709466183128
H -0.12759674051841 -1.38366996491308 4.23413644853449
C -1.26193158729539 -2.07841327309514 -1.15824643613990
C -1.16314505039719 -3.45490441813362 -1.18362497345348
C -1.52965474541254 -4.18775328550960 -0.06483847858757
C -1.98941207749603 -3.54145923941746 1.06973473775901
C -2.09490482834913 -2.16083305047144 1.09851284906891
H -2.43890280254091 -1.66296941229801 1.99321009031093
H -0.97680101270261 -1.47740579885295 -2.02173442794100
H -0.79830678516057 -3.95931752404638 -2.06682883394628
H -1.44912245713620 -5.26477456896227 -0.07570751070465
H -2.26441274834188 -4.11515939285543 1.94285788623495
C -1.33899702123299 2.03521838306450 1.98025828619547
C -3.37070310873479 0.75125660964137 2.07872121054722
C -3.66175048524124 1.32060694174914 3.30460326900669
C -2.79271695562988 2.24020879401778 3.87191884869224
C -1.63622502064262 2.60714685999507 3.20425371868321
H -0.44586719979463 2.32505703036032 1.43797870721434
H -4.06144157566544 0.05636029395033 1.62113501509113
H -4.57328065626997 1.05220506311044 3.81889234490696
H -3.02591061671016 2.68054057363805 4.83024342960527
H -0.96770807874297 3.33835618342170 3.63505826083519
H 4.15918368328721 1.35537509224269 -3.58602614507926
H 3.16709542772868 2.58322614727192 -4.53941332023278

@ -0,0 +1,77 @@
75
energy: -110.830095516537 gnorm: 0.000712094797 xtb: 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54)
Ni 0.08024427094612 0.88030997583889 -1.27008783828989
P 1.41497771575524 -0.00714867347512 -0.22890953738001
P -1.75230087048645 0.38476234738698 -0.19668297223499
N 1.12155635089810 0.89187633675014 -2.75690744217788
C 2.11835491422073 1.37038386158506 -3.21126537312849
C 3.20663630914065 1.80577132901243 -3.79953027379204
H -0.56921926710232 2.03394294791625 -1.90183491699665
C -3.35640013119622 0.64531614208838 -1.03459197146712
C -2.19167612242653 1.08963352859401 1.42248337325409
C -1.73604449502242 -1.42558363427943 -0.02075677851768
C 2.85047996028356 -0.77427535070777 -1.06988803483311
C 2.23102732464868 1.30430346941366 0.75445684312796
C 1.16406330793213 -1.24550160196729 1.10581770386264
C 2.04316351219274 2.62364545972164 0.35287949503565
C 2.63702909124270 3.66182348883229 1.04877405332241
C 3.42859346061043 3.38893750703839 2.15135772444828
C 3.62530705962588 2.07698351868867 2.55418868716394
C 3.03165096172695 1.03769919423120 1.86224563663885
H 3.18634489391197 0.01653532424719 2.18323642540910
H 1.41864774727145 2.83075244737601 -0.51718486505865
H 2.48189467022388 4.68229152170525 0.73032030983572
H 3.89417555723984 4.19615973742794 2.69785870871670
H 4.24648962834332 1.86275192050331 3.41225400171069
C -4.23740995036257 -0.38050985253466 -1.35113551420133
C -3.70054884330393 1.96209283734594 -1.32592360820539
C -4.91291283309764 2.25097092043514 -1.92029499987943
C -5.79091340973570 1.22487334433715 -2.23398191038373
C -5.45011719190370 -0.08641658409241 -1.95128083984541
H -6.13148236137674 -0.88781769554061 -2.19835300335951
H -6.73808829548318 1.44756131814317 -2.70274209774079
H -3.97984794908461 -1.40804659010646 -1.13543502121794
H -2.99817464931393 2.75160439610536 -1.09141928768061
H -5.17453993591038 3.27450180657596 -2.14484095427247
C 4.17459164421984 -0.43722555348943 -0.82745854672754
C 5.18959173561079 -1.05826246679565 -1.53577053393631
C 4.89428678068484 -2.01436632827174 -2.49146766217159
C 3.57373060117103 -2.34628539689413 -2.74828490295612
C 2.55979809734218 -1.72558371015173 -2.04589305342032
H 1.52551876494858 -1.95953203465318 -2.26471231351834
H 4.42153855922872 0.31882863274711 -0.09624713527834
H 6.21772827156207 -0.78621161764932 -1.34288788131147
H 5.69041671558501 -2.49163095531779 -3.04415945671998
H 3.33697654182036 -3.08128169150514 -3.50412762067127
C 1.47536951888857 -2.59063178695704 0.94909652223569
C 1.21909695627136 -3.49190114380949 1.96703994192876
C 0.64633593374008 -3.06497322808563 3.15230736240645
C 0.32245421332866 -1.72796019700436 3.31360343438282
C 0.57351087324393 -0.82840451515219 2.29613616207207
H 1.92858893750176 -2.93798597905753 0.03167440832248
H 1.47213748084837 -4.53388045729795 1.83316640970535
H 0.32152025251750 0.21477047950136 2.43213950541296
H 0.45277013416650 -3.77045479265004 3.94709466183128
H -0.12759674051841 -1.38366996491308 4.23413644853449
C -1.26193158729539 -2.07841327309514 -1.15824643613990
C -1.16314505039719 -3.45490441813362 -1.18362497345348
C -1.52965474541254 -4.18775328550960 -0.06483847858757
C -1.98941207749603 -3.54145923941746 1.06973473775901
C -2.09490482834913 -2.16083305047144 1.09851284906891
H -2.43890280254091 -1.66296941229801 1.99321009031093
H -0.97680101270261 -1.47740579885295 -2.02173442794100
H -0.79830678516057 -3.95931752404638 -2.06682883394628
H -1.44912245713620 -5.26477456896227 -0.07570751070465
H -2.26441274834188 -4.11515939285543 1.94285788623495
C -1.33899702123299 2.03521838306450 1.98025828619547
C -3.37070310873479 0.75125660964137 2.07872121054722
C -3.66175048524124 1.32060694174914 3.30460326900669
C -2.79271695562988 2.24020879401778 3.87191884869224
C -1.63622502064262 2.60714685999507 3.20425371868321
H -0.44586719979463 2.32505703036032 1.43797870721434
H -4.06144157566544 0.05636029395033 1.62113501509113
H -4.57328065626997 1.05220506311044 3.81889234490696
H -3.02591061671016 2.68054057363805 4.83024342960527
H -0.96770807874297 3.33835618342170 3.63505826083519
H 4.15918368328721 1.35537509224269 -3.58602614507926
H 3.16709542772868 2.58322614727192 -4.53941332023278

Binary file not shown.

File diff suppressed because it is too large Load Diff

@ -0,0 +1,160 @@
xtb 07122222053D
xtb: 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54)
75 80 0 0 0 999 V2000
0.0802 0.8803 -1.2701 Ni 0 0 0 0 0 0 0 0 0 0 0 0
1.4150 -0.0071 -0.2289 P 0 0 0 0 0 0 0 0 0 0 0 0
-1.7523 0.3848 -0.1967 P 0 0 0 0 0 0 0 0 0 0 0 0
1.1216 0.8919 -2.7569 N 0 0 0 0 0 0 0 0 0 0 0 0
2.1184 1.3704 -3.2113 C 0 0 0 0 0 0 0 0 0 0 0 0
3.2066 1.8058 -3.7995 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5692 2.0339 -1.9018 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.3564 0.6453 -1.0346 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1917 1.0896 1.4225 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7360 -1.4256 -0.0208 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8505 -0.7743 -1.0699 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2310 1.3043 0.7545 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1641 -1.2455 1.1058 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0432 2.6236 0.3529 C 0 0 0 0 0 0 0 0 0 0 0 0
2.6370 3.6618 1.0488 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4286 3.3889 2.1514 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6253 2.0770 2.5542 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0317 1.0377 1.8622 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1863 0.0165 2.1832 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4186 2.8308 -0.5172 H 0 0 0 0 0 0 0 0 0 0 0 0
2.4819 4.6823 0.7303 H 0 0 0 0 0 0 0 0 0 0 0 0
3.8942 4.1962 2.6979 H 0 0 0 0 0 0 0 0 0 0 0 0
4.2465 1.8628 3.4123 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.2374 -0.3805 -1.3511 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.7005 1.9621 -1.3259 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.9129 2.2510 -1.9203 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.7909 1.2249 -2.2340 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.4501 -0.0864 -1.9513 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.1315 -0.8878 -2.1984 H 0 0 0 0 0 0 0 0 0 0 0 0
-6.7381 1.4476 -2.7027 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.9798 -1.4080 -1.1354 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9982 2.7516 -1.0914 H 0 0 0 0 0 0 0 0 0 0 0 0
-5.1745 3.2745 -2.1448 H 0 0 0 0 0 0 0 0 0 0 0 0
4.1746 -0.4372 -0.8275 C 0 0 0 0 0 0 0 0 0 0 0 0
5.1896 -1.0583 -1.5358 C 0 0 0 0 0 0 0 0 0 0 0 0
4.8943 -2.0144 -2.4915 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5737 -2.3463 -2.7483 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5598 -1.7256 -2.0459 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5255 -1.9595 -2.2647 H 0 0 0 0 0 0 0 0 0 0 0 0
4.4215 0.3188 -0.0962 H 0 0 0 0 0 0 0 0 0 0 0 0
6.2177 -0.7862 -1.3429 H 0 0 0 0 0 0 0 0 0 0 0 0
5.6904 -2.4916 -3.0442 H 0 0 0 0 0 0 0 0 0 0 0 0
3.3370 -3.0813 -3.5041 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4754 -2.5906 0.9491 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2191 -3.4919 1.9670 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6463 -3.0650 3.1523 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3225 -1.7280 3.3136 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5735 -0.8284 2.2961 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9286 -2.9380 0.0317 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4721 -4.5339 1.8332 H 0 0 0 0 0 0 0 0 0 0 0 0
0.3215 0.2148 2.4321 H 0 0 0 0 0 0 0 0 0 0 0 0
0.4528 -3.7705 3.9471 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.1276 -1.3837 4.2341 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.2619 -2.0784 -1.1582 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1631 -3.4549 -1.1836 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5297 -4.1878 -0.0648 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.9894 -3.5415 1.0697 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.0949 -2.1608 1.0985 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4389 -1.6630 1.9932 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.9768 -1.4774 -2.0217 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.7983 -3.9593 -2.0668 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.4491 -5.2648 -0.0757 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.2644 -4.1152 1.9429 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.3390 2.0352 1.9803 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.3707 0.7513 2.0787 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.6618 1.3206 3.3046 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.7927 2.2402 3.8719 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6362 2.6071 3.2043 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4459 2.3251 1.4380 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.0614 0.0564 1.6211 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.5733 1.0522 3.8189 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.0259 2.6805 4.8302 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.9677 3.3384 3.6351 H 0 0 0 0 0 0 0 0 0 0 0 0
4.1592 1.3554 -3.5860 H 0 0 0 0 0 0 0 0 0 0 0 0
3.1671 2.5832 -4.5394 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 4 1 0 0 0 0
4 5 2 0 0 0 0
5 6 2 0 0 0 0
1 7 1 0 0 0 0
3 8 1 0 0 0 0
3 9 1 0 0 0 0
3 10 1 0 0 0 0
2 11 1 0 0 0 0
2 12 1 0 0 0 0
2 13 1 0 0 0 0
12 14 4 0 0 0 0
14 15 4 0 0 0 0
15 16 4 0 0 0 0
16 17 4 0 0 0 0
12 18 4 0 0 0 0
17 18 4 0 0 0 0
18 19 1 0 0 0 0
14 20 1 0 0 0 0
15 21 1 0 0 0 0
16 22 1 0 0 0 0
17 23 1 0 0 0 0
8 24 4 0 0 0 0
8 25 4 0 0 0 0
25 26 4 0 0 0 0
26 27 4 0 0 0 0
24 28 4 0 0 0 0
27 28 4 0 0 0 0
28 29 1 0 0 0 0
27 30 1 0 0 0 0
24 31 1 0 0 0 0
25 32 1 0 0 0 0
26 33 1 0 0 0 0
11 34 4 0 0 0 0
34 35 4 0 0 0 0
35 36 4 0 0 0 0
36 37 4 0 0 0 0
11 38 4 0 0 0 0
37 38 4 0 0 0 0
38 39 1 0 0 0 0
34 40 1 0 0 0 0
35 41 1 0 0 0 0
36 42 1 0 0 0 0
37 43 1 0 0 0 0
13 44 4 0 0 0 0
44 45 4 0 0 0 0
45 46 4 0 0 0 0
46 47 4 0 0 0 0
13 48 4 0 0 0 0
47 48 4 0 0 0 0
44 49 1 0 0 0 0
45 50 1 0 0 0 0
48 51 1 0 0 0 0
46 52 1 0 0 0 0
47 53 1 0 0 0 0
10 54 4 0 0 0 0
54 55 4 0 0 0 0
55 56 4 0 0 0 0
56 57 4 0 0 0 0
10 58 4 0 0 0 0
57 58 4 0 0 0 0
58 59 1 0 0 0 0
54 60 1 0 0 0 0
55 61 1 0 0 0 0
56 62 1 0 0 0 0
57 63 1 0 0 0 0
9 64 4 0 0 0 0
9 65 4 0 0 0 0
65 66 4 0 0 0 0
66 67 4 0 0 0 0
64 68 4 0 0 0 0
67 68 4 0 0 0 0
64 69 1 0 0 0 0
65 70 1 0 0 0 0
66 71 1 0 0 0 0
67 72 1 0 0 0 0
68 73 1 0 0 0 0
6 74 1 0 0 0 0
6 75 1 0 0 0 0
M END

@ -0,0 +1,59 @@
# CMMDE function for xTB standalone program
import os
def xtb(job,geom,nproc,product,temperature,nrun,npoint,anopt,kpush,kpull,ppull,alp,distance,angle,dihedral,scanmode,maxiter,scan):
with open('run.sh','w') as fout:
print("""#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS={}
cd $PWD""".format(nproc),file=fout)
if 'opt' in job:
print("$XTB_COMMAND {} --opt -P {} > xtb.out".format(geom,nproc),file=fout)
if 'freq' in job:
print("$XTB_COMMAND {} --hess -P {} --input cmmd.in > xtb.out".format(geom,nproc), file=fout)
if 'opt' in job and 'freq' in job:
print("$XTB_COMMAND {} --ohess -P {} --input cmmd.in > xtb.out".format(geom,nproc),file=fout)
if 'path' in job:
print("$XTB_COMMAND {} --path {} --input cmmd.in -P {} > xtb.out".format(geom,product,nproc),file=fout)
if 'scan' in job:
print("$XTB_COMMAND {} --opt -P {} --input cmmd.in > xtb.out".format(geom,nproc), file=fout)
if 'freq' in job:
with open('cmmd.in', 'w') as f:
print("""$thermo
temp={}""".format(temperature),file=f)
if 'path' in job:
with open("cmmd.in", 'w') as f:
print("""$path
nrun={}
npoint={}
anopt={}
kpush={}
kpull={}
ppull={}
alp={}
$end""".format(nrun,npoint,anopt,kpush,kpull,ppull,alp),file=f)
if 'scan' in job:
with open("cmmd.in",'w') as f:
print("$constrain",file=f)
if distance != 'None':
print("distance: {}".format(distance),file=f)
if angle != 'None':
print("angle: {}".format(angle),file=f)
if dihedral != 'None':
print("dihedral: {}".format(dihedral),file=f)
print("$scan",file=f)
if scanmode != 'None':
print("mode = {}".format(scanmode),file=f)
scan = scan.split(";")
for index, i in enumerate(scan):
print("{}: {}".format(index+1,i),file=f)
print("""$opt
maxcycle = {}""".format(maxiter),file=f)
os.system('sbatch run.sh')
Loading…
Cancel
Save