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bug fix opt orca

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Aditya Wibawa Sakti 2 years ago
parent c9e7f4877e
commit 8f94c4518c
17 changed files with 7953 additions and 1 deletions
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  1. 102
      cmmde_gui/molekul/cmmd.engrad
  2. BIN
      cmmde_gui/molekul/cmmd.gbw
  3. 8
      cmmde_gui/molekul/cmmd.in
  4. 3373
      cmmde_gui/molekul/cmmd.opt
  5. 4203
      cmmde_gui/molekul/cmmd.out
  6. BIN
      cmmde_gui/molekul/cmmd.xtbrestart
  7. 24
      cmmde_gui/molekul/cmmd.xyz
  8. 6
      cmmde_gui/molekul/cmmd_property.txt
  9. 192
      cmmde_gui/molekul/cmmd_trj.xyz
  10. 1
      cmmde_gui/molekul/geom.smi
  11. 24
      cmmde_gui/molekul/geom.xyz
  12. 10
      cmmde_gui/molekul/run.sh
  13. 8
      cmmde_gui/molekul/run_babel.sh
  14. 1
      cmmde_gui/molekul/slurm-2879.out
  15. 0
      cmmde_gui/molekul/slurm-2880.out
  16. BIN
      lib/__pycache__/cmmde_orca.cpython-39.pyc
  17. 2
      lib/cmmde_orca.py

102
cmmde_gui/molekul/cmmd.engrad
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#
# Number of atoms
#
22
#
# The current total energy in Eh
#
-24.300689883530
#
# The current gradient in Eh/bohr
#
-0.000078011731
0.000077990155
-0.000172228341
0.000077300972
-0.000042371283
0.000161175655
-0.000052245246
-0.000103228073
0.000049462422
0.000001820626
0.000105051957
0.000094782729
0.000086221104
-0.000080609774
-0.000172014815
-0.000078903466
0.000042802807
0.000160254314
0.000050604245
0.000099415702
0.000049911283
-0.000002512022
-0.000100677629
0.000095940374
0.000056324030
-0.000026054592
0.000017365028
-0.000013951222
-0.000000307285
-0.000009022819
0.000004009247
0.000094374895
-0.000051467186
-0.000008807355
-0.000037453860
-0.000046442953
0.000063131670
-0.000001043091
-0.000026363600
0.000023364226
0.000005993197
-0.000031768002
-0.000049385865
-0.000001522204
0.000014911885
0.000012879917
-0.000000298953
-0.000007152993
-0.000062772195
0.000028037742
0.000014978945
-0.000006117115
-0.000093207811
-0.000053946988
0.000010826250
0.000036672974
-0.000043812282
-0.000063088326
0.000003364246
-0.000026478385
-0.000022753307
-0.000009224066
-0.000032077644
0.000052065564
0.000002294948
0.000013993374
#
# The atomic numbers and current coordinates in Bohr
#
6 -3.1707575 0.2177972 1.6020414
6 -2.8099636 -1.9153359 -0.2995915
6 -0.1693597 -1.4539744 -1.3830761
6 1.9809828 -2.5062842 0.2758215
6 3.1608987 -0.2282573 1.6062985
6 2.8030447 1.9100763 -0.2900301
6 0.1641039 1.4516803 -1.3788482
6 -1.9888064 2.4994425 0.2795973
1 -2.1624375 -0.2154170 3.3453092
1 -5.1516399 0.5292905 2.0710045
1 -4.2110958 -1.7429666 -1.8049678
1 -3.0006371 -3.7835331 0.5439859
1 -0.0290829 -2.2380751 -3.2862394
1 3.3966523 -3.4147175 -0.9171384
1 1.2960176 -3.9106360 1.6159815
1 5.1410759 -0.5410329 2.0774044
1 2.1499317 0.2001714 3.3492010
1 4.2064587 1.7419051 -1.7937487
1 2.9924414 3.7759296 0.5590142
1 0.0267864 2.2409994 -3.2800674
1 -3.4027000 3.4110120 -0.9131000
1 -1.3059498 3.9002107 1.6245537

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cmmde_gui/molekul/cmmd.gbw
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8
cmmde_gui/molekul/cmmd.in
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#CMMDE generated Orca input file
!XTB2 opt
%pal
nprocs 1
end
*xyzfile 0 1 geom.xyz

3373
cmmde_gui/molekul/cmmd.opt
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4203
cmmde_gui/molekul/cmmd.out
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cmmde_gui/molekul/cmmd.xtbrestart
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24
cmmde_gui/molekul/cmmd.xyz
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22
Coordinates from ORCA-job cmmd
C -1.67789262482362 0.11525329869831 0.84776377059116
C -1.48696869578108 -1.01355209578752 -0.15853701195241
C -0.08962128164374 -0.76941009503983 -0.73189236960181
C 1.04829096618154 -1.32626849868764 0.14595842599341
C 1.67267554494252 -0.12078858357241 0.85001656867164
C 1.48330738130646 1.01076883814883 -0.15347731629115
C 0.08684005579747 0.76819612789448 -0.72965504301328
C -1.05243100784612 1.32264799435766 0.14795651490402
H -1.14431262086837 -0.11399375088709 1.77026137692973
H -2.72613042030156 0.28008844485899 1.09592839250909
H -2.22841592956031 -0.92233820827076 -0.95514782836367
H -1.58786878660918 -2.00215949404559 0.28786493139880
H -0.01538998189394 -1.18433834677691 -1.73900299660471
H 1.79743095555466 -1.80699066458022 -0.48532872804034
H 0.68582296618717 -2.06941944989369 0.85514056319983
H 2.72054019275969 -0.28630229679690 1.09931508645209
H 1.13769483539212 0.10592615728604 1.77232082684411
H 2.22596209405418 0.92177649029586 -0.94921094504504
H 1.58353180060076 1.99813590573103 0.29581758406903
H 0.01417474663286 1.18588579823564 -1.73573690178012
H -1.80063130399002 1.80502981213503 -0.48319168424581
H -0.69107888609148 2.06390261669669 0.85967678337543

6
cmmde_gui/molekul/cmmd_property.txt
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-------------------------------------------------------------
----------------------- !PROPERTIES! ------------------------
-------------------------------------------------------------
# -------------------------------------------------------------
----------------------- !GEOMETRIES! ------------------------
# -------------------------------------------------------------

192
cmmde_gui/molekul/cmmd_trj.xyz
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@ -0,0 +1,192 @@
22
Coordinates from ORCA-job cmmd E -24.299620455070
C -1.725240 0.119920 0.813870
C -1.484880 -1.019420 -0.160120
C -0.085570 -0.765670 -0.712320
C 1.044960 -1.324190 0.165240
C 1.718310 -0.124670 0.817500
C 1.480690 1.016080 -0.155250
C 0.082270 0.763840 -0.710460
C -1.047980 1.320790 0.167740
H -1.260210 -0.102750 1.781010
H -2.791150 0.295240 0.986430
H -2.217220 -0.965940 -0.975640
H -1.588450 -1.998500 0.316400
H 0.001250 -1.183270 -1.721800
H 1.770250 -1.843610 -0.474190
H 0.699930 -2.046300 0.911040
H 2.784520 -0.299540 0.991200
H 1.251920 0.094270 1.784860
H 2.214410 0.963270 -0.969600
H 1.584150 1.994690 0.322370
H -0.003520 1.183550 -1.719180
H -1.770860 1.845420 -0.469780
H -0.702050 2.038840 0.917520
22
Coordinates from ORCA-job cmmd E -24.300403307080
C -1.709132 0.115048 0.826880
C -1.487578 -1.020249 -0.164171
C -0.087098 -0.768140 -0.722859
C 1.044630 -1.326248 0.159829
C 1.702747 -0.120052 0.829946
C 1.483786 1.017132 -0.159357
C 0.084088 0.766620 -0.720867
C -1.048130 1.322791 0.162264
H -1.220711 -0.112775 1.776421
H -2.767293 0.286107 1.027865
H -2.223486 -0.956290 -0.969999
H -1.586266 -2.001512 0.300410
H -0.002435 -1.182897 -1.730211
H 1.776008 -1.841904 -0.467851
H 0.685755 -2.046335 0.894657
H 2.760757 -0.291127 1.032519
H 1.212674 0.104640 1.779268
H 2.221057 0.953970 -0.964009
H 1.582348 1.997725 0.306717
H 0.000571 1.183628 -1.727369
H -1.777706 1.842783 -0.463950
H -0.689056 2.039136 0.900706
22
Coordinates from ORCA-job cmmd E -24.300625110610
C -1.688892 0.110555 0.838929
C -1.487880 -1.018290 -0.167108
C -0.088001 -0.769291 -0.731798
C 1.043682 -1.325583 0.154806
C 1.683125 -0.115834 0.841502
C 1.484275 1.015358 -0.162300
C 0.085172 0.767987 -0.729671
C -1.047503 1.322045 0.157119
H -1.173838 -0.122387 1.770474
H -2.740485 0.277951 1.068830
H -2.227954 -0.939663 -0.965143
H -1.583761 -2.004133 0.285749
H -0.005328 -1.182022 -1.738588
H 1.784243 -1.833370 -0.464143
H 0.671687 -2.047435 0.879948
H 2.734248 -0.283624 1.073308
H 1.166063 0.114491 1.772522
H 2.225628 0.937925 -0.959263
H 1.579857 2.000291 0.292581
H 0.003743 1.183225 -1.735509
H -1.786675 1.833075 -0.460894
H -0.675878 2.040782 0.885491
22
Coordinates from ORCA-job cmmd E -24.300658534300
C -1.683044 0.109671 0.842540
C -1.487918 -1.016665 -0.166983
C -0.088217 -0.769447 -0.733107
C 1.044132 -1.324679 0.153495
C 1.677508 -0.115054 0.844955
C 1.484328 1.013785 -0.162146
C 0.085421 0.768184 -0.730926
C -1.048036 1.321107 0.155745
H -1.159198 -0.124866 1.768748
H -2.733089 0.276104 1.081191
H -2.228551 -0.930780 -0.963992
H -1.585189 -2.004851 0.281233
H -0.006427 -1.182147 -1.740251
H 1.788442 -1.826774 -0.465552
H 0.670352 -2.050064 0.874996
H 2.727029 -0.281989 1.085508
H 1.151587 0.116998 1.770600
H 2.226192 0.929376 -0.958172
H 1.581191 2.000949 0.288380
H 0.004934 1.183520 -1.737080
H -1.791083 1.825917 -0.462620
H -0.674835 2.043756 0.880278
22
Coordinates from ORCA-job cmmd E -24.300678425300
C -1.679506 0.109965 0.845350
C -1.487907 -1.014891 -0.165490
C -0.088461 -0.769531 -0.732743
C 1.045298 -1.324031 0.152235
C 1.674171 -0.115440 0.847637
C 1.484310 1.012056 -0.160594
C 0.085683 0.768292 -0.730515
C -1.049284 1.320426 0.154403
H -1.149225 -0.125125 1.768088
H -2.728516 0.275701 1.090181
H -2.228031 -0.922067 -0.962812
H -1.588094 -2.005009 0.278512
H -0.008091 -1.182838 -1.740143
H 1.792681 -1.818304 -0.469956
H 0.673286 -2.055248 0.869460
H 2.722660 -0.281771 1.094218
H 1.141890 0.117227 1.769860
H 2.225618 0.921062 -0.957034
H 1.583975 2.001035 0.286042
H 0.006702 1.184357 -1.736891
H -1.795546 1.816846 -0.467384
H -0.678084 2.049339 0.874415
22
Coordinates from ORCA-job cmmd E -24.300683906960
C -1.679004 0.111083 0.846262
C -1.487774 -1.014271 -0.163796
C -0.088697 -0.769539 -0.732111
C 1.046183 -1.324330 0.151061
C 1.673727 -0.116588 0.848520
C 1.484164 1.011456 -0.158851
C 0.085921 0.768309 -0.729871
C -1.050218 1.320713 0.153178
H -1.147302 -0.123035 1.768607
H -2.727718 0.276560 1.092502
H -2.227597 -0.919980 -0.961478
H -1.589297 -2.004506 0.279483
H -0.009687 -1.183453 -1.739420
H 1.794361 -1.814113 -0.474068
H 0.677052 -2.059360 0.865783
H 2.721959 -0.282692 1.096332
H 1.140182 0.115087 1.770437
H 2.225163 0.919161 -0.955679
H 1.585116 2.000505 0.287191
H 0.008358 1.185007 -1.736149
H -1.797349 1.812418 -0.471664
H -0.682013 2.053620 0.870572
22
Coordinates from ORCA-job cmmd E -24.300687361530
C -1.678599 0.112925 0.847033
C -1.487456 -1.013868 -0.161409
C -0.089093 -0.769496 -0.731792
C 1.047194 -1.325156 0.148943
C 1.673355 -0.118447 0.849285
C 1.483824 1.011070 -0.156406
C 0.086316 0.768274 -0.729552
C -1.051283 1.321534 0.151000
H -1.146019 -0.119120 1.769453
H -2.727060 0.278101 1.094226
H -2.227681 -0.920293 -0.958895
H -1.589279 -2.003498 0.282769
H -0.012172 -1.184023 -1.738944
H 1.795860 -1.810369 -0.479379
H 0.681533 -2.064271 0.860927
H 2.721389 -0.284278 1.097826
H 1.139154 0.111110 1.771394
H 2.225235 0.919623 -0.953037
H 1.585027 1.999483 0.290618
H 0.010904 1.185580 -1.735672
H -1.798966 1.808511 -0.477121
H -0.686652 2.058658 0.865573
22
Coordinates from ORCA-job cmmd E -24.300689883530
C -1.677893 0.115253 0.847764
C -1.486969 -1.013552 -0.158537
C -0.089621 -0.769410 -0.731892
C 1.048291 -1.326268 0.145958
C 1.672676 -0.120789 0.850017
C 1.483307 1.010769 -0.153477
C 0.086840 0.768196 -0.729655
C -1.052431 1.322648 0.147957
H -1.144313 -0.113994 1.770261
H -2.726130 0.280088 1.095928
H -2.228416 -0.922338 -0.955148
H -1.587869 -2.002159 0.287865
H -0.015390 -1.184338 -1.739003
H 1.797431 -1.806991 -0.485329
H 0.685823 -2.069419 0.855141
H 2.720540 -0.286302 1.099315
H 1.137695 0.105926 1.772321
H 2.225962 0.921776 -0.949211
H 1.583532 1.998136 0.295818
H 0.014175 1.185886 -1.735737
H -1.800631 1.805030 -0.483192
H -0.691079 2.063903 0.859677

1
cmmde_gui/molekul/geom.smi
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C2CC1CCCC1C2

24
cmmde_gui/molekul/geom.xyz
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@ -0,0 +1,24 @@
22
C -1.72524 0.11992 0.81387
C -1.48488 -1.01942 -0.16012
C -0.08557 -0.76567 -0.71232
C 1.04496 -1.32419 0.16524
C 1.71831 -0.12467 0.81750
C 1.48069 1.01608 -0.15525
C 0.08227 0.76384 -0.71046
C -1.04798 1.32079 0.16774
H -1.26021 -0.10275 1.78101
H -2.79115 0.29524 0.98643
H -2.21722 -0.96594 -0.97564
H -1.58845 -1.99850 0.31640
H 0.00125 -1.18327 -1.72180
H 1.77025 -1.84361 -0.47419
H 0.69993 -2.04630 0.91104
H 2.78452 -0.29954 0.99120
H 1.25192 0.09427 1.78486
H 2.21441 0.96327 -0.96960
H 1.58415 1.99469 0.32237
H -0.00352 1.18355 -1.71918
H -1.77086 1.84542 -0.46978
H -0.70205 2.03884 0.91752

10
cmmde_gui/molekul/run.sh
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@ -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

8
cmmde_gui/molekul/run_babel.sh
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#!/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

1
cmmde_gui/molekul/slurm-2879.out
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1 molecule converted

0
cmmde_gui/molekul/slurm-2880.out
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lib/__pycache__/cmmde_orca.cpython-39.pyc
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2
lib/cmmde_orca.py
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@ -33,7 +33,7 @@ end""".format(nproc),file=f)
if 'opt' in job: if 'opt' in job:
print("""%geom print("""%geom
maxiter {} maxiter {}
end""".format(maxiter)) end""".format(maxiter),file=f)
if qmatoms != 'None': if qmatoms != 'None':
print("""%qmmm print("""%qmmm
QMAtoms {{ {} }} end QMAtoms {{ {} }} end

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