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MOPAC Support #16

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MOPAC Support #16

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716d2fe
Setup parser for MOPAC cosmo files
mabounassif Feb 28, 2022
6ae9216
Replace 4-Hydroxybenzaldehyde with ethanol for better comparison
mabounassif Feb 28, 2022
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182 changes: 182 additions & 0 deletions profiles/MOPAC_TEST/ethanol.cosmo
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Original file line number Diff line number Diff line change
@@ -0,0 +1,182 @@
EPS=999.0 COSWRT RSOLV=1.4 XYZ AM1 EXTERNAL=POA1.rm1 NSPA=92 VDW(;H=1.416;C=2.0
06;N=1.829;O=1.7936;F=1.7346;S=2.124;P=2.124;CL=2.065;BR=2.183;I=2.3364) GNORM=0
.1 RELSCF=0.1

FINAL HEAT OF FORMATION = -60.66430 KCAL/MOL = -253.81945 KJ/MOL
TOTAL ENERGY = -653.12963 EV
DIELECTRIC ENERGY = -0.14207 EV
COSMO AREA = 94.26 SQUARE ANGSTROMS
COSMO VOLUME = 77.39 CUBIC ANGSTROMS
TOTAL COSMO CHARGE = -0.00118

For more information, see: HTTP://OpenMOPAC.net/Manual/COSWRT.html

ATOMIC DATA
NR. ELEM. COORDINATES RADIUS COSMO-CHARGE AREA SIGMA
1 6 -0.009678 0.002732 -0.003552 2.006000 0.002814 11.321301 0.000249
2 6 1.515342 0.017653 -0.024357 2.006000 -0.003116 6.346116 -0.000491
3 8 2.013053 1.322391 0.020637 1.793600 0.165490 17.560011 0.009424
4 1 -0.418431 0.556032 0.853709 1.416000 -0.009174 9.499533 -0.000966
5 1 -0.397624 -1.023319 0.061536 1.416000 -0.016043 9.604387 -0.001670
6 1 -0.444307 0.450946 -0.908673 1.416000 -0.017067 9.431287 -0.001810
7 1 1.944928 -0.472122 0.876887 1.416000 -0.022158 10.048510 -0.002205
8 1 1.908639 -0.545151 -0.902800 1.416000 -0.021571 10.349708 -0.002084
9 1 1.687030 1.792599 -0.754532 1.416000 -0.080352 10.100212 -0.007955

SEGMENT DATA: NPS= 155
NR. ATOM ELEM. COORDINATES (X, Y, Z) COSMO-CHARGE AREA SIGMA POTENTIAL
1 1 6 -0.080052 -0.676266 -1.864194 0.000265 0.363292 0.000730 0.021114
2 1 6 -1.708031 -0.448836 -0.932118 -0.000238 0.489226 -0.000487 0.020710
3 1 6 -1.604233 -0.693297 0.947273 -0.000302 0.532820 -0.000567 0.015063
4 1 6 -0.077973 -1.281938 1.501582 0.000207 0.338918 0.000610 0.007930
5 1 6 -1.557775 1.230153 0.122049 -0.000178 0.379156 -0.000469 0.014044
6 1 6 0.241324 -1.183681 -1.554570 0.001508 1.113429 0.001354 0.018009
7 1 6 -1.389106 -0.926100 -1.082329 -0.000266 0.395644 -0.000672 0.021818
8 1 6 -0.164224 2.062531 -0.043168 0.000925 0.702298 0.001317 0.003639
9 1 6 -0.864824 1.775580 0.141144 0.000087 0.360706 0.000242 0.008163
10 1 6 -0.387900 -0.933488 -1.736895 0.000077 0.238955 0.000324 0.019843
11 1 6 -1.012077 -0.749470 -1.537313 -0.000105 0.256326 -0.000410 0.022399
12 1 6 -1.897172 -0.538024 -0.269910 -0.000124 0.594284 -0.000209 0.017723
13 1 6 -1.903393 -0.491444 0.436529 -0.000043 0.286756 -0.000151 0.015266
14 1 6 -1.001689 -0.773034 1.510634 -0.000061 0.621492 -0.000098 0.010510
15 1 6 -0.140674 -1.012049 1.721874 0.000112 0.144236 0.000775 0.004053
16 1 6 -1.491943 1.286929 -0.276559 -0.000225 0.341293 -0.000659 0.016852
17 1 6 -1.913013 0.272655 -0.515420 -0.000204 0.492325 -0.000414 0.018236
18 1 6 -1.911637 0.640007 0.018106 -0.000002 0.331315 -0.000006 0.014678
19 1 6 -1.879503 0.399190 0.507538 -0.000171 0.366634 -0.000467 0.013933
20 1 6 -1.752439 -0.170329 0.927334 -0.000192 0.492356 -0.000390 0.013718
21 1 6 -0.090389 -0.354214 1.939010 0.000166 0.259963 0.000638 -0.001022
22 1 6 0.385757 -0.820033 1.756683 0.001375 0.913231 0.001506 -0.000640
23 1 6 -0.703323 -1.232962 -1.388699 -0.000055 0.370115 -0.000148 0.020738
24 1 6 -0.782380 1.806114 -0.311363 0.000015 0.415925 0.000036 0.013909
25 1 6 -2.014034 0.003884 0.077633 0.000116 0.315111 0.000367 0.014487
26 1 6 -0.510041 -0.893635 1.719874 0.000128 0.205496 0.000623 0.006090
27 2 6 2.378676 -1.742792 -0.014019 -0.002290 0.743990 -0.003077 0.022031
28 2 6 3.419979 0.056819 -0.293685 0.003815 0.843656 0.004522 -0.038601
29 2 6 1.290213 0.650001 1.883750 0.003185 0.729198 0.004367 -0.044671
30 2 6 1.539066 -1.954324 -0.325880 -0.000812 0.424052 -0.001915 0.023401
31 2 6 2.998163 -1.273665 -0.182593 -0.001154 0.385124 -0.002996 0.013543
32 2 6 3.358280 -0.464543 -0.505209 -0.000958 0.426129 -0.002248 -0.007042
33 2 6 1.676557 -1.884620 0.486019 -0.000878 0.324840 -0.002702 0.022511
34 2 6 1.889571 -1.934770 0.244037 -0.000307 0.183526 -0.001673 0.022183
35 2 6 3.399449 -0.169374 0.634275 0.000247 0.201698 0.001226 -0.030909
36 2 6 3.494517 -0.278552 0.114094 -0.000147 0.374445 -0.000391 -0.024719
37 2 6 1.241218 0.478433 -1.993561 -0.002265 0.609967 -0.003713 0.044162
38 2 6 1.097102 -1.935743 0.065318 -0.000624 0.669896 -0.000932 0.021068
39 2 6 3.246730 -0.915199 0.163498 -0.000929 0.429594 -0.002161 0.001920
40 3 8 2.713235 2.260614 1.379491 0.005818 0.501452 0.011603 -0.108971
41 3 8 3.756157 1.727790 -0.098697 0.005395 0.501452 0.010758 -0.089154
42 3 8 0.766630 2.360175 0.840755 0.008676 1.021915 0.008490 -0.058494
43 3 8 2.563817 3.027248 -0.063765 0.001085 0.299048 0.003627 -0.044139
44 3 8 1.953284 3.086373 0.086593 0.001771 0.601462 0.002944 -0.035461
45 3 8 1.413323 2.924119 0.560816 0.002431 0.376443 0.006457 -0.054259
46 3 8 2.859349 2.710204 -0.656034 0.000351 0.381911 0.000918 -0.024210
47 3 8 3.087030 2.744373 -0.183180 0.002738 0.418148 0.006549 -0.058298
48 3 8 3.520372 2.283511 -0.125105 0.003968 0.413576 0.009594 -0.078998
49 3 8 2.628907 2.950683 0.452367 0.003171 0.386691 0.008201 -0.073334
50 3 8 2.706202 2.695048 0.943870 0.005391 0.494115 0.010910 -0.095946
51 3 8 3.291081 2.135664 0.980967 0.006713 0.534075 0.012569 -0.107499
52 3 8 3.644593 1.897609 0.494137 0.004603 0.376443 0.012227 -0.102146
53 3 8 3.571866 1.698458 -0.782904 0.004441 0.493497 0.008998 -0.060359
54 3 8 3.121898 1.814726 -1.251168 0.000781 0.449263 0.001738 -0.018218
55 3 8 0.833555 2.627383 0.203995 0.002412 0.598388 0.004031 -0.022441
56 3 8 1.576850 2.625956 1.172786 0.005213 0.456981 0.011407 -0.087773
57 3 8 2.113663 2.438083 1.421391 0.004709 0.376443 0.012510 -0.103148
58 3 8 1.793881 1.393444 1.791905 0.008846 0.645908 0.013695 -0.095697
59 3 8 2.363570 1.852579 1.697849 0.004199 0.336483 0.012478 -0.108420
60 3 8 3.035533 1.599504 1.467960 0.005336 0.416403 0.012815 -0.109132
61 3 8 3.225544 0.803556 1.216929 0.009398 0.791537 0.011873 -0.091700
62 3 8 3.615855 0.914191 0.714468 0.004590 0.386691 0.011871 -0.095234
63 3 8 3.783397 1.246391 0.298320 0.004108 0.336483 0.012210 -0.097238
64 3 8 3.744880 1.110188 -0.394991 0.003847 0.339309 0.011339 -0.078526
65 3 8 3.531637 0.641600 -0.602922 0.004362 0.463183 0.009417 -0.061374
66 3 8 3.019159 0.943328 -1.391981 0.003004 0.903112 0.003326 -0.014082
67 3 8 1.181731 2.274348 1.293305 0.002732 0.191032 0.014303 -0.086057
68 3 8 1.134378 1.723690 1.579306 0.009458 0.849599 0.011132 -0.083502
69 3 8 3.321451 2.251228 -0.780837 0.001852 0.329863 0.005613 -0.044640
70 3 8 3.240380 2.572298 0.405869 0.003502 0.334365 0.010473 -0.088434
71 3 8 2.038422 2.933391 0.808697 0.003296 0.334365 0.009858 -0.078154
72 3 8 2.468839 1.089480 1.725197 0.009820 0.812884 0.012081 -0.094790
73 3 8 3.626105 0.626916 0.216201 0.007056 0.528722 0.013345 -0.083853
74 3 8 3.527703 1.501316 0.964471 0.004439 0.334365 0.013275 -0.107209
75 3 8 3.452080 1.130808 -1.032690 0.002587 0.293787 0.008807 -0.047703
76 3 8 1.704995 2.112109 1.601285 0.003392 0.250620 0.013536 -0.101462
77 4 1 -1.315628 0.051408 1.799707 -0.001095 0.717546 -0.001526 0.011188
78 4 1 -1.597917 1.251458 1.214613 -0.000828 0.558353 -0.001482 0.011494
79 4 1 -0.549781 1.180020 2.118004 -0.001157 0.645423 -0.001792 -0.000831
80 4 1 0.180970 0.171577 2.114773 0.000154 0.754516 0.000203 -0.007468
81 4 1 -0.409483 1.977966 0.845473 -0.000088 0.927001 -0.000095 -0.005999
82 4 1 -1.289260 0.899759 1.916048 -0.001330 0.744941 -0.001785 0.008857
83 4 1 -0.615790 0.385397 2.245466 -0.000887 0.504459 -0.001758 0.003487
84 4 1 -0.692476 -0.189694 2.003484 -0.000345 0.340585 -0.001014 0.006161
85 4 1 -1.749058 0.453093 1.276150 -0.001091 0.650118 -0.001678 0.013729
86 4 1 -0.949064 1.674496 1.541113 -0.001264 0.651016 -0.001941 0.003387
87 4 1 0.301079 0.958477 2.009136 0.000106 1.087039 0.000098 -0.019171
88 4 1 -1.706321 1.079170 0.697186 -0.000547 0.358940 -0.001523 0.013757
89 4 1 0.008312 1.708927 1.557433 0.000025 0.985360 0.000025 -0.019372
90 4 1 -1.204768 1.703900 0.710279 -0.000828 0.574237 -0.001443 0.008959
91 5 1 -1.234021 -1.597846 1.049167 -0.000911 0.586295 -0.001553 0.019016
92 5 1 0.174774 -2.069440 0.825947 -0.001418 1.190132 -0.001192 0.019069
93 5 1 -1.180014 -2.177545 -0.184807 -0.001358 0.736115 -0.001845 0.024069
94 5 1 -1.767518 -1.211077 -0.002839 -0.000819 0.412094 -0.001988 0.021987
95 5 1 0.160195 -2.043063 -0.780734 -0.000951 0.986396 -0.000964 0.022456
96 5 1 -1.005258 -1.557892 -1.076082 -0.000549 0.390574 -0.001406 0.023472
97 5 1 -0.935590 -2.203355 0.630011 -0.001579 0.744941 -0.002120 0.022147
98 5 1 -1.629195 -1.686856 0.280642 -0.001032 0.553568 -0.001864 0.022295
99 5 1 -1.547630 -1.208955 0.807670 -0.000667 0.340225 -0.001960 0.019402
100 5 1 -0.442895 -1.706084 1.266781 -0.001259 0.801400 -0.001571 0.016523
101 5 1 -0.399915 -2.433574 -0.065867 -0.001235 0.602292 -0.002050 0.023684
102 5 1 -1.503268 -1.519182 -0.621265 -0.001291 0.632262 -0.002042 0.023837
103 5 1 -0.609133 -1.980764 -0.922357 -0.001500 0.707219 -0.002122 0.024083
104 5 1 0.408761 -2.158414 0.070555 -0.001475 0.920874 -0.001602 0.022399
105 6 1 -1.369500 1.501036 -0.928962 -0.001032 0.688893 -0.001498 0.023556
106 6 1 -1.626075 0.364796 -1.683951 -0.000895 0.558353 -0.001602 0.026176
107 6 1 -0.568585 1.234881 -2.081301 -0.001344 0.736115 -0.001826 0.034511
108 6 1 -0.432368 -0.216932 -2.124630 -0.000921 0.792142 -0.001163 0.027362
109 6 1 -1.360203 1.146678 -1.734594 -0.001330 0.721797 -0.001843 0.028340
110 6 1 -0.444228 1.716334 -1.546300 -0.002686 1.029317 -0.002610 0.035618
111 6 1 -0.555537 1.894660 -0.905292 -0.000828 0.746194 -0.001110 0.026135
112 6 1 -1.781390 0.853702 -1.008061 -0.001178 0.645283 -0.001826 0.023427
113 6 1 -0.970551 0.452951 -2.223252 -0.001249 0.698653 -0.001787 0.029593
114 6 1 -1.749350 0.073262 -1.224397 -0.000602 0.354105 -0.001701 0.023909
115 6 1 0.195380 0.609657 -2.136447 -0.003990 1.867214 -0.002137 0.037656
116 6 1 -1.243249 -0.259557 -1.804428 -0.001012 0.593221 -0.001705 0.025819
117 7 1 2.790785 -1.605807 0.942765 -0.001532 0.607354 -0.002522 0.014497
118 7 1 1.409591 -1.619094 1.508182 -0.002676 1.167163 -0.002293 0.016132
119 7 1 2.750330 -0.740443 2.010196 -0.001655 0.690769 -0.002396 -0.001480
120 7 1 3.308409 -0.266210 1.050801 -0.001091 0.639595 -0.001706 -0.022031
121 7 1 1.424218 -0.091128 2.150578 -0.001086 0.996069 -0.001091 -0.012391
122 7 1 2.520313 -1.476829 1.692087 -0.001972 0.744941 -0.002648 0.011446
123 7 1 3.201807 -0.956320 1.313767 -0.001465 0.554656 -0.002642 0.000817
124 7 1 3.098733 -1.215837 0.664124 -0.001195 0.347647 -0.003436 0.009155
125 7 1 2.015860 -1.848763 0.978809 -0.002820 0.814175 -0.003463 0.020655
126 7 1 1.980858 -0.928304 2.216911 -0.001671 0.651016 -0.002567 0.004591
127 7 1 2.919796 0.039331 1.703250 -0.001125 0.934170 -0.001205 -0.028576
128 7 1 2.213147 0.108432 2.120946 -0.001738 0.916296 -0.001897 -0.023197
129 7 1 1.160148 -0.962917 1.908731 -0.002131 0.984659 -0.002164 0.007089
130 8 1 2.782174 -1.631177 -0.831220 -0.001622 0.755742 -0.002146 0.019813
131 8 1 3.065260 -0.583362 -1.718781 -0.000938 0.558353 -0.001680 0.015029
132 8 1 2.003597 -1.436946 -1.998583 -0.001237 0.668567 -0.001850 0.024819
133 8 1 1.286864 -1.849762 -1.085046 -0.001182 0.719749 -0.001642 0.024344
134 8 1 1.946128 0.117674 -2.127016 -0.003857 1.233716 -0.003126 0.033722
135 8 1 2.763276 -1.369368 -1.674369 -0.001521 0.744941 -0.002041 0.020510
136 8 1 2.085396 -1.889569 -1.310666 -0.001083 0.553183 -0.001958 0.023816
137 8 1 2.095765 -1.899746 -0.708115 -0.001022 0.356634 -0.002865 0.024532
138 8 1 3.229690 -0.985760 -0.995384 -0.001624 0.667255 -0.002433 0.011663
139 8 1 2.373534 -0.729500 -2.227543 -0.001139 0.651016 -0.001750 0.024223
140 8 1 1.220209 -1.501247 -1.673185 -0.001445 0.763165 -0.001893 0.025520
141 8 1 3.200763 -0.111962 -1.300310 -0.000855 0.560098 -0.001526 0.001501
142 8 1 1.221919 -0.663512 -2.123580 -0.002225 1.399321 -0.001590 0.028779
143 8 1 2.719946 0.068025 -1.883185 -0.001822 0.717967 -0.002537 0.018838
144 9 1 2.074263 1.994301 -2.101537 -0.003707 0.557507 -0.006650 0.053747
145 9 1 0.914888 2.642806 -1.582783 -0.005390 0.759934 -0.007092 0.058615
146 9 1 2.289511 3.002162 -1.177651 -0.004005 0.645720 -0.006202 0.026835
147 9 1 1.232768 3.050053 -0.395225 -0.002928 0.493701 -0.005932 0.017828
148 9 1 0.991876 1.963692 -1.966091 -0.010976 1.127814 -0.009732 0.067655
149 9 1 1.435949 1.267969 -2.068919 -0.011591 1.256030 -0.009229 0.064304
150 9 1 2.006995 3.131021 -0.632316 -0.003517 0.508024 -0.006922 0.013712
151 9 1 1.778419 2.737955 -1.804773 -0.006284 0.793251 -0.007922 0.052346
152 9 1 0.520302 2.532580 -0.787612 -0.014789 1.657318 -0.008924 0.044402
153 9 1 2.482585 1.427757 -1.851548 -0.007457 0.945965 -0.007883 0.038150
154 9 1 1.407560 3.141434 -1.082548 -0.003864 0.553568 -0.006981 0.040196
155 9 1 2.656129 2.430363 -1.516997 -0.005843 0.801379 -0.007291 0.027346
Empty file added profiles/MOPAC_TEST/ethanol.sigma
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13 changes: 13 additions & 0 deletions profiles/to_sigma.py
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Original file line number Diff line number Diff line change
Expand Up @@ -142,6 +142,11 @@ def get_seg_DataFrame(COSMO_contents):
# GAMESS: same unit (Bohr in GAMESS/COSab) as Dmol3 but format is different
sdata = re.search(r"\(X, Y, Z\)[\sa-zA-Z0-9\(\)\./\*]+\n([\s0-9\-\n.]+)(=+)", COSMO_contents, re.DOTALL).group(1).rstrip()
table_assign = ['n','atom','x / a.u.','y / a.u.','z / a.u.','charge / e','area / A^2','charge/area / e/A^2','potential']
elif "OpenMOPAC.net" in COSMO_contents:
# MOPAC: unit in ANGSTROMS
sdata = re.search(r"\(X, Y, Z\)[\sa-zA-Z0-9\(\)/\*\-]+\n([\s0-9\-\n.]+)", COSMO_contents, re.DOTALL).group(1).rstrip()
table_assign = ['n','atom','elem', 'x / a.u.','y / a.u.','z / a.u.','charge / e','area / A^2','charge/area / e/A^2','potential']

# Annotate the columns appropriately with units(!)
return pandas.read_csv(StringIO(sdata), names=table_assign, sep=r'\s+',engine= 'python')

Expand All @@ -158,6 +163,11 @@ def get_atom_DataFrame(COSMO_contents):
# GAMESS: same unit (Angstrom in GAMESS) as Dmol3 but format is different
sdata = re.search(r"EQUILIBRIUM GEOMETRY[\sa-zA-Z0-9\(\)\./\*\n]+\-+\n(\s[\s\S]+)\n\n\n", COSMO_contents, re.DOTALL).group(1)
table_assign = ['atom','charge','x / A','y / A','z / A']
elif "OpenMOPAC.net" in COSMO_contents:
# MOPAC: unit in ANGSTROMS
sdata = re.search(r"ATOMIC\sDATA\s\n[\sa-zA-Z\(\)/\.\*\-]+\n([\s0-9\-\n.]+)\n\n", COSMO_contents, re.DOTALL).group(1)
table_assign = ['atom', 'elem', 'x / A','y / A','z / A', 'r / A', 'charge', 'area', 'sigma']

# Annotate the columns appropriately with units(!)
return pandas.read_csv(StringIO(sdata), names=table_assign, sep=r'\s+',engine = 'python')

Expand All @@ -175,6 +185,9 @@ def get_area_volume(COSMO_contents):
# GAMESS: units of area and volume are same as DMol3
area = float(re.search(r"Total surface area of cavity \(A\*\*2\)\s+=(.+)\n", COSMO_contents).group(1).strip())
volume = float(re.search(r"Total volume of cavity \(A\*\*3\)\s+=(.+)\n", COSMO_contents).group(1).strip())
elif "OpenMOPAC.net" in COSMO_contents:
area = float(re.search(r"COSMO\sAREA\s+=\s+([0-9\-\n.]+)", COSMO_contents).group(1).strip())
volume = float(re.search(r"COSMO\sVOLUME\s+=\s+([0-9\-\n.]+)", COSMO_contents).group(1).strip())

return area, volume

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