source: ThirdParty/mpqc_open/lib/perl/QCResult.pm@ 7516f6

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Last change on this file since 7516f6 was 860145, checked in by Frederik Heber <heber@…>, 8 years ago

Merge commit '0b990dfaa8c6007a996d030163a25f7f5fc8a7e7' as 'ThirdParty/mpqc_open'
  • Property mode set to 100644
File size: 19.1 KB
Line 
1#
2eval 'exec perl $0 $*'
3 if 0;
4
5require QCParse;
6require Molecule;
7
8##########################################################################
9
10package QCResult;
11
12# this seems to not work as expected
13$fltrx = "([-+]?(?:\\d+\\.\\d*|\\d+|\\.\\d+)(?:[eEdD][+-]?\\d+)?)";
14
15$have_nodenum = 0;
16
17sub test {
18 my $i;
19 @nums = ("-1.0", "-1", "-.1", "-1.",
20 "-1.0E-04", "-1E-04", "-.1E-04", "-1.E-04");
21 foreach $i ( @nums ) {
22 $i =~ /$fltrx/;
23 my $flt = $1;
24 printf "%10s %10s %12.8f\n", $i, $flt, $flt;
25 }
26}
27
28sub new {
29 my $this = shift;
30 my $class = ref($this) || $this;
31 my $self = {};
32 bless $self, $class;
33 $self->initialize(@_);
34 return $self;
35}
36
37sub initialize {
38 my $self = shift;
39 my $infile = shift;
40 my $outfile = shift;
41 my $parse = new QCParse();
42 $parse->parse_file($infile);
43 $self->{"qcinput"} = QCInput::new QCInput($parse);
44
45 $self->{"exists"} = 0;
46 $self->{"ok"} = 0;
47 if (-e $outfile) {
48 $self->{"exists"} = 1;
49 open(OUTFILE,"<$outfile");
50 my $first = 1;
51 while (<OUTFILE>) {
52 if ($first && /^ *[0-9]+:/) {
53 $have_nodenum = 1;
54 $first = 0;
55 }
56 s/^ *[0-9]+:// if ($have_nodenum);
57 if (/^\s*MPQC:/) {
58 $self->parse_mpqc(\*OUTFILE);
59 last;
60 }
61 elsif (/^\s*Entering Gaussian System/) {
62 $self->parse_g94(\*OUTFILE);
63 last;
64 }
65 }
66 close(OUTFILE);
67 }
68}
69
70sub parse_g94 {
71 my $self = shift;
72 my $out = shift;
73 my $scfenergy = "";
74 my $mp2energy = "";
75 my $ccsd_tenergy = "";
76 my $t1norm = "";
77 my $optconverged = 0;
78 my $molecule;
79 my $havefreq = 0;
80 my $freq = [];
81 my $ifreq = 0;
82 my $b3pw91energy = "";
83 while (<$out>) {
84 s/^ *[0-9]+:// if ($have_nodenum);
85 if (/^\s*SCF Done: E\(RHF\) =\s*$fltrx\s/) {
86 $scfenergy = $1;
87 }
88 elsif (/^\s*E2\s*=\s*$fltrx\s*EUMP2\s*=\s*$fltrx/) {
89 $mp2energy = $2;
90 }
91 elsif (/^\s*CCSD\(T\)\s*=\s*$fltrx/) {
92 $ccsd_tenergy = $1;
93 $ccsd_tenergy =~ s/[DdE]/e/;
94 }
95 elsif (/E\(RB\+HF-PW91\)\s*=\s*$fltrx/) {
96 $b3pw91energy = $1;
97 $b3pw91energy =~ s/[DdE]/e/;
98 }
99 elsif (/^\s*T1 Diagnostic\s*=\s*$fltrx/) {
100 $t1norm = $1;
101 }
102 elsif (/^\s*-- Stationary point found./
103 || /CONVERGENCE CRITERIA APPARENTLY SATISFIED/) {
104 $optconverged = 1;
105 }
106 elsif ($optconverged
107 && (/^\s*Input orientation:/ || /^\s*Standard orientation:/)) {
108 <$out>; <$out>; <$out>; <$out>;
109 my $molstr = "";
110 while (<$out>) {
111 if (! /^\s+\d+\s+(\d+)\s+$fltrx\s+$fltrx\s+$fltrx\s+/) {
112 last;
113 }
114 $molstr = "${molstr} $1 $2 $3 $4\n";
115 }
116 $molecule = new Molecule($molstr);
117 }
118 elsif (/^\s*Frequencies --\s+$fltrx\s+$fltrx\s+$fltrx/) {
119 $freq->[$ifreq] = $1; $ifreq++;
120 $freq->[$ifreq] = $2; $ifreq++;
121 $freq->[$ifreq] = $3; $ifreq++;
122 $havefreq = 1;
123 }
124 elsif (/^\s*Frequencies --\s+$fltrx\s+$fltrx/) {
125 $freq->[$ifreq] = $1; $ifreq++;
126 $freq->[$ifreq] = $2; $ifreq++;
127 $havefreq = 1;
128 }
129 elsif (/^\s*Frequencies --\s+$fltrx\s/) {
130 $freq->[$ifreq] = $1; $ifreq++;
131 $havefreq = 1;
132 }
133 }
134 $self->{"scfenergy"} = $scfenergy;
135 $self->{"mp2energy"} = $mp2energy;
136 $self->{"b3pw91energy"} = $b3pw91energy;
137 $self->{"optconverged"} = $optconverged;
138 if ($optconverged) {
139 $self->{"optmolecule"} = $molecule;
140 }
141 $self->{"have_frequencies"} = $havefreq;
142 if ($havefreq) {
143 my @tmp = sort(@$freq);
144 $freq = \@tmp;
145 $self->{"freq"} = $freq;
146 }
147 my $qcinput = $self->{"qcinput"};
148 my $method = $qcinput->method();
149 if ($method eq "MP2") {
150 $self->{"energy"} = $mp2energy;
151 }
152 elsif ($method eq "CCSD(T)") {
153 $self->{"energy"} = $ccsd_tenergy;
154 }
155 elsif ($method eq "B3-PW91") {
156 $self->{"energy"} = $b3pw91energy;
157 }
158 elsif ($method eq "SCF"
159 || $method eq "ROSCF") {
160 $self->{"energy"} = $scfenergy;
161 }
162
163 $self->{"t1norm"} = $t1norm;
164
165 $self->{"ok"} = 0;
166 if ($self->{"energy"} ne "") {
167 if ($qcinput->optimize()) {
168 if ($self->{"optconverged"}) {
169 $self->{"ok"} = 1
170 }
171 else {
172 #printf "not ok because not converged\n";
173 }
174 }
175 else {
176 $self->{"ok"} = 1;
177 }
178 if ($qcinput->frequencies() && ! $havefreq) {
179 $self->{"ok"} = 0;
180 #printf "not ok because no freq\n";
181 }
182 }
183 else {
184 #printf "not ok because no energy\n";
185 }
186}
187
188sub parse_mpqc {
189 my $self = shift;
190 my $out = shift;
191 my $scfenergy = "";
192 my $opt1energy = "";
193 my $opt2energy = "";
194 my $zapt2energy = "";
195 my $mp2energy = "";
196 my $optconverged = 0;
197 my $molecule;
198 my $havefreq = 0;
199 my $freq;
200 my $wante = 1;
201 my $ifreq = 0;
202 my $grad;
203 my $ngrad;
204 my $state = "none";
205 my $molecularenergy = "";
206 my $s2norm = "";
207 my $to_angstrom = 0.52917706;
208 my $geometry_conversion = $to_angstrom;
209 my $error = "";
210 my $ccsd_energy = "";
211 my $ccsd_t_energy = "";
212 my $t1norm = "";
213 my $t12norm = "";
214 my $psioutput = "";
215 while (<$out>) {
216 s/^ *[0-9]+:// if ($have_nodenum);
217 if ($state eq "read grad" && $wante) {
218 if (/^\s*([0-9]+\s+[A-Za-z]+\s+)?([\-\.0-9]+)\s+([\-\.0-9]+)\s+([\-\.0-9]+)/) {
219 $grad->[$ngrad + 0] = $2;
220 $grad->[$ngrad + 1] = $3;
221 $grad->[$ngrad + 2] = $4;
222 $ngrad = $ngrad + 3;
223 }
224 elsif (/^\s*([0-9]+\s+)?([\-\.0-9]+)/) {
225 $grad->[$ngrad] = $2;
226 $ngrad = $ngrad + 1;
227 }
228 else {
229 $self->{"grad"} = $grad;
230 $state = "none";
231 }
232 }
233
234 if ($wante && /total scf energy =\s+$fltrx/) {
235 $scfenergy = $1;
236 }
237 elsif ($wante && /OPT1 energy .*:\s+$fltrx/) {
238 $opt1energy = $1;
239 }
240 elsif ($wante && /OPT2 energy .*:\s+$fltrx/) {
241 $opt2energy = $1;
242 }
243 elsif ($wante && /ZAPT2 energy .*:\s+$fltrx/) {
244 $zapt2energy = $1;
245 }
246 elsif ($wante && /MP2 energy .*:\s+$fltrx/) {
247 $mp2energy = $1;
248 }
249 elsif (/CSCF: An SCF program written in C/) {
250 $psioutput = 1;
251 }
252 elsif ($psioutput && $wante
253 && /total energy =\s*$fltrx/) {
254 $scfenergy = $1;
255 }
256 elsif ($psioutput && $wante
257 && /\s*ITER\s+CORRELATION ENERGY\s+T1 2-NORM\s+T1 DIAG/) {
258 # this is a PSI CC output embedded in an MPQC output
259 # grab iteration 0
260 my $ecorr;
261 <$out>;
262 while (<$out>) {
263 if (/^\s*\d+\s+$fltrx\s+$fltrx\s+$fltrx/) {
264 $ecorr = $1;
265 $t12norm = $2;
266 $t1norm = $3;
267 }
268 else {
269 last;
270 }
271 }
272 $ccsd_energy = $ecorr + $scfenergy;
273 }
274# IMBN: Added the following elsif to handle new cc output
275 elsif ($psioutput && $wante
276 && /\s*ITER\s+CORRELATION ENERGY\s+T1 DIAG\s+D1\(CCSD\)/) {
277 # this is a PSI CC output embedded in an MPQC output
278 # grab iteration 0
279 my $ecorr;
280 <$out>;
281 while (<$out>) {
282 if (/^\s*\d+\s+$fltrx\s+$fltrx\s+$fltrx/) {
283 $ecorr = $1;
284 $t1norm = $2;
285 $t12norm = $3;
286 }
287 else {
288 last;
289 }
290 }
291 $ccsd_energy = $ecorr + $scfenergy;
292 }
293 elsif ($wante && /Value of the MolecularEnergy:\s+$fltrx/) {
294 $molecularenergy = $1;
295 }
296 elsif ($wante && /S2\(ov\) matrix 1-norm\s*=\s*$fltrx/) {
297 $self->{"s2matrix1norm"} = $1;
298 }
299 elsif ($wante && /There are degenerate orbitals within an irrep/) {
300 $self->{"degenerate"} = 1;
301 }
302 elsif ($wante && /D1\(MP2\)\s*=\s*$fltrx/) {
303 $self->{"d1mp2"} = $1;
304 }
305 elsif ($wante && /D2\(MP1\)\s*=\s*$fltrx/) {
306 $self->{"d2mp1"} = $1;
307 }
308 elsif ($wante && /S2\(ov\) matrix inf-norm\s*=\s*$fltrx/) {
309 $self->{"s2matrixinfnorm"} = $1;
310 }
311 elsif ($wante && /S2 norm\s*=\s*$fltrx/) {
312 $s2norm = $1;
313 }
314 elsif ($wante && /Largest S2 values.*:/) {
315 my $s2large_coef = [];
316 my $s2large_i = [];
317 my $s2large_a = [];
318 my $is2 = 0;
319 while (<$out>) {
320 if (/^\s*([0-9]+)\s+$fltrx\s+([0-9]+)\s+([A-Za-z0-9\'\"]+)\s+->\s+([0-9]+)\s+([A-Za-z0-9\'\"]+)\s*$/) {
321 $s2large_coef->[$is2] = $2;
322 $s2large_i->[$is2] = "$3$4";
323 $s2large_a->[$is2] = "$5$6";
324 $is2 = $is2 + 1;
325 }
326 else {
327 last;
328 }
329 }
330 $self->{"s2large_coef"} = $s2large_coef;
331 $self->{"s2large_i"} = $s2large_i;
332 $self->{"s2large_a"} = $s2large_a;
333 }
334 elsif ($wante && /Largest first order coefficients.*:/) {
335 my $d1large_coef = [];
336 my $d1large_i = [];
337 my $d1large_j = [];
338 my $d1large_a = [];
339 my $d1large_b = [];
340 my $d1large_spin = [];
341 my $id1 = 0;
342 while (<$out>) {
343 if (/^\s*([0-9]+)\s+$fltrx\s+([0-9]+)\s+([A-Za-z0-9\'\"]+)\s+([0-9]+)\s+([A-Za-z0-9\'\"]+)\s+->\s+([0-9]+)\s+([A-Za-z0-9\'\"]+)\s+([0-9]+)\s+([A-Za-z0-9\'\"]+)\s+\((....)\)\s*$/) {
344 $d1large_coef->[$id1] = $2;
345 $d1large_i->[$id1] = "$3$4";
346 $d1large_j->[$id1] = "$5$6";
347 $d1large_a->[$id1] = "$7$8";
348 $d1large_b->[$id1] = "$9$10";
349 $d1large_spin->[$id1] = $11;
350 $id1 = $id1 + 1;
351 }
352 else {
353 last;
354 }
355 }
356 $self->{"d1large_coef"} = $d1large_coef;
357 $self->{"d1large_i"} = $d1large_i;
358 $self->{"d1large_j"} = $d1large_j;
359 $self->{"d1large_a"} = $d1large_a;
360 $self->{"d1large_b"} = $d1large_b;
361 $self->{"d1large_spin"} = $d1large_spin;
362 }
363 elsif ($wante && /^\s*Natural\s+Population\s+Analysis:\s*$/) {
364 my $npacharge = [];
365 my $npashellpop = [];
366 <$out>;
367 my $iatom = 0;
368 while (<$out>) {
369 if (/^\s*\d+\s+[A-Za-z]+\s+$fltrx\s+$fltrx\s*$/) {
370 $npacharge->[$iatom] = $1;
371 $npashellpop->[$iatom] = [ $2 ];
372 }
373 elsif (/^\s*\d+\s+[A-Za-z]+\s+$fltrx\s+$fltrx\s+$fltrx\s*$/) {
374 $npacharge->[$iatom] = $1;
375 $npashellpop->[$iatom] = [ $2, $3 ];
376 }
377 elsif (/^\s*\d+\s+[A-Za-z]+\s+$fltrx\s+$fltrx\s+$fltrx\s+$fltrx\s*$/) {
378 $npacharge->[$iatom] = $1;
379 $npashellpop->[$iatom] = [ $2, $3, $4 ];
380 }
381 elsif (/^\s*\d+\s+[A-Za-z]+\s+$fltrx\s+$fltrx\s+$fltrx\s+$fltrx\s+$fltrx\s*$/) {
382 $npacharge->[$iatom] = $1;
383 $npashellpop->[$iatom] = [ $2, $3, $4, $5 ];
384 }
385 elsif (/^\s*\d+\s+[A-Za-z]+\s+$fltrx\s+$fltrx\s+$fltrx\s+$fltrx\s+$fltrx\s+$fltrx\s*$/) {
386 $npacharge->[$iatom] = $1;
387 $npashellpop->[$iatom] = [ $2, $3, $4, $5, $6 ];
388 }
389 elsif (/^\s*\d+\s+[A-Za-z]+\s+$fltrx\s+$fltrx\s+$fltrx\s+$fltrx\s+$fltrx\s+$fltrx\s+$fltrx\s*$/) {
390 $npacharge->[$iatom] = $1;
391 $npashellpop->[$iatom] = [ $2, $3, $4, $5, $6, $7 ];
392 }
393 elsif (/^\s*$/) {
394 last;
395 }
396 else {
397 die "AM too high to read NPA shell populations (line=$_)";
398 }
399 $iatom = $iatom + 1;
400 }
401 $self->{"npacharge"} = $npacharge;
402 $self->{"npashellpop"} = $npashellpop;
403 }
404 elsif (/The optimization has converged/) {
405 $optconverged = 1;
406 }
407 elsif (/^\s*Beginning displacement/) {
408 # don't grab energies for displaced geometries
409 $wante = 0;
410 }
411 elsif ($optconverged
412 && /^\s+n\s+atom\s+label\s+x\s+y\s+z\s+mass\s*$/) {
413 # old style geometry
414 my $molstr = "";
415 while (<$out>) {
416 s/^ *[0-9]+:// if ($have_nodenum);
417 if (! /^\s+\d+\s+(\w+)\s+$fltrx\s+$fltrx\s+$fltrx\s+/
418 && ! /^\s+\d+\s+(\w+)\s+\S+\s+$fltrx\s+$fltrx\s+$fltrx\s+/) {
419 last;
420 }
421 $molstr = sprintf "%s %s %16.14f %16.14f %16.14f\n",
422 ${molstr}, $1, $2 * $to_angstrom,
423 $3 * $to_angstrom, $4 * $to_angstrom;
424 }
425 $molecule = new Molecule($molstr);
426 }
427 elsif (/^\s*molecule<Molecule>:/) {
428 $geometry_conversion = $to_angstrom;
429 }
430 elsif (/^\s*unit = \"angstrom\"\s*/) { # "
431 $geometry_conversion = 1.0;
432 }
433 elsif ($optconverged
434 && /n\s+atoms\s+(atom_labels\s+)?geometry/) {
435 # new style geometry
436 my $molstr = "";
437 while (<$out>) {
438 s/^ *[0-9]+:// if ($have_nodenum);
439 if (! /^\s+\d+\s+(\w+)\s+\[\s*$fltrx\s+$fltrx\s+$fltrx\s*\]/
440 && ! /^\s+\d+\s+(\w+)\s+\"[^\"]*\"+\s+\[\s*$fltrx\s+$fltrx\s+$fltrx\s*\]/) { # " (unconfuse emacs)
441 last;
442 }
443 $molstr = sprintf "%s %s %16.14f %16.14f %16.14f\n",
444 ${molstr}, $1, $2 * $geometry_conversion,
445 $3 * $geometry_conversion, $4 * $geometry_conversion;
446 }
447 $molecule = new Molecule($molstr);
448 }
449 elsif (/^\s+Total (MP2 )?[Gg]radient/) {
450 $state = "read grad";
451 $grad = [];
452 $ngrad = 0;
453 }
454 elsif (/^\s+Frequencies .*:\s*$/) {
455 # read the frequencies
456 while (<$out>) {
457 s/^ *[0-9]+:// if ($have_nodenum);
458 if (/^\s+\d+\s+$fltrx\s*$/) {
459 $freq->[$ifreq] = $1;
460 $ifreq++;
461 }
462 elsif (/THERMODYNAMIC ANALYSIS/) {
463 last;
464 }
465 }
466 $havefreq = 1;
467 }
468 }
469 $self->{"t1norm"} = $t1norm;
470 $self->{"t1matrix2norm"} = $t12norm;
471 $self->{"s2norm"} = $s2norm;
472 $self->{"ccsdenergy"} = $ccsd_energy;
473 $self->{"ccsd_tenergy"} = $ccsd_t_energy;
474 $self->{"scfenergy"} = $scfenergy;
475 $self->{"opt1energy"} = $opt1energy;
476 $self->{"opt2energy"} = $opt2energy;
477 $self->{"zapt2energy"} = $zapt2energy;
478 $self->{"mp2energy"} = $mp2energy;
479 $self->{"optconverged"} = $optconverged;
480 $self->{"molecularenergy"} = $molecularenergy;
481 if ($optconverged) {
482 $self->{"optmolecule"} = $molecule;
483 }
484 $self->{"have_frequencies"} = $havefreq;
485 if ($havefreq) {
486 my @tmp = sort(@$freq);
487 $freq = \@tmp;
488 $self->{"freq"} = $freq;
489 }
490 my $qcinput = $self->{"qcinput"};
491 my $method = $qcinput->method();
492 #printf "qcinput ok = %d\n", $qcinput->ok();
493 if ($method eq "MP2") {
494 if ($mp2energy ne "") {
495 $self->{"energy"} = $mp2energy;
496 }
497 elsif ($qcinput->mult() == 1) {
498 $self->{"energy"} = $zapt2energy;
499 }
500 }
501 elsif ($method eq "OPT1[2]") {
502 $self->{"energy"} = $opt1energy;
503 }
504 elsif ($method eq "OPT2[2]") {
505 $self->{"energy"} = $opt2energy;
506 }
507 elsif ($method eq "CCSD") {
508 $self->{"energy"} = $ccsd_energy;
509 }
510 elsif ($method eq "CCSD(T)") {
511 $self->{"energy"} = $ccsd_t_energy;
512 }
513 elsif ($qcinput->ok()
514 && ($method eq "SCF" || $method eq "ROSCF")) {
515 $self->{"energy"} = $scfenergy;
516 }
517
518 if ($self->{"energy"} eq "") {
519 $self->{"energy"} = $self->{"molecularenergy"};
520 }
521
522 $self->{"ok"} = 0;
523 if ($self->{"energy"} ne "") {
524 if ($qcinput->optimize()) {
525 if ($self->{"optconverged"}) {
526 $self->{"ok"} = 1;
527 }
528 else {
529 $error = "$error geom not converged\n";
530 }
531 }
532 else {
533 $self->{"ok"} = 1;
534 }
535 if ($qcinput->frequencies() && ! $havefreq) {
536 $self->{"ok"} = 0;
537 $error = "$error no freq\n";
538 }
539 }
540 else {
541 $error = "$error no energy\n";
542 }
543
544 if (! $qcinput->ok()) {
545 $self->{"ok"} = 0;
546 $error = "$error qcinput error: $qcinput->{'error'}";
547 }
548
549 $self->{"error"} = $error;
550}
551
552sub ok {
553 my $self = shift;
554 $self->{"ok"}
555}
556
557sub error {
558 my $self = shift;
559 $self->{"error"};
560}
561
562sub exists {
563 my $self = shift;
564 $self->{"exists"}
565}
566
567sub input {
568 my $self = shift;
569 $self->{"qcinput"}
570}
571
572sub inputok {
573 my $self = shift;
574 $self->{"qcinput"}->ok();
575}
576
577sub energy {
578 my $self = shift;
579 $self->{"energy"}
580}
581
582sub s2norm {
583 my $self = shift;
584 $self->{"s2norm"}
585}
586
587sub s2matrix1norm {
588 my $self = shift;
589 $self->{"s2matrix1norm"}
590}
591
592sub degenerate {
593 my $self = shift;
594 $self->{"degenerate"}
595}
596
597sub d1mp2 {
598 my $self = shift;
599 $self->{"d1mp2"}
600}
601
602sub d2mp1 {
603 my $self = shift;
604 $self->{"d2mp1"}
605}
606
607sub s2matrixinfnorm {
608 my $self = shift;
609 $self->{"s2matrixinfnorm"}
610}
611
612sub t1norm {
613 my $self = shift;
614 $self->{"t1norm"}
615}
616
617sub t1matrix2norm {
618 my $self = shift;
619 $self->{"t1matrix2norm"}
620}
621
622sub optmolecule {
623 my $self = shift;
624 $self->{"optmolecule"};
625}
626
627sub gradient {
628 my $self = shift;
629 $self->{"grad"};
630}
631
632sub frequencies {
633 my $self = shift;
634 $self->{"freq"}
635}
636
637sub d1large_coef {
638 my $self = shift;
639 $self->{"d1large_coef"}
640}
641
642sub d1large_i {
643 my $self = shift;
644 $self->{"d1large_i"}
645}
646
647sub d1large_j {
648 my $self = shift;
649 $self->{"d1large_j"}
650}
651
652sub d1large_a {
653 my $self = shift;
654 $self->{"d1large_a"}
655}
656
657sub d1large_b {
658 my $self = shift;
659 $self->{"d1large_b"}
660}
661
662sub d1large_spin {
663 my $self = shift;
664 $self->{"d1large_spin"}
665}
666
667sub s2large_coef {
668 my $self = shift;
669 $self->{"s2large_coef"}
670}
671
672sub s2large_i {
673 my $self = shift;
674 $self->{"s2large_i"}
675}
676
677sub s2large_a {
678 my $self = shift;
679 $self->{"s2large_a"}
680}
681
682sub npacharge {
683 my $self = shift;
684 $self->{"npacharge"}
685}
686
687sub npashellpop {
688 my $self = shift;
689 $self->{"npashellpop"}
690}
691
6921;
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