MOPAC: withdraw the VIBIR entry -- it killed eccejobmonitor on every job

Shipped this morning, withdrawn the same evening. Live testing:

    FATAL ERROR: JobOutputGet: end of file encountered while reading
    parse type VIBIR
    eccejobmonitor terminating abnormally, exit status 1

repeating forever as the monitor restarted. MOPAC jobs ran but could
never be monitored, and Reconnect did not help.

eccejobmonitor tails a file that is STILL BEING WRITTEN. If it matches a
Begin and then reaches EOF before finding the End, that is FATAL -- not
"wait and try again on the next poll". So an End must be a string
guaranteed to appear, and "SYMMETRY NUMBER FOR POINT-GROUP" is not:
MOPAC does not print it for every molecule or every runtype.

Invisible to tests/parsers by construction. That suite replays COMPLETE
files, so the End is always found. My own note in this file says to run
every runtype through the simulation, and I did -- the simulation cannot
model a partially-written file, which is the condition that matters.
Recorded there so the next End-anchored entry gets thought about at EOF
rather than only on finished output.

The entry is kept commented out rather than deleted, with the
diagnosis: mopac.vibir is correct and verified against a real CH4 run
(the T2 modes carry intensity, A1 and E come out silent, which is right
for Td). What is wrong is only the framing. A blank-line End will not do
either -- MOPAC separates individual VIBRATION stanzas with blank lines,
so it would close after the first and report one mode's intensity as
though it were all of them, which is worse than nothing.

Reopening #103 with this.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFMUNbw2UpRPmgsqviAowb

Author: andy

scripts/parsers/mopac.desc

@@ -176,34 +176,62 @@ Frequency=last
 End=MASS-WEIGHTED COORDINATE ANALYSIS
 [END]
 
-# IR intensities, from the DESCRIPTION OF VIBRATIONS block.  Without
-# VIBIR (or VIBRAM) NModePanel::fillGraph() returns false and
-# initialize() falls back to showTable(), which is why MOPAC alone showed
-# a table where every other code shows the spectrum plot.
-#
-# Boundary check, per the End-line starvation hazard this file's header
-# warns about: Begin is DESCRIPTION OF VIBRATIONS, which lies after
-# [VIBFREQ]'s End (MASS-WEIGHTED COORDINATE ANALYSIS), so nothing is
-# eaten from under it.  End is SYMMETRY NUMBER FOR POINT-GROUP, which is
-# no other entry's Begin -- [PNTGRP] anchors on MOLECULAR POINT GROUP,
-# and every occurrence of that in a real FORCE or GEO+VIB run comes
-# BEFORE this block, so consuming this line starves nothing.
-#
-# Skip=1 starts feeding at the line after Begin, which is blank;
-# mopac.vibir scans for its own markers and ignores everything else, so
-# the usual off-by-one that silently produces zero output does not apply.
-#
-# The block collapses degenerate modes (4 stanzas for CH4's 9 modes);
-# mopac.vibir expands them back out.  See its header for why that is
-# structural rather than a frequency match, and for why the value is the
-# square of the transition dipole on a relative scale.
-[VIBIR]
-Script=mopac.vibir
-Begin=DESCRIPTION OF VIBRATIONS
-Skip=1
-Frequency=last
-End=SYMMETRY NUMBER FOR POINT-GROUP
-[END]
+# IR INTENSITIES ARE DISABLED. The entry below is kept, commented out,
+# because the parser (mopac.vibir) is correct and verified -- what is
+# wrong is the framing, and the fix belongs with someone who can test it
+# live.
+#
+# Shipped briefly on 2026-09-22 and withdrawn the same evening: it made
+# eccejobmonitor die on every MOPAC job.
+#
+#   FATAL ERROR: JobOutputGet: end of file encountered while reading
+#   parse type VIBIR
+#   eccejobmonitor terminating abnormally, exit status 1
+#
+# eccejobmonitor tails a file that is STILL BEING WRITTEN. If it matches
+# a Begin and then reaches EOF before finding the End, that is fatal --
+# not "try again next poll". So an End must be a string that is
+# guaranteed to appear, and "SYMMETRY NUMBER FOR POINT-GROUP" is not:
+# MOPAC does not print it for every molecule or every runtype.
+#
+# This is invisible to tests/parsers, which replays COMPLETE files and
+# therefore always finds the End. Any End-anchored entry needs thinking
+# about at EOF, not just on a finished output.
+#
+# A fix needs an End that always follows the block. A blank line will
+# not do -- MOPAC separates the individual VIBRATION stanzas with blank
+# lines, so it would close after the first one and report a single
+# mode's intensity as though it were all of them, which is worse than
+# nothing. See issue #103.
+#
+# # IR intensities, from the DESCRIPTION OF VIBRATIONS block.  Without
+# # VIBIR (or VIBRAM) NModePanel::fillGraph() returns false and
+# # initialize() falls back to showTable(), which is why MOPAC alone showed
+# # a table where every other code shows the spectrum plot.
+# #
+# # Boundary check, per the End-line starvation hazard this file's header
+# # warns about: Begin is DESCRIPTION OF VIBRATIONS, which lies after
+# # [VIBFREQ]'s End (MASS-WEIGHTED COORDINATE ANALYSIS), so nothing is
+# # eaten from under it.  End is SYMMETRY NUMBER FOR POINT-GROUP, which is
+# # no other entry's Begin -- [PNTGRP] anchors on MOLECULAR POINT GROUP,
+# # and every occurrence of that in a real FORCE or GEO+VIB run comes
+# # BEFORE this block, so consuming this line starves nothing.
+# #
+# # Skip=1 starts feeding at the line after Begin, which is blank;
+# # mopac.vibir scans for its own markers and ignores everything else, so
+# # the usual off-by-one that silently produces zero output does not apply.
+# #
+# # The block collapses degenerate modes (4 stanzas for CH4's 9 modes);
+# # mopac.vibir expands them back out.  See its header for why that is
+# # structural rather than a frequency match, and for why the value is the
+# # square of the transition dipole on a relative scale.
+# [VIBIR]
+# Script=mopac.vibir
+# Begin=DESCRIPTION OF VIBRATIONS
+# Skip=1
+# Frequency=last
+# End=SYMMETRY NUMBER FOR POINT-GROUP
+# [END]
 
 # "          ZERO POINT ENERGY      10.115 KCAL/MOL" -- already in
 # kcal/mol, the Energy converter's base unit, so no conversion.

tests/parsers/expected/mopac-ch4-force.txt

@@ -67,17 +67,6 @@ args:    '.' 'Vibration' 'SE' 'RPM7' '0'
       values: -0.000000000000000e+00 -0.000000000000000e+00 -0.000000000000000e+00 0.000000000000000e+00 2.495000000000000e-01 1.590000000000000e-02 2.352000000000000e-01 8.320000000000000e-02 -1.590000000000000e-02 -1.306000000000000e-01 -1.571000000000000e-01 1.440000000000000e-01 -1.046000000000000e-01 -1.755000000000000e-01 -1.440000000000000e-01 -0.000000000000000e+00 0.000000000000000e+00 0.00000000000000 ...[3034 chars]
       units: Angstrom
 
-[VIBIR]  Script=mopac.vibir  Freq=last  Skip=1  Lines=-
-  Begin=DESCRIPTION OF VIBRATIONS
-  End=SYMMETRY NUMBER FOR POINT-GROUP
-  begins=1 delivered=1 buffered_away=0
-  block 1: begin-line=254 fed=35 rc=0 first-fed=''
-    key: VIBIR
-      size: 9
-      rowlabels: 1 2 3 4 5 6 7 8 9
-      values: 0.0000 0.0000 1.0920 1.0920 1.0920 0.4558 0.4558 0.4558 0.0000
-      units: arb. units
-
 [EZEROPT]  Script=mopac.ezeropt  Freq=last  Skip=0  Lines=1
   Begin=ZERO POINT ENERGY
   begins=1 delivered=1 buffered_away=0

tests/parsers/expected/mopac-ch4-geovib.txt

@@ -109,17 +109,6 @@ args:    '.' 'GeoVib' 'SE' 'RPM7' '0'
       values: 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -0.000000000000000e+00 -2.127000000000000e-01 -1.314000000000000e-01 -2.005000000000000e-01 -7.090000000000000e-02 1.314000000000000e-01 2.076000000000000e-01 6.590000000000000e-02 -1.228000000000000e-01 -7.100000000000000e-03 2.177000000000000e-01 1.228000000000000e-01 0.000000000000000e+00 0.000000000000000e+00 -0.000000000000000e ...[3035 chars]
       units: Angstrom
 
-[VIBIR]  Script=mopac.vibir  Freq=last  Skip=1  Lines=-
-  Begin=DESCRIPTION OF VIBRATIONS
-  End=SYMMETRY NUMBER FOR POINT-GROUP
-  begins=1 delivered=1 buffered_away=0
-  block 1: begin-line=438 fed=35 rc=0 first-fed=''
-    key: VIBIR
-      size: 9
-      rowlabels: 1 2 3 4 5 6 7 8 9
-      values: 0.0000 0.0000 1.0922 1.0922 1.0922 0.4556 0.4556 0.4556 0.0000
-      units: arb. units
-
 [EZEROPT]  Script=mopac.ezeropt  Freq=last  Skip=0  Lines=1
   Begin=ZERO POINT ENERGY
   begins=1 delivered=1 buffered_away=0