MOPAC: re-enable IR intensities, with an End that cannot starve (#103)

The parser was already written and verified.  It was disabled on
2026-09-22 because its End anchor, "SYMMETRY NUMBER FOR POINT-GROUP",
is not printed for every molecule or runtype, and eccejobmonitor treats
reaching EOF inside an open block as fatal:

  FATAL ERROR: JobOutputGet: end of file encountered while reading
  parse type VIBIR

Two traps stood between that and a working End, and both were hit here
rather than reasoned about:

  "FORCE CONSTANT" appears INSIDE every VIBRATION stanza, so ending on
  it closes the block after the first mode and reports one mode's
  intensity as though it were all of them.  The withdrawal note
  predicted exactly this for a blank line; the stanza field has the
  same shape.

  "SYMBOL  FORCE CONSTANT" -- the header of the table that follows --
  cannot match a stanza line and is present exactly once in every
  fixture that has a vibrations block.  But with THERMO that table is a
  long way past the stanzas (438 to 647 in ch4_geovib) and the
  thermochemistry table sits between them at 492, so ending there
  swallowed [ENTHALPY]...'s Begin and stopped MOPAC thermochemistry
  being extracted at all.  The suite caught it immediately: "expected
  parse type [ENTHALPY]... never delivered a block".

The End is therefore an alternation.  "SYSTEM IS A GROUND STATE" is
printed straight after the stanzas whenever THERMO is on, closing the
block before the thermochemistry; the table header closes it otherwise.

Units say "arb. units" and mean it.  MOPAC prints a transition dipole
in Debye -- confirmed against its own manual, which gives the formula
and explicitly offers no conversion -- and IR intensity goes as the
square.  The stored value is that square on a relative scale, so peak
positions and relative heights are right and the y-axis is not
comparable with another code's km/mol.

The geovib case now pins VIBIR at length 9 alongside the
thermochemistry, so the two cannot silently trade places again.

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

@@ -273,62 +273,70 @@ Frequency=last
 End=MASS-WEIGHTED COORDINATE ANALYSIS
 [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.
+# 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.
 #
-# Shipped briefly on 2026-09-22 and withdrawn the same evening: it made
-# eccejobmonitor die on every MOPAC job.
+# THE End IS THE WHOLE STORY HERE.  This shipped on 2026-09-22 anchored
+# on "SYMMETRY NUMBER FOR POINT-GROUP" and was withdrawn the same
+# evening, because 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.
+# The monitor tails a file that is still being written.  Matching a
+# Begin and then reaching EOF without the End is fatal, not "try again
+# next poll", so an End has to be a string that reliably appears --
+# and MOPAC does not print that one for every molecule or 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.
+# The obvious replacement is a trap: "FORCE CONSTANT" appears INSIDE
+# every VIBRATION stanza, so ending on it would close the block after
+# the first mode and report one mode's intensity as though it were all
+# of them -- worse than nothing, and exactly what the withdrawal note
+# warned a blank line would do.
 #
-# 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.
+# "SYMBOL  FORCE CONSTANT" is the header of the force-constant table
+# that follows the block, and cannot match a stanza line (those read
+# " FORCE CONSTANT      0.2475", with no SYMBOL).  Checked across every
+# MOPAC fixture: present exactly once in each output that has a
+# DESCRIPTION OF VIBRATIONS block, always after it, and absent from
+# every output that has no such block.
 #
-# # 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]
+# It is NOT sufficient on its own, and the alternation is not
+# decoration.  With THERMO the force-constant table comes a long way
+# after the stanzas -- 438 to 647 in the ch4_geovib fixture -- and the
+# thermochemistry table sits between them at 492.  Ending only on the
+# table header therefore swallowed [ENTHALPY]...'s Begin and starved it
+# completely: MOPAC thermochemistry stopped being extracted the moment
+# this entry was re-enabled.  "SYSTEM IS A GROUND STATE" is printed
+# immediately after the stanzas whenever THERMO is on, so the
+# alternation closes the block before the thermochemistry in that case
+# and on the table header otherwise.
+#
+# Boundary check per this file's header: Begin lies after [VIBFREQ]'s
+# End (MASS-WEIGHTED COORDINATE ANALYSIS), so nothing is eaten from
+# under it, and the End line is no other entry's Begin.
+#
+# 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, so VIBIR comes out the same length
+# as VIBFREQ.  The value is the square of the transition dipole on a
+# relative scale: MOPAC prints a transition dipole in Debye and gives no
+# conversion to km/mol, so the units say "arb. units" rather than
+# claiming an absolute intensity.  Peak positions and relative heights
+# are right; the y-axis is not comparable with another code's.
+[VIBIR]
+Script=mopac.vibir
+Begin=DESCRIPTION OF VIBRATIONS
+Skip=1
+Frequency=last
+End=SYSTEM IS A GROUND STATE|SYMBOL\s+FORCE CONSTANT
+[END]
 
 # "          ZERO POINT ENERGY      10.115 KCAL/MOL" -- already in
 # kcal/mol, the Energy converter's base unit, so no conversion.

tests/parsers/cases.py

@@ -1007,6 +1007,19 @@
             #  H.O.F. - RT.  The two values below differ by exactly
             #  RT = 1.987204259 * 298.00 / 1000 kcal/mol, which is ORCA's
             #  own "H = U + kB*T" seen from the other side.
+            #  VIBIR must be exactly as long as VIBFREQ.  MOPAC's
+            #  DESCRIPTION OF VIBRATIONS collapses degenerate modes --
+            #  four stanzas for CH4's nine modes -- and mopac.vibir
+            #  expands them back out; a short vector would silently
+            #  misalign the spectrum against the frequencies.
+            #
+            #  Its presence here is also the regression guard for the
+            #  End that had to be an alternation: ending only on the
+            #  force-constant table header swallowed the thermochemistry
+            #  entry's Begin on this very fixture, so if VIBIR appears
+            #  and the thermochemistry below does not, the End has drifted
+            #  too far again.
+            'VIBIR': dict(blocks=1, keys={'VIBIR': {'size': '9'}}),
             'ENTHALPY][ETHERM][ENTROPY][HEATCAP][THERMOTEMP': dict(
                 blocks=1, keys={
                     'ENTHALPY': {'values': '-0.022954235107774',

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

@@ -119,6 +119,17 @@ args:    '.' 'Vibration' 'SE' 'PM7' '0'
       values: 0.000000000000000e+00 0.000000000000000e+00 -0.000000000000000e+00 -0.000000000000000e+00 -1.829000000000000e-01 -1.705000000000000e-01 -1.724000000000000e-01 -6.080000000000000e-02 1.705000000000000e-01 2.254000000000000e-01 2.330000000000000e-02 -1.055000000000000e-01 -5.300000000000000e-02 2.204000000000000e-01 1.055000000000000e-01 0.000000000000000e+00 -0.000000000000000e+00 0.000000000000000 ...[3036 chars]
       units: Angstrom
 
+[VIBIR]  Script=mopac.vibir  Freq=last  Skip=1  Lines=-
+  Begin=DESCRIPTION OF VIBRATIONS
+  End=SYSTEM IS A GROUND STATE|SYMBOL\s+FORCE CONSTANT
+  begins=1 delivered=1 buffered_away=0
+  block 1: begin-line=435 fed=38 rc=0 first-fed=''
+    key: VIBIR
+      size: 9
+      rowlabels: 1 2 3 4 5 6 7 8 9
+      values: 0.0000 0.0000 1.0935 1.0935 1.0935 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

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

@@ -88,6 +88,17 @@ 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=SYSTEM IS A GROUND STATE|SYMBOL\s+FORCE CONSTANT
+  begins=1 delivered=1 buffered_away=0
+  block 1: begin-line=254 fed=38 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

@@ -140,6 +140,17 @@ 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=SYSTEM IS A GROUND STATE|SYMBOL\s+FORCE CONSTANT
+  begins=1 delivered=1 buffered_away=0
+  block 1: begin-line=438 fed=38 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