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andy
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Merge remote-tracking branch 'origin/main' into wip/mac-gl-fit
2 parents 772ad85 + a844c55 commit d098996

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‎CMakeLists.txt‎

Lines changed: 16 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -429,6 +429,13 @@ target_link_libraries(eccejobmaster PRIVATE
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add_executable(ecce-localdata src/apps/localdata/ecce-localdata.C)
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target_include_directories(ecce-localdata PRIVATE ${XercesC_INCLUDE_DIRS})
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target_link_libraries(ecce-localdata PRIVATE ecceutil ${XercesC_LIBRARIES})
432+
# An MO's atomic-orbital composition from a calculation folder (#161).
433+
# Installed as bin/mocomp; its wrapper is ecce-mocomp like every CLI app's.
434+
add_executable(mocomp src/apps/mocomp/mocomp.C)
435+
target_include_directories(mocomp PRIVATE ${XercesC_INCLUDE_DIRS})
436+
target_link_libraries(mocomp PRIVATE
437+
eccedsi eccedav eccecipc eccefaces eccexml eccetdat eccedsi eccexml ecceutil
438+
${XercesC_LIBRARIES})
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# flock(1) for the session scripts where util-linux is absent (macOS).
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add_executable(ecce-flock src/apps/flock/ecce-flock.c)
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# The server half of "ecce -admin" on a -remote client (SiteRequest).
@@ -847,7 +854,6 @@ export ECCE_REALUSERHOME=\${ECCE_REALUSERHOME:-$HOME}
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exec \"$ECCE_HOME/bin/ecce-site-admin\" \"$@\"
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")
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install(PROGRAMS ${_sadm_wrapper} DESTINATION ${ECCE_WRAPPER_DESTINATION} COMPONENT client)
850-
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foreach(_ds start stop status adduser)
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set(_ds_wrapper ${CMAKE_BINARY_DIR}/wrappers/ecce-dataserver-${_ds})
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file(WRITE ${_ds_wrapper}
@@ -895,7 +901,7 @@ set(ECCE_GUI_APPS
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mddynamics mdenergy mdoptimize mdprepare msgdialog metadyn organizer
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passdialog hostkeydialog pertable polyed solvate builder vizthumbnail)
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set(ECCE_CLI_APPS
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load_tgbs ecmd eccejobmaster eccejobstore ecce-localdata ecce-flock ecce-site-admin
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load_tgbs ecmd eccejobmaster eccejobstore ecce-localdata ecce-flock ecce-site-admin mocomp
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autosym getfrag genmol genmollat cleansym symops)
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install(TARGETS ${ECCE_GUI_APPS} ${ECCE_CLI_APPS} RUNTIME DESTINATION bin
@@ -2011,6 +2017,14 @@ if(PYTHON3_EXECUTABLE)
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$<TARGET_FILE:importmeta>)
20122018
set_tests_properties(importmeta PROPERTIES TIMEOUT 300 ENVIRONMENT
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"ECCE_HOME=${CMAKE_SOURCE_DIR};ECCE_REALUSER=fragreaders")
2020+
# tests/mocomp: ecce-mocomp's Mulliken and c^2 compositions against
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# checked-in Multiwfn numbers (#161); re-derives them where Multiwfn is
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# installed (MULTIWFN, or Multiwfn_noGUI on PATH).
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add_test(NAME mocomp
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COMMAND ${PYTHON3_EXECUTABLE}
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${CMAKE_CURRENT_SOURCE_DIR}/tests/mocomp/run_tests.py
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${CMAKE_BINARY_DIR})
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set_tests_properties(mocomp PROPERTIES TIMEOUT 300)
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add_test(NAME fragreaders
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COMMAND fragreaders ${CMAKE_CURRENT_SOURCE_DIR}/tests/fragreaders/data)
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file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/fragreaders-home)

‎data/client/config/verify/Gaussian-16.words‎

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Original file line numberDiff line numberDiff line change
@@ -105,7 +105,9 @@ $wrote
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3pd
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4-31g
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5d
108+
6-21g
108109
6-31++g
110+
6-31++g*
109111
6-31++g**
110112
6-31+g*
111113
6-311++g
@@ -141,6 +143,7 @@ activeelectrons
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activeorbitals
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activities\
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additional
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ahlrichs
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ai.gauss09
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ai.gauss09\n
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ai.gauss16
@@ -246,6 +249,7 @@ cartesian
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cas
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casscf
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category
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cbsb7
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cc
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cc-pv5z
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cc-pv6z
@@ -255,6 +259,9 @@ cc-pvtz
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cc.convergenceenergy.value
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cc.convergenceiterations
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cd-demon\n
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cep-121g
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cep-31g
264+
cep-4g
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cerium
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cesium
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charge
@@ -311,14 +318,21 @@ d6d
311318
d6h
312319
d8h
313320
d95
321+
d95**
314322
d95v
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def2-qzv
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def2-qzvp
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def2-sv
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def2-svp
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def2-tzv
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def2-tzvp
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def2-tzvpp
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def2qzv
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def2qzvp
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def2sv
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def2svp
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def2svpp
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def2tzv
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def2tzvp
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def2tzvpp
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density
@@ -331,6 +345,7 @@ dftxcfitting
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dictionary
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dielectric
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difference
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differs
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diis
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direct
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directly
@@ -345,6 +360,7 @@ dunning
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dunning-hay
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dysprosium
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dz
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dzp
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e
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ecce
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ecce_ai_debug
@@ -355,6 +371,8 @@ empiricaldispersion
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end\n
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energy
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enonly
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epr-ii
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epr-iii
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erbium
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error
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error:
@@ -495,6 +513,7 @@ job
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kcis
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krypton
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lanl2dz
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lanl2mb
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lanthanum
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lawrencium
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lc-whpbe
@@ -649,6 +668,7 @@ promethium
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protactinium
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pseudo
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punch
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pvdz
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pw6b95
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pw6b95d3
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pw91
@@ -709,6 +729,7 @@ scf.levelshiftsize
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scrf
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scripts
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sd
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sdd
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sdq
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se
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seaborgium
@@ -741,6 +762,7 @@ stepsize
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sto-2g
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sto-3g
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sto-3g*
765+
sto-6g
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strontium
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sub
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subroutine
@@ -750,6 +772,7 @@ sulfur
750772
super
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superfine
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sv
775+
svp
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svwn
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svwn5
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symmetry
@@ -794,9 +817,12 @@ true
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ts
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tungsten
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type:
820+
tzv
821+
tzvp
797822
u
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uccd
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udft
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ugbs
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uhf
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ultra
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ultrafine
@@ -816,6 +842,7 @@ user
816842
useroutecard
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usesymmetry
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vanadium
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vdz
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version\n
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very
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verytight

‎data/client/config/verify/ORCA.words‎

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Original file line numberDiff line numberDiff line change
@@ -84,8 +84,10 @@ $wrote
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2pd
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2}\n
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3-21g
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3-21gsp
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3df
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3pd
90+
4-22gsp
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6-31++g**
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6-31+g*
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6-311++g
@@ -115,6 +117,7 @@ $wrote
115117
a
116118
activities
117119
activities.\n
120+
ahlrichs
118121
ai.orca
119122
ai.orca:
120123
also
@@ -125,12 +128,29 @@ are
125128
argument
126129
as
127130
atoms!\n
131+
aug-cc-pcvdz
132+
aug-cc-pcvqz
133+
aug-cc-pcvtz
128134
aug-cc-pv5z
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aug-cc-pv6z
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aug-cc-pvdz
131137
aug-cc-pvqz
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aug-cc-pvtz
139+
aug-cc-pwcvdz
140+
aug-cc-pwcvqz
141+
aug-cc-pwcvtz
142+
aug-pc-0
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aug-pc-1
144+
aug-pc-2
145+
aug-pc-3
146+
aug-pcseg-0
147+
aug-pcseg-1
148+
aug-pcseg-2
149+
aug-pcseg-3
150+
aug-pcsseg-0
151+
aug-pcsseg-1
152+
aug-pcsseg-2
153+
aug-pcsseg-3
134154
b2gp-plyp
135155
b2plyp
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b3lyp
@@ -164,12 +184,20 @@ cam-b3lyp
164184
cannot
165185
category
166186
cc
187+
cc-pcvdz
188+
cc-pcvqz
189+
cc-pcvtz
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cc-pv5z
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cc-pv6z
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cc-pvdz
170193
cc-pvdz-dk
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cc-pvqz
195+
cc-pvqz-dk
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cc-pvtz
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cc-pvtz-dk
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cc-pwcvdz
199+
cc-pwcvqz
200+
cc-pwcvtz
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ccsd
174202
charge
175203
charges
@@ -214,13 +242,15 @@ descriptive
214242
details
215243
dft
216244
dictionary
245+
differs
217246
directly
218247
dlpno-ccsd
219248
dlpno-mp2
220249
dropped
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dsd-blyp
222251
dsd-pbep86
223252
dump
253+
ecce
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ecce_ai_debug
225255
ecp
226256
end\n
@@ -272,10 +302,13 @@ h
272302
has
273303
help\n
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hf
305+
huzinaga
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hybrid
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i
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idx
278309
if
310+
iglo-ii
311+
iglo-iii
279312
ih
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implausible
281314
in
@@ -306,6 +339,8 @@ maxiter
306339
mb/core
307340
memorysize
308341
method
342+
midi
343+
mini
309344
missing
310345
model
311346
molecular
@@ -340,13 +375,26 @@ p
340375
pbe
341376
pbe0
342377
pc-1
378+
pc-2
379+
pc-3
380+
pc-4
381+
pcseg-1
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pcseg-2
383+
pcseg-3
384+
pcseg-4
385+
pcsseg-0
386+
pcsseg-1
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pcsseg-2
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pcsseg-3
389+
pcsseg-4
343390
pertab.pl
344391
pick
345392
polar
346393
polarization
347394
potential
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print[p_mos]
349396
print[p_orben]
397+
pvdz
350398
pwpb95
351399
quadrupole
352400
r
@@ -385,6 +433,8 @@ substitution
385433
such
386434
supported.\n
387435
supported:
436+
sv
437+
svp
388438
symbol
389439
symmetry
390440
t
@@ -409,7 +459,9 @@ tpssh
409459
treating
410460
true\n
411461
turn
462+
tzv
412463
udft
464+
ugbs
413465
uhf
414466
uks
415467
ump2
@@ -420,6 +472,7 @@ use
420472
useroutecard
421473
usesym
422474
value
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vdz
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version\n
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very
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verytightopt

‎docs/claude/mo-diagram/index.md‎

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@@ -31,3 +31,4 @@ MOPAC → spec) is the bridge it would reuse.
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- [Without `symops` every fragment column is empty and no line is drawn](empty-and-no-line-is-drawn.md)
3232
- [A fragment column is not sorted by energy](not-sorted-by-energy.md)
3333
- [Fragment columns may be opened out for legibility; the molecular column never is](fragment-columns-may-be-opened-out-for.md)
34+
- [MO composition: MoAoBasis, Mulliken by default (#161)](mo-composition-is-moaobasis-mulliken-by-default.md)
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1+
---
2+
type: map
3+
title: "MO composition: MoAoBasis, Mulliken by default (#161)"
4+
area: mo-diagram
5+
section: "The MO correlation diagram (#132)"
6+
paths: ["include/tdat/MoAoBasis.H", "src/tdat/chemistry/MoAoBasis.C", "src/apps/mocomp/mocomp.C", "src/apps/builder/MoPanel.C", "tests/mocomp"]
7+
issues: [161, 132]
8+
---
9+
`MoAoBasis` (tdat, no wx) owns the walk that says what each MO coefficient
10+
column is: atom, l, nth shell of that l, component, and the real overlap
11+
matrix. `MoDiagramPanel`'s `functionsPerAtom()`/`buildBasisOverlap()` are thin
12+
wrappers on it, so the diagram, the MOs panel text, View Coeff's `%` column and
13+
`ecce-mocomp` cannot disagree about the basis.
14+
15+
Default method is Mulliken `c_i (S c)_i / c.S.c` (the diagram's own share);
16+
`c^2` is the option. Mulliken parts are unbounded: do not threshold on them
17+
(that is what the Lowdin share in `MoComposition` is for).
18+
19+
Checked against Multiwfn (Mulliken and Ros-Schuit) for ORCA water, benzene,
20+
CH3 (UHF), Cr(CO)6 and Gaussian 16 formaldehyde with Cartesian d: worst
21+
difference about 0.001 percentage point. `tests/mocomp/README.md` says how the
22+
fixtures and references were made. The fixtures are local-data calculation
23+
folders (`.ecce-meta`), not the data-server `.DAV` folders of `tests/modiagram`,
24+
which `ecce-mocomp` cannot open.
25+
26+
Headless screenshots of the Builder need `ECCE_PANEL_MODE=classic`: in the
27+
default `detail` mode the molecule and the MOs pane did not appear in a
28+
private-Xvfb run, with or without this feature.

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