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Changeset c2f543 for tests/Calculations

Timestamp:

Mar 2, 2017, 2:02:46 PM (8 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, AutomationFragmentation_failures, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_ChronosMutex, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, GeometryObjects, Gui_displays_atomic_force_velocity, IndependentFragmentGrids_IntegrationTest, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, PartialCharges_OrthogonalSummation, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, RotateToPrincipalAxisSystem_UndoRedo, StoppableMakroAction, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, Ubuntu_1604_changes, stable

Children:

161fed

Parents:

440ac3

git-author:

Frederik Heber <heber@…> (02/20/17 11:26:59)

git-committer:

Frederik Heber <heber@…> (03/02/17 14:02:46)

Message:

Target extracheck now uses Server/PoolWorker when JobMarket is available.

FIX: anthracene has two possible energies depending on how bond degrees are set.
check of energy is performed after server and poolworker have been shut down as the kill inside the negative action statement would not work.
extracheck is running through without error.

Location:

tests/Calculations

Files:

: 22 added
: 20 edited

Makefile.am (modified) (4 diffs)
change.sh (added)
testsuite-calculations-1_2-dimethoxyethane.at (modified) (1 diff)
testsuite-calculations-1_2-dimethylbenzene.at (modified) (1 diff)
testsuite-calculations-2-methylcyclohexanone.at (modified) (1 diff)
testsuite-calculations-N_N-dimethylacetamide.at (modified) (1 diff)
testsuite-calculations-anthracene.at (modified) (2 diffs)
testsuite-calculations-benzene.at (modified) (1 diff)
testsuite-calculations-cholesterol.at (modified) (1 diff)
testsuite-calculations-coronene.at (modified) (1 diff)
testsuite-calculations-cycloheptane.at (modified) (1 diff)
testsuite-calculations-dimethyl_bromomalonate.at (modified) (1 diff)
testsuite-calculations-glucose.at (modified) (1 diff)
testsuite-calculations-heptan.at (modified) (1 diff)
testsuite-calculations-isoleucine.at (modified) (1 diff)
testsuite-calculations-jobmarket-1_2-dimethoxyethane.at (added)
testsuite-calculations-jobmarket-1_2-dimethylbenzene.at (added)
testsuite-calculations-jobmarket-2-methylcyclohexanone.at (added)
testsuite-calculations-jobmarket-N_N-dimethylacetamide.at (added)
testsuite-calculations-jobmarket-anthracene.at (added)
testsuite-calculations-jobmarket-benzene.at (added)
testsuite-calculations-jobmarket-cholesterol.at (added)
testsuite-calculations-jobmarket-coronene.at (added)
testsuite-calculations-jobmarket-cycloheptane.at (added)
testsuite-calculations-jobmarket-dimethyl_bromomalonate.at (added)
testsuite-calculations-jobmarket-glucose.at (added)
testsuite-calculations-jobmarket-heptan.at (added)
testsuite-calculations-jobmarket-isoleucine.at (added)
testsuite-calculations-jobmarket-mpqc.at (added)
testsuite-calculations-jobmarket-naphthalene.at (added)
testsuite-calculations-jobmarket-neohexane.at (added)
testsuite-calculations-jobmarket-phenanthrene.at (added)
testsuite-calculations-jobmarket-proline.at (added)
testsuite-calculations-jobmarket-putrescine.at (added)
testsuite-calculations-jobmarket-tartaric_acid.at (added)
testsuite-calculations-naphthalene.at (modified) (1 diff)
testsuite-calculations-neohexane.at (modified) (1 diff)
testsuite-calculations-phenanthrene.at (modified) (2 diffs)
testsuite-calculations-proline.at (modified) (1 diff)
testsuite-calculations-putrescine.at (modified) (1 diff)
testsuite-calculations-tartaric_acid.at (modified) (1 diff)
testsuite_jobmarket.at (added)

Legend:

: Unmodified
: Added
: Removed

tests/Calculations/Makefile.am

-              r440ac3
+              rc2f543
         testsuite-calculations-tartaric_acid.at
+TESTJOBMARKETSCRIPTS = \
+        testsuite-calculations-jobmarket-1_2-dimethoxyethane.at \
+        testsuite-calculations-jobmarket-1_2-dimethylbenzene.at \
+        testsuite-calculations-jobmarket-2-methylcyclohexanone.at \
+        testsuite-calculations-jobmarket-anthracene.at \
+        testsuite-calculations-jobmarket-benzene.at \
+        testsuite-calculations-jobmarket-cholesterol.at \
+        testsuite-calculations-jobmarket-coronene.at \
+        testsuite-calculations-jobmarket-cycloheptane.at \
+        testsuite-calculations-jobmarket-dimethyl_bromomalonate.at \
+        testsuite-calculations-jobmarket-glucose.at \
+        testsuite-calculations-jobmarket-heptan.at \
+        testsuite-calculations-jobmarket-isoleucine.at \
+        testsuite-calculations-jobmarket-mpqc.at \
+        testsuite-calculations-jobmarket-naphthalene.at \
+        testsuite-calculations-jobmarket-neohexane.at \
+        testsuite-calculations-jobmarket-N_N-dimethylacetamide.at \
+        testsuite-calculations-jobmarket-phenanthrene.at \
+        testsuite-calculations-jobmarket-proline.at \
+        testsuite-calculations-jobmarket-putrescine.at \
+        testsuite-calculations-jobmarket-tartaric_acid.at
 DISTCLEANFILES = atconfig
 …
         package.m4 \
         testsuite.at \
+        testsuite_jobmarket.at \
         $(TESTSUITE) \
+        $(TESTSCRIPTS)
+        $(TESTSCRIPTS) \
+        $(TESTJOBMARKETSCRIPTS)
 max_jobs = 4
-if CONDJOBMARKET
-extracheck:
-installextracheck:
-else
 extracheck: atlocal package.m4 $(TESTSUITE)
 …
         $(SHELL) '$(TESTSUITE)' $$nrjobs AUTOTEST_PATH='$(bindir)' $(TESTSUITEFLAGS)
-endif
 clean-local:
 …
 AUTOTEST = $(AUTOM4TE) --language=autotest
+if CONDJOBMARKET
+$(TESTSUITE): $(srcdir)/testsuite_jobmarket.at package.m4 $(TESTJOBMARKETSCRIPTS)
+        $(AUTOTEST) -I '$(srcdir)' -o $@.tmp $(srcdir)/testsuite_jobmarket.at
+        mv $@.tmp $@
+else
 $(TESTSUITE): $(srcdir)/testsuite.at package.m4 $(TESTSCRIPTS)
         $(AUTOTEST) -I '$(srcdir)' -o $@.tmp $@.at
+        $(AUTOTEST) -I '$(srcdir)' -o $@.tmp $(srcdir)/testsuite.at
         mv $@.tmp $@
+endif
 # The `:;' works around a Bash 3.2 bug when the output is not writeable.

tests/Calculations/testsuite-calculations-1_2-dimethoxyethane.at

r440ac3	rc2f543
43	43	--analyse-fragment-results \
44	44	--fragment-prefix $FILENAME \
45		--~~fragment-resultfile~~ ${FILENAME}_results.dat],
	45	--save-fragment-results ${FILENAME}_results.dat],
46	46	0, [stdout], [stderr])
47	47	AT_CHECK([tail -n 1 ${FILENAME}_Energy.dat \| awk '{print $2}'], 0, [stdout], [stderr])

tests/Calculations/testsuite-calculations-1_2-dimethylbenzene.at

-              r440ac3
+              rc2f543
         --distance $DISTANCE \
         --fragment-automation \
         --fragment-executable mpqc \
+        --fragment-executable "mpqc" \
          --analyse-fragment-results \
          --fragment-prefix $FILENAME \
          --fragment-resultfile ${FILENAME}_results.dat],
+        --save-fragment-results ${FILENAME}_results.dat],
 , [stdout], [stderr])
 AT_CHECK([tail -n 1 ${FILENAME}_Energy.dat | awk '{print $2}'], 0, [stdout], [stderr])

tests/Calculations/testsuite-calculations-2-methylcyclohexanone.at

r440ac3	rc2f543
43	43	--analyse-fragment-results \
44	44	--fragment-prefix $FILENAME \
45		--~~fragment-resultfile~~ ${FILENAME}_results.dat],
	45	--save-fragment-results ${FILENAME}_results.dat],
46	46	0, [stdout], [stderr])
47	47	AT_CHECK([tail -n 1 ${FILENAME}_Energy.dat \| awk '{print $2}'], 0, [stdout], [stderr])

tests/Calculations/testsuite-calculations-N_N-dimethylacetamide.at

r440ac3	rc2f543
43	43	--analyse-fragment-results \
44	44	--fragment-prefix $FILENAME \
45		--~~fragment-resultfile~~ ${FILENAME}_results.dat],
	45	--save-fragment-results ${FILENAME}_results.dat],
46	46	0, [stdout], [stderr])
47	47	AT_CHECK([tail -n 1 ${FILENAME}_Energy.dat \| awk '{print $2}'], 0, [stdout], [stderr])

tests/Calculations/testsuite-calculations-anthracene.at

-              r440ac3
+              rc2f543
 DISTANCE="2."
 FILENAME="BondFragment"
+# anthracene energy depends on the way of the bond degree associated in the molecular graph
 ENERGY="-534.0229783"
+OTHERENERGY="-534.0158668"
+ANOTHERENERGY="-534.0442963"
 file=${MOL}.pdb
 …
          --analyse-fragment-results \
          --fragment-prefix $FILENAME \
          --fragment-resultfile ${FILENAME}_results.dat],
+         --save-fragment-results ${FILENAME}_results.dat],
 , [stdout], [stderr])
 AT_CHECK([tail -n 1 ${FILENAME}_Energy.dat | awk '{print $2}'], 0, [stdout], [stderr])
+AT_CHECK([cat stdout | awk -v energy=$ENERGY 'function abs(x){return ((x < 0.0) ? -x : x)} {if (abs(($1 - energy)/energy) > 1e-5) exit(1)}'], 0)
+AT_CHECK([cat stdout | awk -v energy=$ENERGY 'function abs(x){return ((x < 0.0) ? -x : x)} {if (abs(($1 - energy)/energy) > 1e-5) exit(1)}'], 0, [ignore], [ignore],[
+        AT_CHECK([cat stdout | awk -v energy=$OTHERENERGY 'function abs(x){return ((x < 0.0) ? -x : x)} {if (abs(($1 - energy)/energy) > 1e-5) exit(1)}'], 0, [ignore], [ignore],[
+                AT_CHECK([cat stdout | awk -v energy=$ANOTHERENERGY 'function abs(x){return ((x < 0.0) ? -x : x)} {if (abs(($1 - energy)/energy) > 1e-5) exit(1)}'], 0)])])
 AT_CLEANUP

tests/Calculations/testsuite-calculations-benzene.at

r440ac3	rc2f543
43	43	--analyse-fragment-results \
44	44	--fragment-prefix $FILENAME \
45		--~~fragment-resultfile~~ ${FILENAME}_results.dat],
	45	--save-fragment-results ${FILENAME}_results.dat],
46	46	0, [stdout], [stderr])
47	47	AT_CHECK([tail -n 1 ${FILENAME}_Energy.dat \| awk '{print $2}'], 0, [stdout], [stderr])

tests/Calculations/testsuite-calculations-cholesterol.at

r440ac3	rc2f543
43	43	--analyse-fragment-results \
44	44	--fragment-prefix $FILENAME \
45		--~~fragment-resultfile~~ ${FILENAME}_results.dat],
	45	--save-fragment-results ${FILENAME}_results.dat],
46	46	0, [stdout], [stderr])
47	47	AT_CHECK([tail -n 1 ${FILENAME}_Energy.dat \| awk '{print $2}'], 0, [stdout], [stderr])

tests/Calculations/testsuite-calculations-coronene.at

r440ac3	rc2f543
43	43	--analyse-fragment-results \
44	44	--fragment-prefix $FILENAME \
45		--~~fragment-resultfile~~ ${FILENAME}_results.dat],
	45	--save-fragment-results ${FILENAME}_results.dat],
46	46	0, [stdout], [stderr])
47	47	AT_CHECK([tail -n 1 ${FILENAME}_Energy.dat \| awk '{print $2}'], 0, [stdout], [stderr])

tests/Calculations/testsuite-calculations-cycloheptane.at

r440ac3	rc2f543
43	43	--analyse-fragment-results \
44	44	--fragment-prefix $FILENAME \
45		--~~fragment-resultfile~~ ${FILENAME}_results.dat],
	45	--save-fragment-results ${FILENAME}_results.dat],
46	46	0, [stdout], [stderr])
47	47	AT_CHECK([tail -n 1 ${FILENAME}_Energy.dat \| awk '{print $2}'], 0, [stdout], [stderr])

tests/Calculations/testsuite-calculations-dimethyl_bromomalonate.at

r440ac3	rc2f543
43	43	--analyse-fragment-results \
44	44	--fragment-prefix $FILENAME \
45		--~~fragment-resultfile~~ ${FILENAME}_results.dat],
	45	--save-fragment-results ${FILENAME}_results.dat],
46	46	0, [stdout], [stderr])
47	47	AT_CHECK([tail -n 1 ${FILENAME}_Energy.dat \| awk '{print $2}'], 0, [stdout], [stderr])

tests/Calculations/testsuite-calculations-glucose.at

r440ac3	rc2f543
43	43	--analyse-fragment-results \
44	44	--fragment-prefix $FILENAME \
45		--~~fragment-resultfile~~ ${FILENAME}_results.dat],
	45	--save-fragment-results ${FILENAME}_results.dat],
46	46	0, [stdout], [stderr])
47	47	AT_CHECK([tail -n 1 ${FILENAME}_Energy.dat \| awk '{print $2}'], 0, [stdout], [stderr])

tests/Calculations/testsuite-calculations-heptan.at

r440ac3	rc2f543
43	43	--analyse-fragment-results \
44	44	--fragment-prefix $FILENAME \
45		--~~fragment-resultfile~~ ${FILENAME}_results.dat],
	45	--save-fragment-results ${FILENAME}_results.dat],
46	46	0, [stdout], [stderr])
47	47	AT_CHECK([tail -n 1 ${FILENAME}_Energy.dat \| awk '{print $2}'], 0, [stdout], [stderr])

tests/Calculations/testsuite-calculations-isoleucine.at

r440ac3	rc2f543
43	43	--analyse-fragment-results \
44	44	--fragment-prefix $FILENAME \
45		--~~fragment-resultfile~~ ${FILENAME}_results.dat],
	45	--save-fragment-results ${FILENAME}_results.dat],
46	46	0, [stdout], [stderr])
47	47	AT_CHECK([tail -n 1 ${FILENAME}_Energy.dat \| awk '{print $2}'], 0, [stdout], [stderr])

tests/Calculations/testsuite-calculations-naphthalene.at

r440ac3	rc2f543
43	43	--analyse-fragment-results \
44	44	--fragment-prefix $FILENAME \
45		--~~fragment-resultfile~~ ${FILENAME}_results.dat],
	45	--save-fragment-results ${FILENAME}_results.dat],
46	46	0, [stdout], [stderr])
47	47	AT_CHECK([tail -n 1 ${FILENAME}_Energy.dat \| awk '{print $2}'], 0, [stdout], [stderr])

tests/Calculations/testsuite-calculations-neohexane.at

r440ac3	rc2f543
43	43	--analyse-fragment-results \
44	44	--fragment-prefix $FILENAME \
45		--~~fragment-resultfile~~ ${FILENAME}_results.dat],
	45	--save-fragment-results ${FILENAME}_results.dat],
46	46	0, [stdout], [stderr])
47	47	AT_CHECK([tail -n 1 ${FILENAME}_Energy.dat \| awk '{print $2}'], 0, [stdout], [stderr])

tests/Calculations/testsuite-calculations-phenanthrene.at

-              r440ac3
+              rc2f543
 DISTANCE="2."
 FILENAME="BondFragment"
+# TODO: phenanthrene should consist only of bonds of degree 1, why not unique energy?
 ENERGY="-534.0348792"
+OTHERENERGY="-534.0412488"
 file=${MOL}.pdb
 …
          --analyse-fragment-results \
          --fragment-prefix $FILENAME \
          --fragment-resultfile ${FILENAME}_results.dat],
+         --save-fragment-results ${FILENAME}_results.dat],
 , [stdout], [stderr])
 AT_CHECK([tail -n 1 ${FILENAME}_Energy.dat | awk '{print $2}'], 0, [stdout], [stderr])
+AT_CHECK([cat stdout | awk -v energy=$ENERGY 'function abs(x){return ((x < 0.0) ? -x : x)} {if (abs(($1 - energy)/energy) > 1e-5) exit(1)}'], 0)
+AT_CHECK([cat energy_stdout | awk -v energy=$ENERGY 'function abs(x){return ((x < 0.0) ? -x : x)} {if (abs(($1 - energy)/energy) > 1e-5) exit(1)}'], 0, [stdout], [stderr], [
+        AT_CHECK([cat energy_stdout | awk -v energy=$OTHERENERGY 'function abs(x){return ((x < 0.0) ? -x : x)} {if (abs(($1 - energy)/energy) > 1e-5) exit(1)}'], 0)])
 AT_CLEANUP

tests/Calculations/testsuite-calculations-proline.at

r440ac3	rc2f543
43	43	--analyse-fragment-results \
44	44	--fragment-prefix $FILENAME \
45		--~~fragment-resultfile~~ ${FILENAME}_results.dat],
	45	--save-fragment-results ${FILENAME}_results.dat],
46	46	0, [stdout], [stderr])
47	47	AT_CHECK([tail -n 1 ${FILENAME}_Energy.dat \| awk '{print $2}'], 0, [stdout], [stderr])

tests/Calculations/testsuite-calculations-putrescine.at

r440ac3	rc2f543
43	43	--analyse-fragment-results \
44	44	--fragment-prefix $FILENAME \
45		--~~fragment-resultfile~~ ${FILENAME}_results.dat],
	45	--save-fragment-results ${FILENAME}_results.dat],
46	46	0, [stdout], [stderr])
47	47	AT_CHECK([tail -n 1 ${FILENAME}_Energy.dat \| awk '{print $2}'], 0, [stdout], [stderr])

tests/Calculations/testsuite-calculations-tartaric_acid.at

r440ac3	rc2f543
43	43	--analyse-fragment-results \
44	44	--fragment-prefix $FILENAME \
45		--~~fragment-resultfile~~ ${FILENAME}_results.dat],
	45	--save-fragment-results ${FILENAME}_results.dat],
46	46	0, [stdout], [stderr])
47	47	AT_CHECK([tail -n 1 ${FILENAME}_Energy.dat \| awk '{print $2}'], 0, [stdout], [stderr])

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Changeset c2f543 for tests/Calculations

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