Changeset ebcade


Ignore:
Timestamp:
Oct 6, 2009, 5:56:15 PM (16 years ago)
Author:
Frederik Heber <heber@…>
Branches:
Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable
Children:
e9f8f9
Parents:
cee0b57
git-author:
Frederik Heber <heber@…> (10/06/09 17:37:50)
git-committer:
Frederik Heber <heber@…> (10/06/09 17:56:15)
Message:

Extended the testsuite to encompass the vital areas of molecuilder.

  • the vital areas are: simple geometry, Graph, fragmentation, tesselation
  • in molecuilder/tests a dir regression was added for each case with pre and post dirs. Pre contains files needed for the test, post contains results to compare to
  • builder.cpp: check for commands that need extra arguments that first arguments does not begin with '-' missing for many cases
Files:
69 added
3 edited

Legend:

Unmodified
Added
Removed

  • src/builder.cpp

    rcee0b57 rebcade  
    13821382            cout << "\t-p <file>\tParse given xyz file and create raw config file from it." << endl;
    13831383            cout << "\t-P <file>\tParse given forces file and append as an MD step to config file via Verlet." << endl;
    1384             cout << "\t-r\t\tConvert file from an old pcp syntax." << endl;
    1385             cout << "\t-R\t\tRemove all atoms out of sphere around a given one." << endl;
     1384            cout << "\t-r <id>\t\tRemove an atom with given id." << endl;
     1385            cout << "\t-R <id> <radius>\t\tRemove all atoms out of sphere around a given one." << endl;
    13861386            cout << "\t-s x1 x2 x3\tScale all atom coordinates by this vector (x1,x2,x3)." << endl;
    13871387            cout << "\t-S <file> Store temperatures from the config file in <file>." << endl;
    … …  
    14801480          switch(argv[argptr-1][1]) {
    14811481            case 'p':
    1482               ExitFlag = 1;
     1482              if (ExitFlag == 0) ExitFlag = 1;
    14831483              if ((argptr >= argc) || (argv[argptr][0] == '-')) {
    14841484                ExitFlag = 255;
    … …  
    14961496              break;
    14971497            case 'a':
    1498               ExitFlag = 1;
     1498              if (ExitFlag == 0) ExitFlag = 1;
    14991499              if ((argptr >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr+1]))) {
    15001500                ExitFlag = 255;
    … …  
    15351535              break;
    15361536            case 'D':
    1537               ExitFlag = 1;
     1537              if (ExitFlag == 0) ExitFlag = 1;
    15381538              {
    15391539                cout << Verbose(1) << "Depth-First-Search Analysis." << endl;
    … …  
    15681568              break;
    15691569            case 'E':
    1570               ExitFlag = 1;
     1570              if (ExitFlag == 0) ExitFlag = 1;
    15711571              if ((argptr+1 >= argc) || (!IsValidNumber(argv[argptr])) || (argv[argptr+1][0] == '-')) {
    15721572                ExitFlag = 255;
    … …  
    15811581              break;
    15821582            case 'F':
    1583               ExitFlag = 1;
     1583              if (ExitFlag == 0) ExitFlag = 1;
    15841584              if (argptr+5 >=argc) {
    15851585                ExitFlag = 255;
    … …  
    16191619              break;
    16201620            case 'A':
    1621               ExitFlag = 1;
     1621              if (ExitFlag == 0) ExitFlag = 1;
    16221622              if ((argptr >= argc) || (argv[argptr][0] == '-')) {
    16231623                ExitFlag =255;
    … …  
    16321632              break;
    16331633            case 'N':
    1634               ExitFlag = 1;
     1634              if (ExitFlag == 0) ExitFlag = 1;
    16351635              if ((argptr+1 >= argc) || (argv[argptr+1][0] == '-')){
    16361636                ExitFlag = 255;
    … …  
    16521652              break;
    16531653            case 'S':
    1654               ExitFlag = 1;
     1654              if (ExitFlag == 0) ExitFlag = 1;
    16551655              if ((argptr >= argc) || (argv[argptr][0] == '-')) {
    16561656                ExitFlag = 255;
    … …  
    16691669              break;
    16701670            case 'L':
    1671               ExitFlag = 1;
     1671              if (ExitFlag == 0) ExitFlag = 1;
    16721672              if ((argptr >= argc) || (argv[argptr][0] == '-')) {
    16731673                ExitFlag = 255;
    … …  
    16861686              break;
    16871687            case 'P':
    1688               ExitFlag = 1;
     1688              if (ExitFlag == 0) ExitFlag = 1;
    16891689              if ((argptr >= argc) || (argv[argptr][0] == '-')) {
    16901690                ExitFlag = 255;
    … …  
    17011701              break;
    17021702            case 'R':
    1703               ExitFlag = 1;
    1704               if ((argptr+1 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])))  {
     1703              if (ExitFlag == 0) ExitFlag = 1;
     1704              if ((argptr+1 >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])))  {
    17051705                ExitFlag = 255;
    17061706                cerr << "Not enough or invalid arguments given for removing atoms: -R <id> <distance>" << endl;
    … …  
    17261726              break;
    17271727            case 't':
    1728               ExitFlag = 1;
    1729               if ((argptr+2 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
     1728              if (ExitFlag == 0) ExitFlag = 1;
     1729              if ((argptr+2 >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
    17301730                ExitFlag = 255;
    17311731                cerr << "Not enough or invalid arguments given for translation: -t <x> <y> <z>" << endl;
    17321732              } else {
    1733                 ExitFlag = 1;
     1733                if (ExitFlag == 0) ExitFlag = 1;
    17341734                SaveFlag = true;
    17351735                cout << Verbose(1) << "Translating all ions by given vector." << endl;
    … …  
    17411741              break;
    17421742            case 'T':
    1743               ExitFlag = 1;
    1744               if ((argptr+2 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
     1743              if (ExitFlag == 0) ExitFlag = 1;
     1744              if ((argptr+2 >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
    17451745                ExitFlag = 255;
    17461746                cerr << "Not enough or invalid arguments given for periodic translation: -T <x> <y> <z>" << endl;
    17471747              } else {
    1748                 ExitFlag = 1;
     1748                if (ExitFlag == 0) ExitFlag = 1;
    17491749                SaveFlag = true;
    17501750                cout << Verbose(1) << "Translating all ions periodically by given vector." << endl;
    … …  
    17561756              break;
    17571757            case 's':
    1758               ExitFlag = 1;
    1759               if ((argptr >= argc) || (!IsValidNumber(argv[argptr])) ) {
     1758              if (ExitFlag == 0) ExitFlag = 1;
     1759              if ((argptr >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) ) {
    17601760                ExitFlag = 255;
    17611761                cerr << "Not enough or invalid arguments given for scaling: -s <factor/[factor_x]> [factor_y] [factor_z]" << endl;
    … …  
    17831783              break;
    17841784            case 'b':
    1785               ExitFlag = 1;
    1786               if ((argptr+5 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) || (!IsValidNumber(argv[argptr+3])) || (!IsValidNumber(argv[argptr+4])) || (!IsValidNumber(argv[argptr+5])) ) {
     1785              if (ExitFlag == 0) ExitFlag = 1;
     1786              if ((argptr+5 >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) || (!IsValidNumber(argv[argptr+3])) || (!IsValidNumber(argv[argptr+4])) || (!IsValidNumber(argv[argptr+5])) ) {
    17871787                ExitFlag = 255;
    17881788                cerr << "Not enough or invalid arguments given for centering in box: -b <xx> <xy> <xz> <yy> <yz> <zz>" << endl;
    … …  
    18001800              break;
    18011801            case 'B':
    1802               ExitFlag = 1;
    1803               if ((argptr+5 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) || (!IsValidNumber(argv[argptr+3])) || (!IsValidNumber(argv[argptr+4])) || (!IsValidNumber(argv[argptr+5])) ) {
     1802              if (ExitFlag == 0) ExitFlag = 1;
     1803              if ((argptr+5 >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) || (!IsValidNumber(argv[argptr+3])) || (!IsValidNumber(argv[argptr+4])) || (!IsValidNumber(argv[argptr+5])) ) {
    18041804                ExitFlag = 255;
    18051805                cerr << "Not enough or invalid arguments given for bounding in box: -B <xx> <xy> <xz> <yy> <yz> <zz>" << endl;
    … …  
    18171817              break;
    18181818            case 'c':
    1819               ExitFlag = 1;
    1820               if ((argptr+2 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
     1819              if (ExitFlag == 0) ExitFlag = 1;
     1820              if ((argptr+2 >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
    18211821                ExitFlag = 255;
    18221822                cerr << "Not enough or invalid arguments given for centering with boundary: -c <boundary_x> <boundary_y> <boundary_z>" << endl;
    … …  
    18411841              break;
    18421842            case 'O':
    1843               ExitFlag = 1;
     1843              if (ExitFlag == 0) ExitFlag = 1;
    18441844              SaveFlag = true;
    18451845              cout << Verbose(1) << "Centering atoms on edge and setting box dimensions." << endl;
    … …  
    18501850              break;
    18511851            case 'r':
    1852               ExitFlag = 1;
    1853               SaveFlag = true;
    1854               cout << Verbose(1) << "Converting config file from supposed old to new syntax." << endl;
     1852              if (ExitFlag == 0) ExitFlag = 1;
     1853              if ((argptr >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])))  {
     1854                ExitFlag = 255;
     1855                cerr << "Not enough or invalid arguments given for removing atoms: -r <id>" << endl;
     1856              } else {
     1857                SaveFlag = true;
     1858                cout << Verbose(1) << "Removing atom " << argv[argptr] << "." << endl;
     1859                atom *first = mol->FindAtom(atoi(argv[argptr]));
     1860                mol->RemoveAtom(first);
     1861                argptr+=1;
     1862              }
    18551863              break;
    18561864            case 'f':
    1857               ExitFlag = 1;
    1858               if ((argptr+1 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1]))) {
     1865              if (ExitFlag == 0) ExitFlag = 1;
     1866              if ((argptr+1 >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1]))) {
    18591867                ExitFlag = 255;
    18601868                cerr << "Not enough or invalid arguments for fragmentation: -f <max. bond distance> <bond order>" << endl;
    … …  
    18741882              break;
    18751883            case 'm':
    1876               ExitFlag = 1;
     1884              if (ExitFlag == 0) ExitFlag = 1;
    18771885              j = atoi(argv[argptr++]);
    18781886              if ((j<0) || (j>1)) {
    … …  
    18881896              break;
    18891897            case 'o':
    1890               ExitFlag = 1;
     1898              if (ExitFlag == 0) ExitFlag = 1;
    18911899              if ((argptr+1 >= argc) || (argv[argptr][0] == '-')){
    18921900                ExitFlag = 255;
    … …  
    19081916              break;
    19091917            case 'U':
    1910               ExitFlag = 1;
    1911               if ((argptr+1 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) ) {
     1918              if (ExitFlag == 0) ExitFlag = 1;
     1919              if ((argptr+1 >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) ) {
    19121920                ExitFlag = 255;
    19131921                cerr << "Not enough or invalid arguments given for suspension with specified volume: -U <volume> <density>" << endl;
    … …  
    19181926              }
    19191927            case 'u':
    1920               ExitFlag = 1;
    1921               if ((argptr >= argc) || (!IsValidNumber(argv[argptr])) ) {
     1928              if (ExitFlag == 0) ExitFlag = 1;
     1929              if ((argptr >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) ) {
    19221930                if (volume != -1)
    19231931                  ExitFlag = 255;
    … …  
    19421950              break;
    19431951            case 'd':
    1944               ExitFlag = 1;
    1945               if ((argptr+2 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
     1952              if (ExitFlag == 0) ExitFlag = 1;
     1953              if ((argptr+2 >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
    19461954                ExitFlag = 255;
    19471955                cerr << "Not enough or invalid arguments given for repeating cells: -d <repeat_x> <repeat_y> <repeat_z>" << endl;

  • tests/Makefile.am

    rcee0b57 rebcade  
    11AUTOM4TE = autom4te
    2 EXTRA_DIST = testsuite.at $(TESTSUITE) atlocal.in
     2EXTRA_DIST = testsuite.at $(TESTSUITE) atlocal.in regression
    33TESTSUITE = $(srcdir)/testsuite
    44

  • tests/testsuite.at

    rcee0b57 rebcade  
    11# Process with autom4te to create an -*- Autotest -*- test suite.
    2 
     2#
     3# see regression/... subdirs wherein for each of the cases and each check (enumerated) is a pre and post dir.
     4# In pre initial files are placed, in post results can be found to be checked by diff in this testsuite.
    35
    46AT_INIT([Molecular Builder])
    … …  
    79AT_BANNER([MoleCuilder - standard options])
    810AT_SETUP([Standard Options])
     11AT_KEYWORDS([options])
    912AT_CHECK([pwd],[ignore],[ignore])
    1013AT_CHECK([../../molecuilder -v], 0, [stdout], [ignore])
    … …  
    1821AT_CLEANUP
    1922
     23
    2024AT_BANNER([MoleCuilder - molecular config creation from xyz file and atom adding])
    21 AT_SETUP([Simple configuration])
    22 # 1. create a fake element database with the only element we need
    23 AT_DATA([elements.db],[#        Covalent        radius  of      each    element in      Angstroem       from    CSD     (binding        is:     [Rcov(A)+Rcov(B)-t,Rcov(A)+Rcov(B)+t]   with    t       =       0.4A
    24 #Element        Name    Symbol  Period  Group   Block   Atomic  Number  AtomicWeight    Covalent        Radius  vdW     Radius
    25 Hydrogen        H       1       1       s       1       1.008   0.23    1.09
    26 ])
    27 # 2. create some simplest molecular geometry
     25AT_KEYWORDS([Atom handling])
     26# 1. create some simplest molecular geometry
     27AT_SETUP([Simple configuration - xyz file generation])
    2828AT_DATA([test.xyz], [[1
    2929 # test configuration, created by molecuilder test suite
    3030H       10.     10.     10.
    3131]])
    32 # 3. make sure config is empty and not remnant from last test with broken dirs
    33 AT_DATA([test.conf], [])
    34 AT_CHECK([../../molecuilder test.conf -e ./ -p test.xyz], 0, [ignore], [ignore])
     32AT_CHECK([file=test.xyz; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/1/post/$file], 0, [ignore], [ignore])
     33AT_CLEANUP
     34
     35# 2. parsing an xyz
     36AT_SETUP([Simple configuration - parsing xyz file])
     37AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/2/pre/test.xyz .], 0)
     38AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -p test.xyz], 0, [ignore], [ignore])
    3539AT_CHECK([fgrep "Ion_Type1_1" test.conf], 0, [Ion_Type1_1       10.000000000    10.000000000    10.000000000    0 # molecule nr 0
    3640], [ignore])
    37 AT_CHECK([mv test.conf main_pcp_linux], 0, [ignore], [ignore])
    38 AT_DATA([input], [maa 10. 10. 10. 1
    39 s
    40 q
    41 ])
    42 AT_CHECK([../../molecuilder test.conf -e ./ <input], 0, [ignore], [ignore])
    43 AT_CHECK([diff main_pcp_linux test.conf], 0, [ignore], [ignore])
    44 # 4. test some more configuration
    45 AT_CHECK([../../molecuilder test.conf -e ./ -t -s -b -E -c -b -a -U -T -u], 0, [ignore], [stderr])
     41AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
     42AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
     43AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
     44
     45# 3. add atom
     46AT_CLEANUP
     47AT_SETUP([Simple configuration - adding atom])
     48AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -a 1 10. 10. 10.], 0, [ignore], [ignore])
     49AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
     50AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
     51AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
     52AT_CLEANUP
     53
     54# 4. change the element
     55AT_SETUP([Simple configuration - Changing element])
     56AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/4/pre/test.conf test.conf], 0)
     57AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -E 0 6], 0, [ignore], [ignore])
     58AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/4/post/$file], 0, [ignore], [ignore])
     59AT_CLEANUP
     60
     61# 5. remove atom
     62AT_SETUP([Simple configuration - Atom removal])
     63AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/5/pre/test.conf .], 0)
     64AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -r 0], 0, [ignore], [ignore])
     65AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
     66AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
     67AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
     68AT_CLEANUP
     69
     70# 6. test some more configuration that all desire parameters and count how many complain
     71AT_SETUP([Simple configuration - invalid commands on empty configs])
     72AT_CHECK([../../molecuilder empty.conf -e ${abs_top_srcdir}/src/ -t -s -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
     73AT_CHECK([fgrep -c "Not enough or invalid" stderr], 0, [1
     74], [ignore])
     75AT_CLEANUP
     76
     77# 7. test some more configuration that all need parameters and count how many complain
     78AT_SETUP([Simple configuration - invalid commands on present configs])
     79AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/7/pre/test.conf .], 0)
     80AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -t -s -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
    4681AT_CHECK([fgrep -c "Not enough or invalid" stderr], 0, [9
    4782], [ignore])
    4883AT_CLEANUP
    4984
     85
     86AT_BANNER([MoleCuilder - Graph routines test])
     87AT_KEYWORDS([graph])
     88AT_SETUP([Graph - DFS analysis])
     89AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Graph/1/pre/test.conf .], 0)
     90AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -D 2.], 0, [stdout], [stderr])
     91AT_CHECK([fgrep -c "No rings were detected in the molecular structure." stdout], 0, [1
     92], [ignore])
     93AT_CLEANUP
     94
    5095AT_BANNER([MoleCuilder - Fragmentation and Re-fragmentation test])
    51 AT_SETUP([Fragmentation])
    52 # 1. create a fake element database with the only two elements we need
    53 AT_DATA([elements.db],[#  Covalent  radius  of  each  element in  Angstroem from  CSD (binding  is: [Rcov(A)+Rcov(B)-t,Rcov(A)+Rcov(B)+t] with  t = 0.4A
    54 #Element  Name  Symbol  Period  Group Block Atomic  Number  AtomicWeight  Covalent  Radius  vdW Radius
    55 Hydrogen  H 1 1 s 1 1.008 0.23  1.09
    56 Carbon  C       2       14      p       6       12.011  0.68    1.70
    57 ])
    58 # 2. create molecular geometry
    59 AT_DATA([test.xyz], [[11
    60  # test configuration, created by molecuilder test suite
    61 C       9.782085945     3.275186040     3.535886037
    62 C       8.532785963     4.158586027     3.535886037
    63 C       7.283585982     3.275186040     3.535886037
    64 H       9.782085945     2.645886050     2.645886050
    65 H       9.782085945     2.645886050     4.425886024
    66 H       10.672039608    3.904536878     3.535886037
    67 H       8.532785963     4.787886018     2.645886050
    68 H       8.532785963     4.787886018     4.425886024
    69 H       6.393632318     3.904536877     3.535886037
    70 H       7.283585982     2.645886050     2.645886050
    71 H       7.283585982     2.645886050     4.425886024
    72 ]])
    73 # 3. make sure config is empty and not remnant from last test with broken dirs
    74 AT_DATA([test.conf], [])
    75 # 4. create the config and check it
    76 AT_CHECK([../../molecuilder test.conf -e ./ -p test.xyz], 0, [ignore], [ignore])
     96AT_KEYWORDS([fragmentation])
     97# 1. check config
     98AT_SETUP([Fragmentation - Checking present config])
     99AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Fragmentation/1/pre/test.conf .], 0)
    77100AT_CHECK([fgrep "Ion_Type1_4" test.conf], 0, [Ion_Type1_4       8.532785963     4.787886018     2.645886050     0 # molecule nr 6
    78101], [ignore])
    79102AT_CHECK([fgrep "Ion_Type2_4" test.conf], 1, [ignore], [ignore])
    80 # 5. fragment the molecule and check the number of configs
    81 AT_CHECK([../../molecuilder test.conf -e ./ -f 1.55 2], 0, [ignore], [ignore], [mkdir std; mv BondFragment*.conf* std/])
     103AT_CLEANUP
     104# 2. fragment the molecule and check the number of configs
     105AT_SETUP([Fragmentation - Fragmentation])
     106AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Fragmentation/2/pre/test.conf .], 0)
     107AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -f 1.55 2], 0, [ignore], [ignore], [mkdir std; mv BondFragment*.conf* std/])
    82108AT_CHECK([mkdir std; mv BondFragment*.conf* std/], 0)
    83109AT_CHECK([ls -l std/BondFragment*.conf | wc -l], 0, [5
    84110], [ignore])
    85 # 3a. check whether parsing of BondFragment files and re-rwriting config files is working (exit code is 2 as we don't need to continue wrt to ...OrderAtSite)
    86 AT_CHECK([../../molecuilder test.conf -e ./ -f 1.55 2], 2, [ignore], [ignore], [mkdir new; mv BondFragment*.conf* new/])
     111AT_CLEANUP
     112# 3. check whether parsing of BondFragment files and re-rwriting config files is working (exit code is 2 as we don't need to continue wrt to ...OrderAtSite)
     113AT_SETUP([Fragmentation - Fragmentation is at MaxOrder])
     114AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Fragmentation/3/pre/* .], 0)
     115AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -f 1.55 2], 2, [ignore], [ignore], [mkdir new; mv BondFragment*.conf* new/])
    87116AT_CHECK([mkdir new; mv BondFragment*.conf* new/], 0)
    88 # 6. compare both dirs by diff'ing
    89 AT_CHECK([diff -I '.*Created by molecuilder.*' std/ new/], 0, [], [])
    90117AT_CLEANUP
    91118
     119
     120AT_BANNER([MoleCuilder - Tesselation test])
     121AT_KEYWORDS([Tesselation])
     122# 1. Non convex tesselation
     123AT_SETUP([Tesselation - Non-Convex Envelope])
     124AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/1/pre/* .], 0)
     125AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 4. NonConvexEnvelope], 0, [stdout], [stderr])
     126AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/1/post/$file], 0, [ignore], [ignore])
     127AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/1/post/$file], 0, [ignore], [ignore])
     128AT_CLEANUP
     129
     130# 2. convex tesselation (where the non-convex is already convex)
     131AT_SETUP([Tesselation - Convex Envelope])
     132AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/2/pre/* .], 0)
     133AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o ConvexEnvelope NonConvexEnvelope], 0, [stdout], [stderr])
     134AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/2/post/$file], 0, [ignore], [ignore])
     135AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/2/post/$file], 0, [ignore], [ignore])
     136AT_CHECK([fgrep "RESULT: The summed volume is 16.401577 angstrom^3" stdout], 0, [ignore], [ignore])
     137AT_CHECK([diff ConvexEnvelope.dat NonConvexEnvelope.dat], 0, [ignore], [ignore])
     138AT_CLEANUP
     139
     140# 3. Big Non convex tesselation
     141AT_SETUP([Tesselation - Big non-Convex Envelope])
     142AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/3/pre/* .], 0)
     143AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 4. NonConvexEnvelope], 0, [stdout], [stderr])
     144AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/3/post/$file], 0, [ignore], [ignore])
     145AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/3/post/$file], 0, [ignore], [ignore])
     146AT_CLEANUP
     147
     148# 4. Big convex tesselation - is not working yet
     149#AT_SETUP([Tesselation - big convex Envelope])
     150#AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/4/pre/* .], 0)
     151#AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o ConvexEnvelope NonConvexEnvelope], 0, [stdout], [stderr])
     152#AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/4/post/$file], 0, [ignore], [ignore])
     153#AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/4/post/$file], 0, [ignore], [ignore])
     154#AT_CHECK([fgrep "RESULT: The summed volume is 16.401577 angstrom^3" stdout], 0, [ignore], [ignore])
     155#AT_CLEANUP
     156
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