Changeset 86cff86

Timestamp:

Jul 7, 2010, 11:53:05 AM (15 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:

ed6dd8

Parents:

192f6e

Message:

InputAction now parses all possible formats, not only pcp.

• new function FormatParserStorage::get() that checks on the suffix and calls the load() function of the respective specialized FormatParser.
• InputAction changed such that ...
  • prefix and suffix are extracted.
  • FormatParserStorage::get() is used.
  • empty configs are handled, too.
• FormatParserStorage::ParserSuffix changed, removed ".conf".
• TESTFIX: renamed all files to diff accordingly: .conf.xyz -> .xyz, .conf.in -> .in
• BUGFIX: xyz files were written without initial tab in front of comment, fix in ParserUnitTest necessary (i.e. a tab was missing there as we always write it now)
• ChangeElementAction: now needs --atom-by-id and takes the element as argument

Files:

• src/Actions/AtomAction/ChangeElementAction.cpp (modified) (1 diff)
• src/Actions/MapOfActions.cpp (modified) (1 diff)
• src/Actions/WorldAction/InputAction.cpp (modified) (2 diffs)
• src/Parser/FormatParserStorage.cpp (modified) (2 diffs)
• src/Parser/FormatParserStorage.hpp (modified) (1 diff)
• src/Parser/XyzParser.cpp (modified) (2 diffs)
• src/unittests/ParserUnitTest.cpp (modified) (1 diff)
• tests/regression/Domain/6/post/test-x.xyz (moved) (moved from tests/regression/Domain/6/post/test-x.conf.xyz )
• tests/regression/Domain/6/post/test-y.xyz (moved) (moved from tests/regression/Domain/6/post/test-y.conf.xyz )
• tests/regression/Domain/6/post/test-z.xyz (moved) (moved from tests/regression/Domain/6/post/test-z.conf.xyz )
• tests/regression/Domain/6/post/test.xyz (moved) (moved from tests/regression/Domain/6/post/test.conf.xyz )
• tests/regression/Fragmentation/2/post/BondFragment0.xyz (moved) (moved from tests/regression/Fragmentation/2/post/BondFragment0.conf.xyz )
• tests/regression/Fragmentation/2/post/BondFragment1.xyz (moved) (moved from tests/regression/Fragmentation/2/post/BondFragment1.conf.xyz )
• tests/regression/Fragmentation/2/post/BondFragment2.xyz (moved) (moved from tests/regression/Fragmentation/2/post/BondFragment2.conf.xyz )
• tests/regression/Fragmentation/2/post/BondFragment3.xyz (moved) (moved from tests/regression/Fragmentation/2/post/BondFragment3.conf.xyz )
• tests/regression/Fragmentation/2/post/BondFragment4.xyz (moved) (moved from tests/regression/Fragmentation/2/post/BondFragment4.conf.xyz )
• tests/regression/Molecules/6/post/test2.conf (moved) (moved from tests/regression/Simple_configuration/4/post/test.conf ) (4 diffs)
• tests/regression/Molecules/6/pre/test2.conf (added)
• tests/regression/Simple_configuration/2/post/test.in (moved) (moved from tests/regression/Simple_configuration/2/post/test.conf.in )
• tests/regression/Simple_configuration/2/post/test.xyz (moved) (moved from tests/regression/Simple_configuration/2/post/test.conf.xyz )
• tests/regression/Simple_configuration/3/post/test.in (moved) (moved from tests/regression/Simple_configuration/3/post/test.conf.in )
• tests/regression/Simple_configuration/3/post/test.xyz (moved) (moved from tests/regression/Simple_configuration/3/post/test.conf.xyz )
• tests/regression/Simple_configuration/3/post/test2.conf (moved) (moved from tests/regression/Simple_configuration/4/pre/test.conf ) (4 diffs)
• tests/regression/Simple_configuration/3/post/test2.in (added)
• tests/regression/Simple_configuration/3/post/test2.xyz (added)
• tests/regression/Simple_configuration/4/post/test.conf.xyz (deleted)
• tests/regression/Simple_configuration/4/post/test.xyz (added)
• tests/regression/Simple_configuration/4/pre/test.xyz (added)
• tests/regression/Simple_configuration/5/post/test.in (moved) (moved from tests/regression/Simple_configuration/5/post/test.conf.in )
• tests/regression/Simple_configuration/5/post/test.xyz (moved) (moved from tests/regression/Simple_configuration/5/post/test.conf.xyz )
• tests/regression/Simple_configuration/8/post/test.xyz (moved) (moved from tests/regression/Simple_configuration/8/post/test.conf.xyz )
• tests/regression/Simple_configuration/8/post/test.xyz-sorted (added)
• tests/regression/testsuite-domain.at (modified) (1 diff)
• tests/regression/testsuite-simple_configuration.at (modified) (5 diffs)

src/Actions/AtomAction/ChangeElementAction.cpp

@@ -38 +38 @@
   std::vector<element *> elements;
 
-  dialog->queryAtom(NAME, &first, MapOfActions::getInstance().getDescription(NAME));
-  dialog->queryElement("element", &elements, MapOfActions::getInstance().getDescription("element"));
+  dialog->queryElement(NAME, &elements, MapOfActions::getInstance().getDescription(NAME));
+  dialog->queryAtom("atom-by-id", &first, MapOfActions::getInstance().getDescription("atom-by-id"));
 
   if(dialog->display()) {

src/Actions/MapOfActions.cpp

@@ -270 +270 @@
   TypeMap["center-in-box"] = Box;
   TypeMap["change-box"] = Box;
-  TypeMap["change-element"] = Atom;
+  TypeMap["change-element"] = Element;
   TypeMap["change-molname"] = String;
   TypeMap["convex-envelope"] = Molecule;

src/Actions/WorldAction/InputAction.cpp

@@ -38 +38 @@
   MoleculeListClass *molecules = World::getInstance().getMolecules();
   molecule *mol = NULL;
-  string filename;
+  std::string filename;
   std::ifstream test;
 
@@ -45 +45 @@
   if(dialog->display()) {
     DoLog(0) && (Log() << Verbose(0) << "Config file given." << endl);
-    std::string FilenamePrefix = filename.substr(0,filename.find('.'));
-    FormatParserStorage::getInstance().SetOutputPrefixForAll(FilenamePrefix);
-    DoLog(1) && (Log() << Verbose(1) << "Setting config file name prefix to " << FilenamePrefix << "." << endl);
-    test.open(filename.c_str());
-    if (test == NULL) {
-      DoLog(1) && (Log() << Verbose(1) << "Specified config file " << filename << " not found." << endl);
+    if (filename.find('.') != string::npos) {
+      std::string FilenamePrefix = filename.substr(0,filename.find_last_of('.'));
+      std::string FilenameSuffix = filename.substr(filename.find_last_of('.')+1, filename.length());
+      DoLog(1) && (Log() << Verbose(1) << "Setting config file name prefix to " << FilenamePrefix << "." << endl);
+      test.open(filename.c_str());
+      if (test == NULL) {
+        DoLog(1) && (Log() << Verbose(1) << "Specified config file " << filename << " not found." << endl);
+      } else {
+        DoLog(1) && (Log() << Verbose(1) << "Specified config file found, parsing ... ");
+        FormatParserStorage::getInstance().get((std::istream &)test, FilenameSuffix);
+        test.close();
+      }
+      FormatParserStorage::getInstance().SetOutputPrefixForAll(FilenamePrefix);
+      // set mol to first active molecule
+      if (molecules->ListOfMolecules.size() != 0) {
+        for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
+          if ((*ListRunner)->ActiveFlag) {
+            mol = *ListRunner;
+            break;
+          }
+      }
+      if (mol == NULL) {
+        mol = World::getInstance().createMolecule();
+        mol->ActiveFlag = true;
+        molecules->insert(mol);
+      }
+      mol->SetNameFromFilename(filename.substr(0,filename.find('.')).c_str());
     } else {
-      DoLog(1) && (Log() << Verbose(1) << "Specified config file found, parsing ... ");
-      FormatParserStorage::getInstance().getPcp().load(&test);
-      test.close();
+      DoeLog(1) && (eLog() << Verbose(1) << "Input file does not have a suffix, cannot recognize format." << endl);
     }
-    // set mol to first active molecule
-    if (molecules->ListOfMolecules.size() != 0) {
-      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
-        if ((*ListRunner)->ActiveFlag) {
-          mol = *ListRunner;
-          break;
-        }
-    }
-    if (mol == NULL) {
-      mol = World::getInstance().createMolecule();
-      mol->ActiveFlag = true;
-      molecules->insert(mol);
-    }
-    mol->SetNameFromFilename(filename.c_str());
     delete dialog;
     return Action::success;

src/Parser/FormatParserStorage.cpp

@@ -42 +42 @@
   ParserSuffix.resize(ParserTypes_end, "");
 
-  ParserSuffix[mpqc] = "conf.in";
+  ParserSuffix[mpqc] = "in";
   ParserSuffix[pcp] = "conf";
-  ParserSuffix[tremolo] = "conf.data";
-  ParserSuffix[xyz] = "conf.xyz";
+  ParserSuffix[tremolo] = "data";
+  ParserSuffix[xyz] = "xyz";
 }
 
@@ -133 +133 @@
 }
 
+/** Parses an istream depending on its suffix
+ * \param &input input stream
+ * \param suffix
+ * \return true - parsing ok, false - suffix unknown
+ */
+bool FormatParserStorage::get(std::istream &input, std::string suffix)
+{
+  if (suffix == ParserSuffix[mpqc]) {
+    getMpqc().load(&input);
+  } else if (suffix == ParserSuffix[pcp]) {
+    getPcp().load(&input);
+  } else if (suffix == ParserSuffix[tremolo]) {
+    getTremolo().load(&input);
+  } else if (suffix == ParserSuffix[xyz]) {
+    getXyz().load(&input);
+  } else {
+    DoeLog(1) && (eLog() << Verbose(1) << "Unknown suffix to for FormatParserStorage::get()." << endl);
+    return false;
+  }
+  return true;
+}
+
 /** Returns reference to the output MpqcParser, adds if not present.
  * \return reference to the output MpqcParser

src/Parser/FormatParserStorage.hpp

@@ -41 +41 @@
   void addXyz();
 
+  bool get(std::istream &input, std::string suffix);
   MpqcParser &getMpqc();
   PcpParser &getPcp();

src/Parser/XyzParser.cpp

@@ -59 +59 @@
   if (comment == "") {
     time_t now = time((time_t *)NULL);   // Get the system time and put it into 'now' as 'calender time'
-    comment = "\tCreated by molecuilder on ";
+    comment = "Created by molecuilder on ";
     // ctime ends in \n\0, we have to cut away the newline
     std::string time(ctime(&now));
@@ -68 +68 @@
       comment += time;
   }
-  *file << World::getInstance().numAtoms() << endl << comment << endl;
+  *file << World::getInstance().numAtoms() << endl << "\t" << comment << endl;
 
   vector<atom*> atoms = World::getInstance().getAllAtoms();

src/unittests/ParserUnitTest.cpp

@@ -131 +131 @@
 \tmolecule = $:molecule\n\
 )\n";
-static string waterXyz = "3\nH2O: water molecule\nO\t0\t0\t0\nH\t0.758602\t0\t0.504284\nH\t0.758602\t0\t-0.504284\n";
+static string waterXyz = "3\n\tH2O: water molecule\nO\t0\t0\t0\nH\t0.758602\t0\t0.504284\nH\t0.758602\t0\t-0.504284\n";
 static string Tremolo_Atomdata1 = "# ATOMDATA\tId\tname\tType\tx=3\n";
 static string Tremolo_Atomdata2 = "#\n#ATOMDATA Id name Type x=3\n1 hydrogen H 3.0 4.5 0.1\n\n";

tests/regression/Molecules/6/post/test2.conf

@@ -35 +35 @@
 RelEpsTotalE    1e-07   # relative change in total energy
 RelEpsKineticE  1e-05   # relative change in kinetic energy
-MaxMinStopStep  2       # check every ..th steps
+MaxMinStopStep  10      # check every ..th steps
 MaxMinGapStopStep       1       # check every ..th steps
 
@@ -42 +42 @@
 InitRelEpsTotalE        1e-05   # relative change in total energy
 InitRelEpsKineticE      0.0001  # relative change in kinetic energy
-InitMaxMinStopStep      2       # check every ..th steps
+InitMaxMinStopStep      10      # check every ..th steps
 InitMaxMinGapStopStep   1       # check every ..th steps
 
@@ -55 +55 @@
 RiemannTensor   0       # (Use metric)
 PsiType         0       # 0 - doubly occupied, 1 - SpinUp,SpinDown
-MaxPsiDouble    2       # here: specifying both maximum number of SpinUp- and -Down-states
-PsiMaxNoUp      2       # here: specifying maximum number of SpinUp-states
-PsiMaxNoDown    2       # here: specifying maximum number of SpinDown-states
+MaxPsiDouble    10      # here: specifying both maximum number of SpinUp- and -Down-states
+PsiMaxNoUp      10      # here: specifying maximum number of SpinUp-states
+PsiMaxNoDown    10      # here: specifying maximum number of SpinDown-states
 AddPsis         0       # Additional unoccupied Psis for bandgap determination
 
@@ -64 +64 @@
 IsAngstroem     1       # 0 - Bohr, 1 - Angstroem
 RelativeCoord   0       # whether ion coordinates are relative (1) or absolute (0)
-MaxTypes        1       # maximum number of different ion types
+MaxTypes        2       # maximum number of different ion types
 
 # Ion type data (PP = PseudoPotential, Z = atomic number)
 #Ion_TypeNr.    Amount  Z       RGauss  L_Max(PP)L_Loc(PP)IonMass       # chemical name, symbol
-Ion_Type1       1       6       1.0     3       3       12.01100000000  Carbon  C
+Ion_Type1       8       1       1.0     3       3       1.00800000000   Hydrogen        H
+Ion_Type2       3       6       1.0     3       3       12.01100000000  Carbon  C
 #Ion_TypeNr._Nr.R[0]    R[1]    R[2]    MoveType (0 MoveIon, 1 FixedIon)
-Ion_Type1_1     10.000000000    10.000000000    10.000000000    0 # molecule nr 0
+Ion_Type1_1     8.782085945     1.645886050     1.645886050     0 # molecule nr 0
+Ion_Type1_2     8.782085945     1.645886050     3.425886024     0 # molecule nr 1
+Ion_Type1_3     9.672039608     2.904536878     2.535886037     0 # molecule nr 2
+Ion_Type1_4     7.532785963     3.787886018     1.645886050     0 # molecule nr 3
+Ion_Type1_5     7.532785963     3.787886018     3.425886024     0 # molecule nr 4
+Ion_Type1_6     5.393632318     2.904536877     2.535886037     0 # molecule nr 5
+Ion_Type1_7     6.283585982     1.645886050     1.645886050     0 # molecule nr 6
+Ion_Type1_8     6.283585982     1.645886050     3.425886024     0 # molecule nr 7
+Ion_Type2_1     8.782085945     2.275186040     2.535886037     0 # molecule nr 8
+Ion_Type2_2     7.532785963     3.158586027     2.535886037     0 # molecule nr 9
+Ion_Type2_3     6.283585982     2.275186040     2.535886037     0 # molecule nr 10

tests/regression/Simple_configuration/3/post/test2.conf

@@ -35 +35 @@
 RelEpsTotalE    1e-07   # relative change in total energy
 RelEpsKineticE  1e-05   # relative change in kinetic energy
-MaxMinStopStep  0       # check every ..th steps
+MaxMinStopStep  1       # check every ..th steps
 MaxMinGapStopStep       0       # check every ..th steps
 
@@ -42 +42 @@
 InitRelEpsTotalE        1e-05   # relative change in total energy
 InitRelEpsKineticE      0.0001  # relative change in kinetic energy
-InitMaxMinStopStep      0       # check every ..th steps
+InitMaxMinStopStep      1       # check every ..th steps
 InitMaxMinGapStopStep   0       # check every ..th steps
 
@@ -54 +54 @@
 Level0Factor    2       # factor by which node number increases from S to 0 level
 RiemannTensor   0       # (Use metric)
-PsiType         0       # 0 - doubly occupied, 1 - SpinUp,SpinDown
+PsiType         1       # 0 - doubly occupied, 1 - SpinUp,SpinDown
 MaxPsiDouble    0       # here: specifying both maximum number of SpinUp- and -Down-states
 PsiMaxNoUp      0       # here: specifying maximum number of SpinUp-states
-PsiMaxNoDown    0       # here: specifying maximum number of SpinDown-states
+PsiMaxNoDown    1       # here: specifying maximum number of SpinDown-states
 AddPsis         0       # Additional unoccupied Psis for bandgap determination
 
@@ -70 +70 @@
 Ion_Type1       1       1       1.0     3       3       1.00800000000   Hydrogen        H
 #Ion_TypeNr._Nr.R[0]    R[1]    R[2]    MoveType (0 MoveIon, 1 FixedIon)
-Ion_Type1_1     10.000000000    10.000000000    10.000000000    0 # molecule nr 0
+Ion_Type1_1     0.000000000     0.000000000     -1.000000000    0 # molecule nr 0

tests/regression/testsuite-domain.at

@@ -45 +45 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/pre/test.conf .], 0)
 AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -o xyz -d "1, 1, 1"], 0, [stdout], [stderr])
-AT_CHECK([file=test.conf.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
-AT_CHECK([file=test.conf.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
-AT_CHECK([file=test.conf.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
+AT_CHECK([file=test.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
+AT_CHECK([file=test.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
+AT_CHECK([file=test.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/pre/test.conf test-x.conf], 0)
 AT_CHECK([../../molecuilder -i test-x.conf -e ${abs_top_srcdir}/src/ -o xyz -d "2, 1, 1"], 0, [stdout], [stderr])
-AT_CHECK([file=test-x.conf.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
-AT_CHECK([file=test-x.conf.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
-AT_CHECK([file=test-x.conf.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
+AT_CHECK([file=test-x.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
+AT_CHECK([file=test-x.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
+AT_CHECK([file=test-x.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/pre/test.conf test-y.conf], 0)
 AT_CHECK([../../molecuilder -i test-y.conf -e ${abs_top_srcdir}/src/ -o xyz -d "1, 2, 1"], 0, [stdout], [stderr])
-AT_CHECK([file=test-y.conf.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
-AT_CHECK([file=test-y.conf.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
-AT_CHECK([file=test-y.conf.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
+AT_CHECK([file=test-y.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
+AT_CHECK([file=test-y.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
+AT_CHECK([file=test-y.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/pre/test.conf test-z.conf], 0)
 AT_CHECK([../../molecuilder -i test-z.conf -e ${abs_top_srcdir}/src/ -o xyz -d "1, 1, 2"], 0, [stdout], [stderr])
-AT_CHECK([file=test-z.conf.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
-AT_CHECK([file=test-z.conf.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
-AT_CHECK([file=test-z.conf.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
+AT_CHECK([file=test-z.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
+AT_CHECK([file=test-z.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
+AT_CHECK([file=test-z.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
 #AT_CHECK([/bin/false], 12, [ignore], [ignore])
 AT_CLEANUP

tests/regression/testsuite-simple_configuration.at

@@ -18 +18 @@
 ], [ignore])
 AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
-AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
-AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
+AT_CHECK([file=test.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
+AT_CHECK([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP
 
@@ -27 +27 @@
 AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -o mpqc pcp xyz -a 1 --position "10., 10., 10."], 0, [ignore], [ignore])
 AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
-AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
-AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
+AT_CHECK([file=test.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
+AT_CHECK([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
 AT_CHECK([../../molecuilder -i test2.conf -e ${abs_top_srcdir}/src/ -o mpqc pcp xyz -a 1 --position "0., 0., -1."], 0, [ignore], [ignore])
 AT_CHECK([file=test2.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
-AT_CHECK([file=test2.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
-AT_CHECK([file=test2.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
+AT_CHECK([file=test2.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
+AT_CHECK([file=test2.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP
 
@@ -38 +38 @@
 AT_SETUP([Simple configuration - Changing element])
 AT_KEYWORDS([configuration])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/pre/test.conf test.conf], 0)
-AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -E 0 --element 6], 0, [ignore], [ignore])
-AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/post/$file], 0, [ignore], [ignore])
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/pre/test.xyz test.xyz], 0)
+AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ -E 6 --atom-by-id 0], 0, [ignore], [ignore])
+AT_CHECK([file=test.xyz; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP
 
@@ -49 +49 @@
 AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -o mpqc pcp xyz -r 0], 0, [ignore], [ignore])
 AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
-AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
-AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
+AT_CHECK([file=test.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
+AT_CHECK([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP
 
@@ -80 +80 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/pre/test.* .], 0)
 AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -o xyz -R 7. --position "7.283585982, 3.275186040, 3.535886037"], 0, [stdout], [stderr])
-AT_CHECK([sort -n test.conf.xyz | grep -v "Created by" >test.conf.xyz-sorted], 0, [ignore], [ignore])
-AT_CHECK([sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/post/test.conf.xyz  | grep -v "Created by" >${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/post/test.conf.xyz-sorted], 0, [ignore], [ignore])
-AT_CHECK([file=test.conf.xyz-sorted; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/post/$file], 0, [ignore], [ignore])
+AT_CHECK([sort -n test.xyz | grep -v "Created by" >test.xyz-sorted], 0, [ignore], [ignore])
+AT_CHECK([sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/post/test.xyz  | grep -v "Created by" >${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/post/test.xyz-sorted], 0, [ignore], [ignore])
+AT_CHECK([file=test.xyz-sorted; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP