Changeset 2382d7


Ignore:
Timestamp:
Jun 13, 2012, 5:39:02 PM (13 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:
8ea3e7
Parents:
7951b9
git-author:
Frederik Heber <heber@…> (05/10/12 08:57:41)
git-committer:
Frederik Heber <heber@…> (06/13/12 17:39:02)
Message:

FillRegularGrid now uses std::vector<unsigned int> instead of Vector.

  • with the new validators it possible to constrain number of entries to 3 easily.
  • added unimplemented StreamOperator for vectopr<unsigned int>.
  • TESTFIX: option mesh-size needs its arguments now as 5 5 11, not "5,5,11", hence changed regression tests in Filling/RegularGrid.
Files:
5 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/FillAction/FillRegularGridAction.def

    r7951b9 r2382d7  
    1515// ValueStorage by the token "Z" -> first column: int, Z, "Z"
    1616// "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
    17 #define paramtypes (Vector)(Vector)(double)(double)(double)(double)(bool)
     17#define paramtypes (std::vector< unsigned int >)(Vector)(double)(double)(double)(double)(bool)
    1818#define paramtokens ("mesh-size")("mesh-offset")("min-distance")("tesselation-radius")("random-atom-displacement")("random-molecule-displacement")("DoRotate")
    1919#define paramdescriptions ("number of points per axis")("offset to start of partition, must be in [0,1)")("Minimum distance to other atoms")("radius of rolling sphere in tesselating selected molecule's surfaces")("magnitude of random atom displacement")("magnitude of random molecule displacement")("whether to rotate or not")

  • src/Filling/Mesh/CubeMesh.cpp

    r7951b9 r2382d7  
    4141CubeMesh::CubeMesh(const Vector &counts, const Vector &offset, const RealSpaceMatrix &M)
    4242{
    43   RealSpaceMatrix partition;
    44   int n[NDIM];
    45 
    4643#ifndef NDEBUG
    4744  for (size_t i=0;i<NDIM;++i) {
    … …  
    4946        "CubeMesh::CubeMesh() - offset coordinates must be in [0,1) but offset["
    5047        +toString(i)+"] is "+toString(offset[i])+".");
    51     ASSERT(counts[i] != 0.,
    52         "CubeMesh::CubeMesh() - counts["+toString(i)+"] must be != "+toString(counts[i])+".");
     48    ASSERT(counts[i] == (int)counts[i],
     49        "CubeMesh::CubeMesh() - counts["+toString(i)+"] must be integer: != "+toString(counts[i])+".");
    5350  }
    5451#endif
     52
     53  std::vector< unsigned int> size_counts;
     54  for (size_t i=0;i<NDIM;++i) {
     55    size_counts.push_back( (int)counts[i] );
     56  }
     57  init(size_counts, offset, M);
     58}
     59
     60/** Constructor for class CubeMesh.
     61 *
     62 * Here, we generate nodes homogeneously distributed over a cuboid.
     63 *
     64 * \a offset shifts the coordinates, e.g. if counts = 2, we would set nodes at
     65 * 0 and 0.5 with offset = 0 and 0.4999... and 0.9999.. with offset = 0.999...
     66 *
     67 * @param counts number of points per axis
     68 * @param offset offset Vector (coordinates in [0,1))
     69 * @param M matrix to transform the default cuboid from (0,0,0) to (1,1,1).
     70 */
     71CubeMesh::CubeMesh(const std::vector< unsigned int > &counts, const Vector &offset, const RealSpaceMatrix &M)
     72{
     73  ASSERT(counts.size() == 3,
     74      "CubeMesh::CubeMesh() - counts does not have three but "
     75      +toString(counts.size())+" entries.");
     76
     77  init(counts, offset, M);
     78}
     79
     80void CubeMesh::init(const std::vector< unsigned int > &counts, const Vector &offset, const RealSpaceMatrix &M)
     81{
     82  RealSpaceMatrix partition;
    5583
    5684  partition.setZero();
    … …  
    5987  LOG(1, "INFO: partition is " << partition << ".");
    6088
    61 
    6289  // go over [0,1]^3 filler grid
     90  int n[NDIM];
    6391  for (n[0] = 0; n[0] < counts[0]; n[0]++)
    6492    for (n[1] = 0; n[1] < counts[1]; n[1]++)

  • src/Filling/Mesh/CubeMesh.hpp

    r7951b9 r2382d7  
    2525public:
    2626  CubeMesh(const Vector &counts, const Vector &offset, const RealSpaceMatrix &M);
     27  CubeMesh(const std::vector< unsigned int > &counts, const Vector &offset, const RealSpaceMatrix &M);
    2728  virtual ~CubeMesh();
    2829
     30  void init(const std::vector< unsigned int > &counts, const Vector &offset, const RealSpaceMatrix &M);
    2931};
    3032

  • tests/regression/Filling/RegularGrid/testsuite-molecules-fill-regular-grid-with-surface.at

    r7951b9 r2382d7  
    88AT_CHECK([chmod u+w $file], 0)
    99# check that specifying radius but selecting no atoms is wrong
    10 AT_CHECK([../../molecuilder --parse-tremolo-potentials ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/sles.potentials -i $file -B "14.199,0,21.6216,0,0,33.9159" --load ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/water.data --select-molecule-by-order -1 --fill-regular-grid --mesh-size "5,7,11" --mesh-offset "0.5,0.5,0.5" --tesselation-radius 10 --min-distance .5], 5, [stdout], [stderr])
     10AT_CHECK([../../molecuilder --parse-tremolo-potentials ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/sles.potentials -i $file -B "14.199,0,21.6216,0,0,33.9159" --load ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/water.data --select-molecule-by-order -1 --fill-regular-grid --mesh-size 5 7 11 --mesh-offset "0.5,0.5,0.5" --tesselation-radius 10 --min-distance .5], 5, [stdout], [stderr])
    1111
    1212AT_CLEANUP
    … …  
    1818AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/double_sles.data $file], 0)
    1919AT_CHECK([chmod u+w $file], 0)
    20 AT_CHECK([../../molecuilder --parse-tremolo-potentials ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/sles.potentials -i $file --select-all-atoms -B "14.199,0,21.6216,0,0,33.9159" --load ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/water.data --select-molecule-by-order -1 --fill-regular-grid --mesh-size "5,7,11" --mesh-offset "0.5,0.5,0.5" --tesselation-radius 10 --min-distance .5], 0, [stdout], [stderr])
     20AT_CHECK([../../molecuilder --parse-tremolo-potentials ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/sles.potentials -i $file --select-all-atoms -B "14.199,0,21.6216,0,0,33.9159" --load ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/water.data --select-molecule-by-order -1 --fill-regular-grid --mesh-size 5 7 11 --mesh-offset "0.5,0.5,0.5" --tesselation-radius 10 --min-distance .5], 0, [stdout], [stderr])
    2121AT_CHECK([grep "366 out of 385 returned true from predicate" stdout], 0, [ignore], [ignore])
    2222AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/post/$file], 0, [ignore], [ignore])
    … …  
    3131AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/double_sles.data $file], 0)
    3232AT_CHECK([chmod u+w $file], 0)
    33 AT_CHECK([../../molecuilder --parse-tremolo-potentials ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/sles.potentials -i $file --select-all-atoms -B "14.199,0,21.6216,0,0,33.9159" --load ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/water.data --select-molecule-by-order -1 --fill-regular-grid --mesh-size "5,7,11" --mesh-offset "0.5,0.5,0.5" --tesselation-radius 10 --min-distance .5 --undo], 0, [stdout], [stderr])
     33AT_CHECK([../../molecuilder --parse-tremolo-potentials ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/sles.potentials -i $file --select-all-atoms -B "14.199,0,21.6216,0,0,33.9159" --load ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/water.data --select-molecule-by-order -1 --fill-regular-grid --mesh-size 5 7 11 --mesh-offset "0.5,0.5,0.5" --tesselation-radius 10 --min-distance .5 --undo], 0, [stdout], [stderr])
    3434AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/post/double_sles-undo.data], 0, [ignore], [ignore])
    3535
    … …  
    4343AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/double_sles.data $file], 0)
    4444AT_CHECK([chmod u+w $file], 0)
    45 AT_CHECK([../../molecuilder --parse-tremolo-potentials ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/sles.potentials -i $file --select-all-atoms -B "14.199,0,21.6216,0,0,33.9159" --load ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/water.data --select-molecule-by-order -1 --fill-regular-grid --mesh-size "5,7,11" --mesh-offset "0.5,0.5,0.5" --tesselation-radius 10 --min-distance .5 --undo --redo], 0, [stdout], [stderr])
     45AT_CHECK([../../molecuilder --parse-tremolo-potentials ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/sles.potentials -i $file --select-all-atoms -B "14.199,0,21.6216,0,0,33.9159" --load ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/water.data --select-molecule-by-order -1 --fill-regular-grid --mesh-size 5 7 11 --mesh-offset "0.5,0.5,0.5" --tesselation-radius 10 --min-distance .5 --undo --redo], 0, [stdout], [stderr])
    4646AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/post/$file], 0, [ignore], [ignore])
    4747

  • tests/regression/Filling/RegularGrid/testsuite-molecules-fill-regular-grid.at

    r7951b9 r2382d7  
    77AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/single_sles.data $file], 0)
    88AT_CHECK([chmod u+w $file], 0)
    9 AT_CHECK([../../molecuilder --parse-tremolo-potentials ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/sles.potentials -i $file -B "14.199,0,16.6216,0,0,33.9159" --load ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/water.data --select-molecule-by-order -1 --fill-regular-grid --mesh-size "5,5,11" --mesh-offset "0.5,0.5,0.5" --min-distance 3.1], 0, [stdout], [stderr])
     9AT_CHECK([../../molecuilder --parse-tremolo-potentials ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/sles.potentials -i $file -B "14.199,0,16.6216,0,0,33.9159" --load ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/water.data --select-molecule-by-order -1 --fill-regular-grid --mesh-size 5 5 11 --mesh-offset "0.5,0.5,0.5" --min-distance 3.1], 0, [stdout], [stderr])
    1010AT_CHECK([grep "222 out of 275 returned true from predicate" stdout], 0, [ignore], [ignore])
    1111AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/post/$file], 0, [ignore], [ignore])
    … …  
    2020AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/single_sles.data $file], 0)
    2121AT_CHECK([chmod u+w $file], 0)
    22 AT_CHECK([../../molecuilder --parse-tremolo-potentials ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/sles.potentials -i $file -B "14.199,0,16.6216,0,0,33.9159" --load ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/water.data --select-molecule-by-order -1 --fill-regular-grid --mesh-size "5,5,11" --mesh-offset "0.5,0.5,0.5" --min-distance 3.1 --undo], 0, [stdout], [stderr])
     22AT_CHECK([../../molecuilder --parse-tremolo-potentials ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/sles.potentials -i $file -B "14.199,0,16.6216,0,0,33.9159" --load ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/water.data --select-molecule-by-order -1 --fill-regular-grid --mesh-size 5 5 11 --mesh-offset "0.5,0.5,0.5" --min-distance 3.1 --undo], 0, [stdout], [stderr])
    2323AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/post/single_sles-undo.data], 0, [ignore], [ignore])
    2424
    … …  
    3232AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/single_sles.data $file], 0)
    3333AT_CHECK([chmod u+w $file], 0)
    34 AT_CHECK([../../molecuilder --parse-tremolo-potentials ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/sles.potentials -i $file -B "14.199,0,16.6216,0,0,33.9159" --load ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/water.data --select-molecule-by-order -1 --fill-regular-grid --mesh-size "5,5,11" --mesh-offset "0.5,0.5,0.5" --min-distance 3.1 --undo --redo], 0, [stdout], [stderr])
     34AT_CHECK([../../molecuilder --parse-tremolo-potentials ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/sles.potentials -i $file -B "14.199,0,16.6216,0,0,33.9159" --load ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/pre/water.data --select-molecule-by-order -1 --fill-regular-grid --mesh-size 5 5 11 --mesh-offset "0.5,0.5,0.5" --min-distance 3.1 --undo --redo], 0, [stdout], [stderr])
    3535AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Filling/RegularGrid/post/$file], 0, [ignore], [ignore])
    3636
Note: See TracChangeset for help on using the changeset viewer.