Ignore:
Timestamp:
Jun 12, 2010, 10:19:48 PM (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:
55240c4
Parents:
43dad6
git-author:
Frederik Heber <heber@…> (06/12/10 21:59:36)
git-committer:
Frederik Heber <heber@…> (06/12/10 22:19:48)
Message:

Extended PcpParser, completed MpqcParser.

  • BUGFIX: ConfigFileBuffer::InitFileBuffer() did not clear istream before re-use.
  • class PcpParser
    • operator== - compares every variable by ASSERTs.
    • constructor initializes variables all to sensible values.
  • class MpqcParser
    • new function save() - calls either SaveHessian() or Save() according to flag HessianPresent.
    • new functions SaveHessian() and Save() which contain both parts of config::SaveMPQC().
    • no function load() - this functionality has not been present and is not needed right away.
  • Extended ParserUnitTest
    • new test case readwritePcpTest() - load from static string, store, load again and compare both.
    • new test case writeMpqcTest() - write a state of the world and compare to one from static string.
    • all static strings have been made static and set before all functions.
    • new string containing an example pcp config file.
    • we check whether hydrogen and oxygen are known to the world as we test with these two elements.
  • atom::OutputMPQCLine() - now takes ostream instead of ofstream.
  • config::SaveMPQC() - adapted accordingly (cast is necessary)
File:
1 edited

Legend:

Unmodified
Added
Removed

  • src/unittests/ParserUnitTest.cpp

    r43dad6 r1b2d30  
    1212#include <cppunit/ui/text/TestRunner.h>
    1313
     14#include "Parser/MpqcParser.hpp"
     15#include "Parser/PcpParser.hpp"
     16#include "Parser/TremoloParser.hpp"
    1417#include "Parser/XyzParser.hpp"
    15 #include "Parser/TremoloParser.hpp"
    1618#include "World.hpp"
    1719#include "atom.hpp"
    … …  
    2931CPPUNIT_TEST_SUITE_REGISTRATION( ParserUnitTest );
    3032
     33static string waterPcp = "# ParallelCarParinello - main configuration file - created with molecuilder\n\
     34\n\
     35mainname\tpcp\t# programm name (for runtime files)\n\
     36defaultpath\not specified\t# where to put files during runtime\n\
     37pseudopotpath\not specified\t# where to find pseudopotentials\n\
     38\n\
     39ProcPEGamma\t8\t# for parallel computing: share constants\n\
     40ProcPEPsi\t1\t# for parallel computing: share wave functions\n\
     41DoOutVis\t0\t# Output data for OpenDX\n\
     42DoOutMes\t1\t# Output data for measurements\n\
     43DoOutOrbitals\t0\t# Output all Orbitals\n\
     44DoOutCurr\t0\t# Ouput current density for OpenDx\n\
     45DoOutNICS\t0\t# Output Nucleus independent current shieldings\n\
     46DoPerturbation\t0\t# Do perturbation calculate and determine susceptibility and shielding\n\
     47DoFullCurrent\t0\t# Do full perturbation\n\
     48DoConstrainedMD\t0\t# Do perform a constrained (>0, relating to current MD step) instead of unconstrained (0) MD\n\
     49Thermostat\tBerendsen\t2.5\t# Which Thermostat and its parameters to use in MD case.\n\
     50CommonWannier\t0\t# Put virtual centers at indivual orbits, all common, merged by variance, to grid point, to cell center\n\
     51SawtoothStart\t0.01\t# Absolute value for smooth transition at cell border \n\
     52VectorPlane\t0\t# Cut plane axis (x, y or z: 0,1,2) for two-dim current vector plot\n\
     53VectorCut\t0\t# Cut plane axis value\n\
     54AddGramSch\t1\t# Additional GramSchmidtOrtogonalization to be safe\n\
     55Seed\t1\t# initial value for random seed for Psi coefficients\n\
     56\n\
     57MaxOuterStep\t0\t# number of MolecularDynamics/Structure optimization steps\n\
     58Deltat\t0.01\t# time per MD step\n\
     59OutVisStep\t10\t# Output visual data every ...th step\n\
     60OutSrcStep\t5\t# Output \"restart\" data every ..th step\n\
     61TargetTemp\t0.000950045\t# Target temperature\n\
     62MaxPsiStep\t3\t# number of Minimisation steps per state (0 - default)\n\
     63EpsWannier\t1e-07\t# tolerance value for spread minimisation of orbitals\n\
     64# Values specifying when to stop\n\
     65MaxMinStep\t100\t# Maximum number of steps\n\
     66RelEpsTotalE\t1e-07\t# relative change in total energy\n\
     67RelEpsKineticE\t1e-05\t# relative change in kinetic energy\n\
     68MaxMinStopStep\t0\t# check every ..th steps\n\
     69MaxMinGapStopStep\t1\t# check every ..th steps\n\
     70\n\
     71# Values specifying when to stop for INIT, otherwise same as above\n\
     72MaxInitMinStep\t100\t# Maximum number of steps\n\
     73InitRelEpsTotalE\t1e-05\t# relative change in total energy\n\
     74InitRelEpsKineticE\t0.0001\t# relative change in kinetic energy\n\
     75InitMaxMinStopStep\t0\t# check every ..th steps\n\
     76InitMaxMinGapStopStep\t1\t# check every ..th steps\n\
     77\n\
     78BoxLength\t# (Length of a unit cell)\n\
     7920\n\
     800\t20\n\
     810\t0\t20\n\
     82\n\
     83ECut\t128\t# energy cutoff for discretization in Hartrees\n\
     84MaxLevel\t5\t# number of different levels in the code, >=2\n\
     85Level0Factor\t2\t# factor by which node number increases from S to 0 level\n\
     86RiemannTensor\t0\t# (Use metric)\n\
     87PsiType\t0\t# 0 - doubly occupied, 1 - SpinUp,SpinDown\n\
     88MaxPsiDouble\t0\t# here: specifying both maximum number of SpinUp- and -Down-states\n\
     89PsiMaxNoUp\t0\t# here: specifying maximum number of SpinUp-states\n\
     90PsiMaxNoDown\t0\t# here: specifying maximum number of SpinDown-states\n\
     91AddPsis\t0\t# Additional unoccupied Psis for bandgap determination\n\
     92\n\
     93RCut\t20\t# R-cut for the ewald summation\n\
     94StructOpt\t0\t# Do structure optimization beforehand\n\
     95IsAngstroem\t1\t# 0 - Bohr, 1 - Angstroem\n\
     96RelativeCoord\t0\t# whether ion coordinates are relative (1) or absolute (0)\n\
     97MaxTypes\t2\t# maximum number of different ion types\n\
     98\n\
     99# Ion type data (PP = PseudoPotential, Z = atomic number)\n\
     100#Ion_TypeNr.\tAmount\tZ\tRGauss\tL_Max(PP)L_Loc(PP)IonMass\t# chemical name, symbol\n\
     101Ion_Type1\t2\t1\t1.0\t3\t3\t1.008\tHydrogen\tH\n\
     102Ion_Type2\t1\t8\t1.0\t3\t3\t15.999\tOxygen\tO\n\
     103#Ion_TypeNr._Nr.R[0]\tR[1]\tR[2]\tMoveType (0 MoveIon, 1 FixedIon)\n\
     104Ion_Type2_1\t0.000000000\t0.000000000\t0.000000000\t0 # molecule nr 0\n\
     105Ion_Type1_1\t0.758602\t0.000000000\t0.504284\t0 # molecule nr 1\n\
     106Ion_Type1_2\t0.758602\t0.000000000\t-0.504284\t0 # molecule nr 2\n";
     107static string waterMpqc ="% Created by MoleCuilder\n\
     108mpqc: (\n\
     109\tsavestate = no\n\
     110\tdo_gradient = yes\n\
     111\tmole<MBPT2>: (\n\
     112\t\tmaxiter = 200\n\
     113\t\tbasis = $:basis\n\
     114\t\tmolecule = $:molecule\n\
     115\t\treference<CLHF>: (\n\
     116\t\t\tbasis = $:basis\n\
     117\t\t\tmolecule = $:molecule\n\
     118\t\t)\n\
     119\t)\n\
     120)\n\
     121molecule<Molecule>: (\n\
     122\tunit = angstrom\n\
     123\t{ atoms geometry } = {\n\
     124\t\tO [ 0\t0\t0 ]\n\
     125\t\tH [ 0.758602\t0\t0.504284 ]\n\
     126\t\tH [ 0.758602\t0\t-0.504284 ]\n\
     127\t}\n\
     128)\n\
     129basis<GaussianBasisSet>: (\n\
     130\tname = \"3-21G\"\n\
     131\tmolecule = $:molecule\n\
     132)\n";
     133static string waterXyz = "3\nH2O: water molecule\nO\t0.000000\t0.000000\t0.000000\nH\t0.758602\t0.000000\t0.504284\nH\t0.758602\t0.000000\t-0.504284\n";
     134static string Tremolo_Atomdata1 = "# ATOMDATA\tId\tname\tType\tx=3\n";
     135static string Tremolo_Atomdata2 = "#\n#ATOMDATA Id name Type x=3\n1 hydrogen H 3.0 4.5 0.1\n\n";
     136static string Tremolo_invalidkey = "#\n#ATOMDATA Id name foo Type x=3\n\n\n";
     137static string Tremolo_velocity = "#\n#ATOMDATA Id name Type u=3\n1 hydrogen H 3.0 4.5 0.1\n\n";
     138static string Tremolo_neighbours = "#\n#ATOMDATA Id Type neighbors=2\n1 H 3 0\n2 H 3 0\n3 O 1 2\n";
     139static string Tremolo_improper = "#\n#ATOMDATA Id Type imprData\n8 H 9-10\n9 H 10-8,8-10\n10 O -\n";
     140static string Tremolo_torsion = "#\n#ATOMDATA Id Type torsion\n8 H 9-10\n9 H 10-8,8-10\n10 O -\n";
     141static string Tremolo_full = "# ATOMDATA\tx=3\tu=3\tF\tstress\tId\tneighbors=5\timprData\tGroupMeasureTypeNo\tType\textType\tname\tresName\tchainID\tresSeq\toccupancy\ttempFactor\tsegID\tCharge\tcharge\tGrpTypeNo\ttorsion\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t-\t0\tH\t-\t-\t-\t0\t0\t0\t0\t0\t0\t0\t0\t-\t\n";
    31142
    32143void ParserUnitTest::setUp() {
    33144  World::getInstance();
     145
     146  // we need hydrogens and oxygens in the following tests
     147  CPPUNIT_ASSERT(World::getInstance().getPeriode()->FindElement(1) != NULL);
     148  CPPUNIT_ASSERT(World::getInstance().getPeriode()->FindElement(8) != NULL);
    34149}
    35150
    … …  
    43158  cout << "Testing the XYZ parser." << endl;
    44159  XyzParser* testParser = new XyzParser();
    45   string waterXyz = "3\nH2O: water molecule\nO\t0.000000\t0.000000\t0.000000\nH\t0.758602\t0.000000\t0.504284\nH\t0.758602\t0.000000\t-0.504284\n";
    46160  stringstream input;
    47161  input << waterXyz;
    … …  
    62176  TremoloParser* testParser = new TremoloParser();
    63177  stringstream input, output;
    64   string waterTremolo;
    65178
    66179  // Atomdata beginning with "# ATOMDATA"
    67   waterTremolo = "# ATOMDATA\tId\tname\tType\tx=3\n";
    68   input << waterTremolo;
    69   testParser->load(&input);
    70   testParser->save(&output);
    71   CPPUNIT_ASSERT(waterTremolo == output.str());
     180  input << Tremolo_Atomdata1;
     181  testParser->load(&input);
     182  testParser->save(&output);
     183  CPPUNIT_ASSERT(Tremolo_Atomdata1 == output.str());
    72184  input.clear();
    73185  output.clear();
    74186
    75187  // Atomdata beginning with "#ATOMDATA"
    76   waterTremolo = "#\n#ATOMDATA Id name Type x=3\n1 hydrogen H 3.0 4.5 0.1\n\n";
    77   input << waterTremolo;
     188  input << Tremolo_Atomdata2;
    78189  testParser->load(&input);
    79190  testParser->save(&output);
    … …  
    83194
    84195  // Invalid key in Atomdata line
    85   waterTremolo = "#\n#ATOMDATA Id name foo Type x=3\n\n\n";
    86   input << waterTremolo;
     196  input << Tremolo_invalidkey;
    87197  testParser->load(&input);
    88198  //TODO: proove invalidity
    … …  
    93203  TremoloParser* testParser = new TremoloParser();
    94204  stringstream input;
    95   string waterTremolo;
    96205
    97206  // One simple data line
    98   waterTremolo = "#\n#ATOMDATA Id name Type x=3\n1 hydrogen H 3.0 4.5 0.1\n\n";
    99   input << waterTremolo;
     207  input << Tremolo_Atomdata2;
    100208  testParser->load(&input);
    101209  CPPUNIT_ASSERT(World::getInstance().getAtom(AtomByType(1))->x[0] == 3.0);
    … …  
    106214  TremoloParser* testParser = new TremoloParser();
    107215  stringstream input;
    108   string waterTremolo;
    109216
    110217  // One simple data line
    111   waterTremolo = "#\n#ATOMDATA Id name Type u=3\n1 hydrogen H 3.0 4.5 0.1\n\n";
    112   input << waterTremolo;
     218  input << Tremolo_velocity;
    113219  testParser->load(&input);
    114220  CPPUNIT_ASSERT(World::getInstance().getAtom(AtomByType(1))->v[0] == 3.0);
    … …  
    119225  TremoloParser* testParser = new TremoloParser();
    120226  stringstream input;
    121   string waterTremolo;
    122227
    123228  // Neighbor data
    124   waterTremolo = "#\n#ATOMDATA Id Type neighbors=2\n1 H 3 0\n2 H 3 0\n3 O 1 2\n";
    125   input << waterTremolo;
     229  input << Tremolo_neighbours;
    126230  testParser->load(&input);
    127231
    … …  
    135239  TremoloParser* testParser = new TremoloParser();
    136240  stringstream input, output;
    137   string waterTremolo;
    138241
    139242  // Neighbor data
    140   waterTremolo = "#\n#ATOMDATA Id Type imprData\n8 H 9-10\n9 H 10-8,8-10\n10 O -\n";
    141   input << waterTremolo;
     243  input << Tremolo_improper;
    142244  testParser->load(&input);
    143245  testParser->save(&output);
    … …  
    151253  TremoloParser* testParser = new TremoloParser();
    152254  stringstream input, output;
    153   string waterTremolo;
    154255
    155256  // Neighbor data
    156   waterTremolo = "#\n#ATOMDATA Id Type torsion\n8 H 9-10\n9 H 10-8,8-10\n10 O -\n";
    157   input << waterTremolo;
     257  input << Tremolo_torsion;
    158258  testParser->load(&input);
    159259  testParser->save(&output);
    … …  
    173273  testParser->setFieldsForSave("x=3 u=3 F stress Id neighbors=5 imprData GroupMeasureTypeNo Type extType name resName chainID resSeq occupancy tempFactor segID Charge charge GrpTypeNo torsion");
    174274  testParser->save(&output);
    175   CPPUNIT_ASSERT(output.str() == "# ATOMDATA\tx=3\tu=3\tF\tstress\tId\tneighbors=5\timprData\tGroupMeasureTypeNo\tType\textType\tname\tresName\tchainID\tresSeq\toccupancy\ttempFactor\tsegID\tCharge\tcharge\tGrpTypeNo\ttorsion\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t-\t0\tH\t-\t-\t-\t0\t0\t0\t0\t0\t0\t0\t0\t-\t\n");
     275  CPPUNIT_ASSERT(output.str() == Tremolo_full);
    176276
    177277  cout << "testing the tremolo parser is done" << endl;
    178278}
     279
     280void ParserUnitTest::readwritePcpTest() {
     281  stringstream input(waterPcp);
     282  PcpParser* testParser = new PcpParser();
     283  testParser->load(&input);
     284  input.clear();
     285
     286  CPPUNIT_ASSERT_EQUAL(3, World::getInstance().numAtoms());
     287
     288  string newWaterPcp = "";
     289  stringstream output;
     290  testParser->save(&output);
     291
     292  input << output;
     293  PcpParser* testParser2 = new PcpParser();
     294  testParser2->load(&input);
     295
     296  CPPUNIT_ASSERT_EQUAL(6, World::getInstance().numAtoms());
     297
     298  CPPUNIT_ASSERT(*testParser == *testParser2);
     299}
     300
     301void ParserUnitTest::writeMpqcTest() {
     302  // build up water molecule
     303  atom *Walker = NULL;
     304  Walker = World::getInstance().createAtom();
     305  Walker->type = World::getInstance().getPeriode()->FindElement(8);
     306  Walker->x = Vector(0,0,0);
     307  Walker = World::getInstance().createAtom();
     308  Walker->type = World::getInstance().getPeriode()->FindElement(1);
     309  Walker->x = Vector(0.758602,0,0.504284);
     310  Walker = World::getInstance().createAtom();
     311  Walker->type = World::getInstance().getPeriode()->FindElement(1);
     312  Walker->x = Vector(0.758602,0,-0.504284);
     313  CPPUNIT_ASSERT_EQUAL(3, World::getInstance().numAtoms());
     314
     315  // create two stringstreams, one stored, one created
     316  stringstream input(waterMpqc);
     317  MpqcParser* testParser = new MpqcParser();
     318  stringstream output;
     319  testParser->save(&output);
     320
     321  // compare both configs
     322  CPPUNIT_ASSERT(input.str() == output.str());
     323}
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