/* * Project: MoleCuilder * Description: creates and alters molecular systems * Copyright (C) 2010 University of Bonn. All rights reserved. * Please see the LICENSE file or "Copyright notice" in builder.cpp for details. */ /* * ParserCommonUnitTest.cpp * * Created on: Mar 3, 2010 * Author: metzler */ // include config.h #ifdef HAVE_CONFIG_H #include #endif #include "ParserCommonUnitTest.hpp" #include #include #include #include "Parser/MpqcParser.hpp" #include "Parser/PdbParser.hpp" #include "Parser/PcpParser.hpp" #include "Parser/TremoloParser.hpp" #include "Parser/XyzParser.hpp" #include "World.hpp" #include "atom.hpp" #include "element.hpp" #include "periodentafel.hpp" #include "Descriptors/AtomTypeDescriptor.hpp" #ifdef HAVE_TESTRUNNER #include "UnitTestMain.hpp" #endif /*HAVE_TESTRUNNER*/ using namespace std; // Registers the fixture into the 'registry' CPPUNIT_TEST_SUITE_REGISTRATION( ParserCommonUnitTest ); static string waterPcp = "# ParallelCarParinello - main configuration file - created with molecuilder\n\ \n\ mainname\tpcp\t# programm name (for runtime files)\n\ defaultpath\not specified\t# where to put files during runtime\n\ pseudopotpath\not specified\t# where to find pseudopotentials\n\ \n\ ProcPEGamma\t8\t# for parallel computing: share constants\n\ ProcPEPsi\t1\t# for parallel computing: share wave functions\n\ DoOutVis\t0\t# Output data for OpenDX\n\ DoOutMes\t1\t# Output data for measurements\n\ DoOutOrbitals\t0\t# Output all Orbitals\n\ DoOutCurr\t0\t# Ouput current density for OpenDx\n\ DoOutNICS\t0\t# Output Nucleus independent current shieldings\n\ DoPerturbation\t0\t# Do perturbation calculate and determine susceptibility and shielding\n\ DoFullCurrent\t0\t# Do full perturbation\n\ DoConstrainedMD\t0\t# Do perform a constrained (>0, relating to current MD step) instead of unconstrained (0) MD\n\ Thermostat\tBerendsen\t2.5\t# Which Thermostat and its parameters to use in MD case.\n\ CommonWannier\t0\t# Put virtual centers at indivual orbits, all common, merged by variance, to grid point, to cell center\n\ SawtoothStart\t0.01\t# Absolute value for smooth transition at cell border \n\ VectorPlane\t0\t# Cut plane axis (x, y or z: 0,1,2) for two-dim current vector plot\n\ VectorCut\t0\t# Cut plane axis value\n\ AddGramSch\t1\t# Additional GramSchmidtOrtogonalization to be safe\n\ Seed\t1\t# initial value for random seed for Psi coefficients\n\ \n\ MaxOuterStep\t0\t# number of MolecularDynamics/Structure optimization steps\n\ Deltat\t0.01\t# time per MD step\n\ OutVisStep\t10\t# Output visual data every ...th step\n\ OutSrcStep\t5\t# Output \"restart\" data every ..th step\n\ TargetTemp\t0.000950045\t# Target temperature\n\ MaxPsiStep\t3\t# number of Minimisation steps per state (0 - default)\n\ EpsWannier\t1e-07\t# tolerance value for spread minimisation of orbitals\n\ # Values specifying when to stop\n\ MaxMinStep\t100\t# Maximum number of steps\n\ RelEpsTotalE\t1e-07\t# relative change in total energy\n\ RelEpsKineticE\t1e-05\t# relative change in kinetic energy\n\ MaxMinStopStep\t2\t# check every ..th steps\n\ MaxMinGapStopStep\t1\t# check every ..th steps\n\ \n\ # Values specifying when to stop for INIT, otherwise same as above\n\ MaxInitMinStep\t100\t# Maximum number of steps\n\ InitRelEpsTotalE\t1e-05\t# relative change in total energy\n\ InitRelEpsKineticE\t0.0001\t# relative change in kinetic energy\n\ InitMaxMinStopStep\t2\t# check every ..th steps\n\ InitMaxMinGapStopStep\t1\t# check every ..th steps\n\ \n\ BoxLength\t# (Length of a unit cell)\n\ 20\n\ 0\t20\n\ 0\t0\t20\n\ \n\ ECut\t128\t# energy cutoff for discretization in Hartrees\n\ MaxLevel\t5\t# number of different levels in the code, >=2\n\ Level0Factor\t2\t# factor by which node number increases from S to 0 level\n\ RiemannTensor\t0\t# (Use metric)\n\ PsiType\t0\t# 0 - doubly occupied, 1 - SpinUp,SpinDown\n\ MaxPsiDouble\t2\t# here: specifying both maximum number of SpinUp- and -Down-states\n\ PsiMaxNoUp\t2\t# here: specifying maximum number of SpinUp-states\n\ PsiMaxNoDown\t2\t# here: specifying maximum number of SpinDown-states\n\ AddPsis\t0\t# Additional unoccupied Psis for bandgap determination\n\ \n\ RCut\t20\t# R-cut for the ewald summation\n\ StructOpt\t0\t# Do structure optimization beforehand\n\ IsAngstroem\t1\t# 0 - Bohr, 1 - Angstroem\n\ RelativeCoord\t0\t# whether ion coordinates are relative (1) or absolute (0)\n\ MaxTypes\t2\t# maximum number of different ion types\n\ \n\ # Ion type data (PP = PseudoPotential, Z = atomic number)\n\ #Ion_TypeNr.\tAmount\tZ\tRGauss\tL_Max(PP)L_Loc(PP)IonMass\t# chemical name, symbol\n\ Ion_Type1\t2\t1\t1.0\t3\t3\t1.008\tHydrogen\tH\n\ Ion_Type2\t1\t8\t1.0\t3\t3\t15.999\tOxygen\tO\n\ #Ion_TypeNr._Nr.R[0]\tR[1]\tR[2]\tMoveType (0 MoveIon, 1 FixedIon)\n\ Ion_Type2_1\t0.000000000\t0.000000000\t0.000000000\t0 # molecule nr 0\n\ Ion_Type1_1\t0.758602\t0.000000000\t0.504284\t0 # molecule nr 1\n\ Ion_Type1_2\t0.758602\t0.000000000\t-0.504284\t0 # molecule nr 2\n"; //----|----*|---||--*||---|***|-------|-------|-------|-----|---------------|-|- //000000011111111112222222222333333333344444444445555555555666666666677777777778 //345678901234567890123456789012345678901234567890123456789012345678901234567890 static string waterPdb = "\ REMARK This is a test water molecule as written by TREMOLO.\n\ ATOM 1 OT GMT- 0 1.583 1.785 1.480 1.00178.02 O-2\n\ ATOM 2 HT GMT- 0 1.186 1.643 2.213 1.00103.58 H+1\n\ ATOM 3 HT GMT- 0 2.642 1.896 1.730 1.00126.00 H+1\n\ ATOM 4 OT GMT- 1 3.583 1.785 1.480 1.00178.02 O-2\n\ ATOM 5 HT GMT- 1 3.186 1.643 2.213 1.00103.58 H+1\n\ ATOM 6 HT GMT- 1 4.642 1.896 1.730 1.00126.00 H+1\n\ CONECT 1 2 3\n\ CONECT 2 1\n\ CONECT 3 1\n\ CONECT 4 5 6\n\ CONECT 5 4\n\ CONECT 6 4\n\ END"; static string waterMpqc ="% Created by MoleCuilder\n\ mpqc: (\n\ \tsavestate = no\n\ \tdo_gradient = yes\n\ \tmole: (\n\ \t\tmaxiter = 200\n\ \t\tbasis = $:basis\n\ \t\tmolecule = $:molecule\n\ \t\treference: (\n\ \t\t\tbasis = $:basis\n\ \t\t\tmolecule = $:molecule\n\ \t\t)\n\ \t)\n\ )\n\ molecule: (\n\ \tunit = angstrom\n\ \t{ atoms geometry } = {\n\ \t\tO [ -0.505735\t0\t0 ]\n\ \t\tH [ 0.252867\t0\t0.504284 ]\n\ \t\tH [ 0.252867\t0\t-0.504284 ]\n\ \t}\n\ )\n\ basis: (\n\ \tname = \"3-21G\"\n\ \tmolecule = $:molecule\n\ )\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"; void ParserCommonUnitTest::setUp() { World::getInstance(); setVerbosity(2); // we need hydrogens and oxygens in the following tests CPPUNIT_ASSERT(World::getInstance().getPeriode()->FindElement(1) != NULL); CPPUNIT_ASSERT(World::getInstance().getPeriode()->FindElement(8) != NULL); } void ParserCommonUnitTest::tearDown() { ChangeTracker::purgeInstance(); World::purgeInstance(); } /************************************ tests ***********************************/ void ParserCommonUnitTest::rewriteAnXyzTest() { cout << "Testing the XYZ parser." << endl; XyzParser* testParser = new XyzParser(); stringstream input; input << waterXyz; testParser->load(&input); input.clear(); CPPUNIT_ASSERT_EQUAL(3, World::getInstance().numAtoms()); // store and parse in again { stringstream output; std::vector atoms = World::getInstance().getAllAtoms(); testParser->save(&output, atoms); input << output.str(); testParser->load(&input); } // now twice as many CPPUNIT_ASSERT_EQUAL(6, World::getInstance().numAtoms()); // check every atom std::vector atoms = World::getInstance().getAllAtoms(); std::vector::const_iterator firstiter = atoms.begin(); std::vector::const_iterator seconditer = atoms.begin(); for (size_t i=0;i<3;i++) ++seconditer; for (; seconditer != atoms.end(); ++firstiter,++seconditer) { // check position and type (only stuff xyz stores) CPPUNIT_ASSERT_EQUAL((*firstiter)->getPosition(),(*seconditer)->getPosition()); CPPUNIT_ASSERT_EQUAL((*firstiter)->getType(),(*seconditer)->getType()); } } void ParserCommonUnitTest::readwritePcpTest() { stringstream input(waterPcp); PcpParser* testParser = new PcpParser(); testParser->load(&input); input.clear(); CPPUNIT_ASSERT_EQUAL(3, World::getInstance().numAtoms()); // check that equality function is ok CPPUNIT_ASSERT(*testParser == *testParser); stringstream output; std::vector atoms = World::getInstance().getAllAtoms(); testParser->save(&output, atoms); input << output.str(); PcpParser* testParser2 = new PcpParser(); testParser2->load(&input); CPPUNIT_ASSERT_EQUAL(6, World::getInstance().numAtoms()); CPPUNIT_ASSERT(*testParser == *testParser2); } void ParserCommonUnitTest::readwritePdbTest() { stringstream input; input << waterPdb; PdbParser* testParser = new PdbParser(); testParser->load(&input); input.clear(); CPPUNIT_ASSERT_EQUAL(6, World::getInstance().numAtoms()); stringstream output; std::vector atoms = World::getInstance().getAllAtoms(); testParser->save(&output, atoms); // std::cout << "Save PDB is:" << std::endl; // std::cout << output.str() << std::endl; input << output.str(); PdbParser* testParser2 = new PdbParser(); testParser2->load(&input); CPPUNIT_ASSERT_EQUAL(12, World::getInstance().numAtoms()); } void ParserCommonUnitTest::writeMpqcTest() { // build up water molecule atom *Walker = NULL; Walker = World::getInstance().createAtom(); Walker->setType(8); Walker->setPosition(Vector(0,0,0)); Walker = World::getInstance().createAtom(); Walker->setType(1); Walker->setPosition(Vector(0.758602,0,0.504284)); Walker = World::getInstance().createAtom(); Walker->setType(1); Walker->setPosition(Vector(0.758602,0,-0.504284)); CPPUNIT_ASSERT_EQUAL(3, World::getInstance().numAtoms()); // create two stringstreams, one stored, one created stringstream input(waterMpqc); MpqcParser* testParser = new MpqcParser(); stringstream output; std::vector atoms = World::getInstance().getAllAtoms(); testParser->save(&output, atoms); // compare both configs string first = input.str(); string second = output.str(); CPPUNIT_ASSERT(first == second); }