Changes in src/unittests/ParserUnitTest.cpp [2fd80b5:4eb4fe]

File:

• src/unittests/ParserUnitTest.cpp (modified) (11 diffs)

src/unittests/ParserUnitTest.cpp

@@ -12 +12 @@
 #include <cppunit/ui/text/TestRunner.h>
 
-#include "Parser/MpqcParser.hpp"
-#include "Parser/PcpParser.hpp"
+#include "Parser/XyzParser.hpp"
 #include "Parser/TremoloParser.hpp"
-#include "Parser/XyzParser.hpp"
 #include "World.hpp"
 #include "atom.hpp"
@@ -31 +29 @@
 CPPUNIT_TEST_SUITE_REGISTRATION( ParserUnitTest );
 
-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";
-static string waterMpqc ="% Created by MoleCuilder\n\
-mpqc: (\n\
-\tsavestate = no\n\
-\tdo_gradient = yes\n\
-\tmole<MBPT2>: (\n\
-\t\tmaxiter = 200\n\
-\t\tbasis = $:basis\n\
-\t\tmolecule = $:molecule\n\
-\t\treference<CLHF>: (\n\
-\t\t\tbasis = $:basis\n\
-\t\t\tmolecule = $:molecule\n\
-\t\t)\n\
-\t)\n\
-)\n\
-molecule<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<GaussianBasisSet>: (\n\
-\tname = \"3-21G\"\n\
-\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 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";
-static string Tremolo_invalidkey = "#\n#ATOMDATA Id name foo Type x=3\n\n\n";
-static string Tremolo_velocity = "#\n#ATOMDATA Id name Type u=3\n1 hydrogen H 3.0 4.5 0.1\n\n";
-static string Tremolo_neighbours = "#\n#ATOMDATA Id Type neighbors=2\n1 H 3 0\n2 H 3 0\n3 O 1 2\n";
-static string Tremolo_improper = "#\n#ATOMDATA Id Type imprData\n8 H 9-10\n9 H 10-8,8-10\n10 O -\n";
-static string Tremolo_torsion = "#\n#ATOMDATA Id Type torsion\n8 H 9-10\n9 H 10-8,8-10\n10 O -\n";
-static 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";
 
 void ParserUnitTest::setUp() {
   World::getInstance();
-
-  // 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 ParserUnitTest::tearDown() {
-  ChangeTracker::purgeInstance();
   World::purgeInstance();
 }
@@ -159 +43 @@
   cout << "Testing the XYZ parser." << endl;
   XyzParser* testParser = new XyzParser();
+  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";
   stringstream input;
   input << waterXyz;
@@ -177 +62 @@
   TremoloParser* testParser = new TremoloParser();
   stringstream input, output;
+  string waterTremolo;
 
   // Atomdata beginning with "# ATOMDATA"
-  input << Tremolo_Atomdata1;
+  waterTremolo = "# ATOMDATA\tId\tname\tType\tx=3\n";
+  input << waterTremolo;
   testParser->load(&input);
   testParser->save(&output);
-  CPPUNIT_ASSERT(Tremolo_Atomdata1 == output.str());
+  CPPUNIT_ASSERT(waterTremolo == output.str());
   input.clear();
   output.clear();
 
   // Atomdata beginning with "#ATOMDATA"
-  input << Tremolo_Atomdata2;
+  waterTremolo = "#\n#ATOMDATA Id name Type x=3\n1 hydrogen H 3.0 4.5 0.1\n\n";
+  input << waterTremolo;
   testParser->load(&input);
   testParser->save(&output);
@@ -195 +83 @@
 
   // Invalid key in Atomdata line
-  input << Tremolo_invalidkey;
+  waterTremolo = "#\n#ATOMDATA Id name foo Type x=3\n\n\n";
+  input << waterTremolo;
   testParser->load(&input);
   //TODO: proove invalidity
@@ -204 +93 @@
   TremoloParser* testParser = new TremoloParser();
   stringstream input;
+  string waterTremolo;
 
   // One simple data line
-  input << Tremolo_Atomdata2;
+  waterTremolo = "#\n#ATOMDATA Id name Type x=3\n1 hydrogen H 3.0 4.5 0.1\n\n";
+  input << waterTremolo;
   testParser->load(&input);
   CPPUNIT_ASSERT(World::getInstance().getAtom(AtomByType(1))->x[0] == 3.0);
@@ -215 +106 @@
   TremoloParser* testParser = new TremoloParser();
   stringstream input;
+  string waterTremolo;
 
   // One simple data line
-  input << Tremolo_velocity;
+  waterTremolo = "#\n#ATOMDATA Id name Type u=3\n1 hydrogen H 3.0 4.5 0.1\n\n";
+  input << waterTremolo;
   testParser->load(&input);
   CPPUNIT_ASSERT(World::getInstance().getAtom(AtomByType(1))->v[0] == 3.0);
@@ -226 +119 @@
   TremoloParser* testParser = new TremoloParser();
   stringstream input;
+  string waterTremolo;
 
   // Neighbor data
-  input << Tremolo_neighbours;
+  waterTremolo = "#\n#ATOMDATA Id Type neighbors=2\n1 H 3 0\n2 H 3 0\n3 O 1 2\n";
+  input << waterTremolo;
   testParser->load(&input);
 
@@ -240 +135 @@
   TremoloParser* testParser = new TremoloParser();
   stringstream input, output;
+  string waterTremolo;
 
   // Neighbor data
-  input << Tremolo_improper;
+  waterTremolo = "#\n#ATOMDATA Id Type imprData\n8 H 9-10\n9 H 10-8,8-10\n10 O -\n";
+  input << waterTremolo;
   testParser->load(&input);
   testParser->save(&output);
@@ -254 +151 @@
   TremoloParser* testParser = new TremoloParser();
   stringstream input, output;
+  string waterTremolo;
 
   // Neighbor data
-  input << Tremolo_torsion;
+  waterTremolo = "#\n#ATOMDATA Id Type torsion\n8 H 9-10\n9 H 10-8,8-10\n10 O -\n";
+  input << waterTremolo;
   testParser->load(&input);
   testParser->save(&output);
@@ -274 +173 @@
   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");
   testParser->save(&output);
-  CPPUNIT_ASSERT(output.str() == Tremolo_full);
+  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");
 
   cout << "testing the tremolo parser is done" << endl;
 }
-
-void ParserUnitTest::readwritePcpTest() {
-  stringstream input(waterPcp);
-  PcpParser* testParser = new PcpParser();
-  testParser->load(&input);
-  input.clear();
-
-  CPPUNIT_ASSERT_EQUAL(3, World::getInstance().numAtoms());
-
-  string newWaterPcp = "";
-  stringstream output;
-  testParser->save(&output);
-
-  input << output;
-  PcpParser* testParser2 = new PcpParser();
-  testParser2->load(&input);
-
-  CPPUNIT_ASSERT_EQUAL(6, World::getInstance().numAtoms());
-
-  CPPUNIT_ASSERT(*testParser == *testParser2);
-}
-
-void ParserUnitTest::writeMpqcTest() {
-  // build up water molecule
-  atom *Walker = NULL;
-  Walker = World::getInstance().createAtom();
-  Walker->type = World::getInstance().getPeriode()->FindElement(8);
-  Walker->x = Vector(0,0,0);
-  Walker = World::getInstance().createAtom();
-  Walker->type = World::getInstance().getPeriode()->FindElement(1);
-  Walker->x = Vector(0.758602,0,0.504284);
-  Walker = World::getInstance().createAtom();
-  Walker->type = World::getInstance().getPeriode()->FindElement(1);
-  Walker->x = 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;
-  testParser->save(&output);
-
-  // compare both configs
-  string first = input.str();
-  string second = output.str();
-  CPPUNIT_ASSERT(first == second);
-}