diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 66113af126..aaa0b7eb41 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -22,6 +22,7 @@ Version 2021-dev - convert markdown to rst format (#559) - read units stored in H5MD file (#549) - enable CXX only in CMake (#560) +- refactored tests to use files instead of data in source code (#572) Version 1.6.2 (released XX.07.20) ================================= diff --git a/src/tests/CMakeLists.txt b/src/tests/CMakeLists.txt index 0ab6041fe7..f935dd6673 100644 --- a/src/tests/CMakeLists.txt +++ b/src/tests/CMakeLists.txt @@ -23,6 +23,7 @@ foreach(PROG file(GLOB ${PROG}_SOURCES ${PROG}.cc) add_executable(unit_${PROG} ${${PROG}_SOURCES}) + target_compile_definitions(unit_${PROG} PRIVATE CSG_TEST_DATA_FOLDER="${CMAKE_CURRENT_SOURCE_DIR}/DataFiles") if(PROG STREQUAL "test_bondedstatistics" OR PROG STREQUAL "test_tabulatedpotential") target_link_libraries(unit_${PROG} votca_csg_boltzmann) endif() diff --git a/src/tests/DataFiles/lammpsdatareader/test_polymer.data b/src/tests/DataFiles/lammpsdatareader/test_polymer.data new file mode 100644 index 0000000000..b07f992306 --- /dev/null +++ b/src/tests/DataFiles/lammpsdatareader/test_polymer.data @@ -0,0 +1,539 @@ +LAMMPS data file via write_data, version 17 Nov 2015, timestep = 961 + +100 atoms +1 atom types +99 bonds +1 bond types +98 angles +1 angle types +97 dihedrals +1 dihedral types + +0.0000000000000000e+00 1.5850000000000000e+02 xlo xhi +0.0000000000000000e+00 1.5850000000000000e+02 ylo yhi +0.0000000000000000e+00 1.0000000000000000e+02 zlo zhi + +Masses + +1 14.02 + +Pair Coeffs # lj/cut + +1 0.112 4.01 + +Bond Coeffs # harmonic + +1 350 1.53 + +Angle Coeffs # harmonic + +1 60 109.5 + +Atoms # molecular + +5 1 1 5.8137734438047275e+01 5.2820532540049605e+01 5.1610735195303207e+01 0 0 0 +6 1 1 5.7593847093164598e+01 5.3264325139761141e+01 5.0249644669646678e+01 0 0 0 +7 1 1 5.6511930501583258e+01 5.4329619289202022e+01 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a/src/tests/DataFiles/lammpsdatareader/test_polymer3.data b/src/tests/DataFiles/lammpsdatareader/test_polymer3.data new file mode 100644 index 0000000000..b07f992306 --- /dev/null +++ b/src/tests/DataFiles/lammpsdatareader/test_polymer3.data @@ -0,0 +1,539 @@ +LAMMPS data file via write_data, version 17 Nov 2015, timestep = 961 + +100 atoms +1 atom types +99 bonds +1 bond types +98 angles +1 angle types +97 dihedrals +1 dihedral types + +0.0000000000000000e+00 1.5850000000000000e+02 xlo xhi +0.0000000000000000e+00 1.5850000000000000e+02 ylo yhi +0.0000000000000000e+00 1.0000000000000000e+02 zlo zhi + +Masses + +1 14.02 + +Pair Coeffs # lj/cut + +1 0.112 4.01 + +Bond Coeffs # harmonic + +1 350 1.53 + +Angle Coeffs # harmonic + +1 60 109.5 + +Atoms # molecular + +5 1 1 5.8137734438047275e+01 5.2820532540049605e+01 5.1610735195303207e+01 0 0 0 +6 1 1 5.7593847093164598e+01 5.3264325139761141e+01 5.0249644669646678e+01 0 0 0 +7 1 1 5.6511930501583258e+01 5.4329619289202022e+01 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a/src/tests/DataFiles/lammpsdatareader/test_polymer4.data b/src/tests/DataFiles/lammpsdatareader/test_polymer4.data new file mode 100644 index 0000000000..8836d90f96 --- /dev/null +++ b/src/tests/DataFiles/lammpsdatareader/test_polymer4.data @@ -0,0 +1,540 @@ +LAMMPS data file via write_data, version 17 Nov 2015, timestep = 1010 + +100 atoms +1 atom types +99 bonds +1 bond types +98 angles +1 angle types +97 dihedrals +1 dihedral types + +0.0000000000000000e+00 1.5850000000000000e+02 xlo xhi +0.0000000000000000e+00 1.5850000000000000e+02 ylo yhi +0.0000000000000000e+00 1.0000000000000000e+02 zlo zhi + +Masses + +1 14.02 + +Pair Coeffs # lj/cut + +1 0.112 4.01 + +Bond Coeffs # harmonic + +1 350 1.53 + +Angle Coeffs # harmonic + +1 60 109.5 + +Atoms # molecular + +5 1 1 6.3263003185944591e+01 5.4290657368992242e+01 5.9883190680423475e+01 0 0 0 +8 1 1 6.2418305028410344e+01 5.4490261304479837e+01 5.6129058120497604e+01 0 0 0 +9 1 1 6.1735199864545841e+01 5.5858546306169337e+01 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a/src/tests/DataFiles/lammpsdumpreaderwriter/test_thiophene.dump b/src/tests/DataFiles/lammpsdumpreaderwriter/test_thiophene.dump new file mode 100644 index 0000000000..b8cc07f5e6 --- /dev/null +++ b/src/tests/DataFiles/lammpsdumpreaderwriter/test_thiophene.dump @@ -0,0 +1,25 @@ +ITEM: TIMESTEP +1 +ITEM: NUMBER OF ATOMS +16 +ITEM: BOX BOUNDS pp pp pp +0 100.000000 +0 100.000000 +0 100.000000 +ITEM: ATOMS id type x y z vx vy vz fx fy fz +1 0 3.571663 -2.912328 0.627991 0.000000 0.000000 0.000000 0.100000 0.100000 0.100000 +2 0 2.702771 -1.746477 0.724159 0.000000 0.000000 0.000000 0.100000 0.100000 0.100000 +3 0 1.448135 -2.025836 0.308560 0.000000 0.000000 0.000000 0.100000 0.100000 0.100000 +4 0 2.946939 -3.992905 0.161081 0.000000 0.000000 0.000000 0.100000 0.100000 0.100000 +5 1 4.611604 -2.882320 0.919327 0.000000 0.000000 0.000000 0.100000 0.100000 0.100000 +6 2 1.284820 -3.692216 -0.197094 0.000000 0.000000 0.000000 0.100000 0.100000 0.100000 +7 1 3.374874 -4.971104 0.004941 0.000000 0.000000 0.000000 0.100000 0.100000 0.100000 +8 1 3.082680 -0.806748 1.097073 0.000000 0.000000 0.000000 0.100000 0.100000 0.100000 +9 0 0.244597 -1.159273 0.241620 0.000000 0.000000 0.000000 0.100000 0.100000 0.100000 +10 2 -0.599083 -0.820914 -1.247944 0.000000 0.000000 0.000000 0.100000 0.100000 0.100000 +11 0 -0.362405 -0.567118 1.284770 0.000000 0.000000 0.000000 0.100000 0.100000 0.100000 +12 1 -0.017750 -0.642753 2.305544 0.000000 0.000000 0.000000 0.100000 0.100000 0.100000 +13 0 -1.542466 0.201364 0.915934 0.000000 0.000000 0.000000 0.100000 0.100000 0.100000 +14 0 -1.764805 0.138711 -0.400894 0.000000 0.000000 0.000000 0.100000 0.100000 0.100000 +15 1 -2.563883 0.611988 -0.947270 0.000000 0.000000 0.000000 0.100000 0.100000 0.100000 +16 1 -2.121735 0.732859 1.656506 0.000000 0.000000 0.000000 0.100000 0.100000 0.100000 diff --git a/src/tests/DataFiles/pdbreader/Molecule1.pdb b/src/tests/DataFiles/pdbreader/Molecule1.pdb new file mode 100644 index 0000000000..d048e81c05 --- /dev/null +++ b/src/tests/DataFiles/pdbreader/Molecule1.pdb @@ -0,0 +1,24 @@ +COMPND UNNAMED +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +HETATM 1 C UNL 1 -5.249 1.055 -0.000 1.00 0.00 C +HETATM 2 H UNL 1 -6.202 1.521 -0.141 1.00 0.00 H +HETATM 3 H UNL 1 -5.390 0.026 0.255 1.00 0.00 H +HETATM 4 H UNL 1 -4.682 1.124 -0.904 1.00 0.00 H +HETATM 5 H UNL 1 -4.724 1.550 0.790 1.00 0.00 H +HETATM 6 C UNL 2 -2.248 1.671 -0.000 1.00 0.00 C +HETATM 7 H UNL 2 -1.518 2.451 0.051 1.00 0.00 H +HETATM 8 H UNL 2 -3.153 1.999 0.467 1.00 0.00 H +HETATM 9 H UNL 2 -2.442 1.430 -1.024 1.00 0.00 H +HETATM 10 H UNL 2 -1.880 0.804 0.507 1.00 0.00 H +CONECT 1 2 3 4 5 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 1 +CONECT 6 7 8 9 10 +CONECT 7 6 +CONECT 8 6 +CONECT 9 6 +CONECT 10 6 +MASTER 0 0 0 0 0 0 0 0 10 0 10 0 +END diff --git a/src/tests/test_lammpsdatareader.cc b/src/tests/test_lammpsdatareader.cc index 61f08d2ea4..103ce31b7c 100644 --- a/src/tests/test_lammpsdatareader.cc +++ b/src/tests/test_lammpsdatareader.cc @@ -1,5 +1,5 @@ /* - * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org) + * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -38,12 +38,6 @@ using namespace votca::tools; BOOST_AUTO_TEST_SUITE(lammpsdatareaderwriter_test) -// Check if file exists -bool fexists_(const string filename); - -void printTestFile1_(const string filename); -void printTestFile2_(const string filename); - /** * \brief Test the topology reader * @@ -54,17 +48,14 @@ void printTestFile2_(const string filename); */ BOOST_AUTO_TEST_CASE(test_topologyreader) { - string lammpsdatafilename = "test_polymer.data"; - if (fexists_(lammpsdatafilename)) { - remove(lammpsdatafilename.c_str()); - } - printTestFile1_(lammpsdatafilename); + string lammpsdatafilename = + std::string(CSG_TEST_DATA_FOLDER) + "/lammpsdatareader/test_polymer.data"; Topology top; TopologyReader::RegisterPlugins(); TopologyReader *lammpsDataReader; - lammpsDataReader = TopReaderFactory().Create("test.data"); + lammpsDataReader = TopReaderFactory().Create(lammpsdatafilename); lammpsDataReader->ReadTopology(lammpsdatafilename, top); BOOST_CHECK_EQUAL(top.BeadCount(), 100); @@ -103,28 +94,21 @@ BOOST_AUTO_TEST_CASE(test_topologyreader) { BOOST_AUTO_TEST_CASE(test_trajectoryreader) { - string lammpsdatafilename = "test_polymer3.data"; - if (fexists_(lammpsdatafilename)) { - remove(lammpsdatafilename.c_str()); - } - printTestFile1_(lammpsdatafilename); - + string lammpsdatafilename = std::string(CSG_TEST_DATA_FOLDER) + + "/lammpsdatareader/test_polymer3.data"; Topology top; TopologyReader::RegisterPlugins(); TopologyReader *lammpsDataReader; - lammpsDataReader = TopReaderFactory().Create("test.data"); + lammpsDataReader = TopReaderFactory().Create(lammpsdatafilename); lammpsDataReader->ReadTopology(lammpsdatafilename, top); - string lammpsdatafilename2 = "test_polymer4.data"; - if (fexists_(lammpsdatafilename2)) { - remove(lammpsdatafilename2.c_str()); - } - printTestFile2_(lammpsdatafilename2); + string lammpsdatafilename2 = std::string(CSG_TEST_DATA_FOLDER) + + "/lammpsdatareader/test_polymer4.data"; TrajectoryReader::RegisterPlugins(); TrajectoryReader *lammpsDataReaderTrj; - lammpsDataReaderTrj = TrjReaderFactory().Create("test.data"); + lammpsDataReaderTrj = TrjReaderFactory().Create(lammpsdatafilename2); lammpsDataReaderTrj->Open(lammpsdatafilename2); lammpsDataReaderTrj->FirstFrame(top); @@ -158,1908 +142,5 @@ BOOST_AUTO_TEST_CASE(test_trajectoryreader) { votca::Index totalInter = numBondInter + numAngleInter + numDihedralInter; BOOST_CHECK_EQUAL(interaction_cont.size(), totalInter); } -/***************************************************************************** - * Internal test functions * - *****************************************************************************/ - -// Check if file exists -bool fexists_(const string filename) { - std::ifstream ifile(filename); - return (bool)ifile; -} -void printTestFile1_(const string filename) { - - ofstream outfile(filename); - outfile - << "LAMMPS data file via write_data, version 17 Nov 2015, timestep = 961" - << endl; - outfile << "" << endl; - outfile << "100 atoms" << endl; - outfile << "1 atom types" << endl; - outfile << "99 bonds" << endl; - outfile << "1 bond types" << endl; - outfile << "98 angles" << endl; - outfile << "1 angle types" << endl; - outfile << "97 dihedrals" << endl; - outfile << "1 dihedral types" << endl; - outfile << "" << endl; - outfile << "0.0000000000000000e+00 1.5850000000000000e+02 xlo xhi" << endl; - outfile << "0.0000000000000000e+00 1.5850000000000000e+02 ylo yhi" << endl; - outfile << "0.0000000000000000e+00 1.0000000000000000e+02 zlo zhi" << endl; - outfile << "" << endl; - outfile << "Masses" << endl; - outfile << "" << endl; - outfile << "1 14.02" << endl; - outfile << "" << endl; - outfile << "Pair Coeffs # lj/cut" << endl; - outfile << "" << endl; - outfile << "1 0.112 4.01" << endl; - outfile << "" << endl; - outfile << "Bond Coeffs # harmonic" << endl; - outfile << "" << endl; - outfile << "1 350 1.53" << endl; - outfile << "" << endl; - outfile << "Angle Coeffs # harmonic" << endl; - outfile << "" << endl; - outfile << "1 60 109.5" << endl; - outfile << "" << endl; - outfile << "Atoms # molecular" << endl; - outfile << "" << endl; - outfile << "5 1 1 5.8137734438047275e+01 5.2820532540049605e+01 " - "5.1610735195303207e+01 0 0 0" - << endl; - outfile << "6 1 1 5.7593847093164598e+01 5.3264325139761141e+01 " - "5.0249644669646678e+01 0 0 0" - << endl; - outfile << "7 1 1 5.6511930501583258e+01 5.4329619289202022e+01 " - "5.0444704115951488e+01 0 0 0" - << endl; - outfile << "9 1 1 5.8047091053480429e+01 5.6222029048615425e+01 " - "4.9874845165148727e+01 0 0 0" - << endl; - outfile << "8 1 1 5.7157290110423276e+01 5.5616832485184531e+01 " - "5.0964522757346906e+01 0 0 0" - << endl; - outfile << "10 1 1 5.8796606242207154e+01 5.7431388649541120e+01 " - "5.0436740373291755e+01 0 0 0" - << endl; - outfile << "13 1 1 6.1470904287728864e+01 5.8661356795663160e+01 " - "5.0956738288440924e+01 0 0 0" - << endl; - outfile << "14 1 1 6.2318874922711110e+01 5.9820763044333191e+01 " - "5.1482733521136190e+01 0 0 0" - << endl; - outfile << "11 1 1 5.9740399827120577e+01 5.6964684624717705e+01 " - "5.1547015047030342e+01 0 0 0" - << endl; - outfile << "12 1 1 6.0550755372027595e+01 5.8152824805563078e+01 " - "5.2068213576080311e+01 0 0 0" - << endl; - outfile << "15 1 1 6.3220534569625151e+01 5.9309964725714572e+01 " - "5.2607828752412175e+01 0 0 0" - << endl; - outfile << "16 1 1 6.4122151012703725e+01 6.0440684531421851e+01 " - "5.3106224006392388e+01 0 0 0" - << endl; - outfile << "17 1 1 6.4989383763573784e+01 5.9916464190367087e+01 " - "5.4251845650219749e+01 0 0 0" - << endl; - outfile << "18 1 1 6.4098633759524319e+01 5.9598860291991549e+01 " - "5.5454314244516617e+01 0 0 0" - << endl; - outfile << "19 1 1 6.4944652589155282e+01 5.8985111104358268e+01 " - "5.6571073918330995e+01 0 0 0" - << endl; - outfile << "20 1 1 6.5994561083409252e+01 5.9993009252428024e+01 " - "5.7042894764699355e+01 0 0 0" - << endl; - outfile << "22 1 1 6.7926851198445149e+01 6.0321059085483142e+01 " - "5.8608478010470662e+01 0 0 0" - << endl; - outfile << "23 1 1 6.8901563116380558e+01 6.0573575982606258e+01 " - "5.7456282631605447e+01 0 0 0" - << endl; - outfile << "21 1 1 6.6831300248918623e+01 5.9354803574005928e+01 " - "5.8152660598019651e+01 0 0 0" - << endl; - outfile << "1 1 1 6.2806039595490141e+01 5.2512717926489422e+01 " - "4.9887303784980617e+01 0 0 0" - << endl; - outfile << "3 1 1 6.0466882959009020e+01 5.2652416089059159e+01 " - "5.0746419497822217e+01 0 0 0" - << endl; - outfile << "4 1 1 5.9321955572837354e+01 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<< endl; - outfile << "54 -5.7431940873534587e-03 1.0872788768227556e-02 " - "1.3025488593651966e-02" - << endl; - outfile << "55 -2.9248565279124894e-02 2.0601220669770508e-03 " - "-4.7066384051876022e-03" - << endl; - outfile << "56 -2.6726844290510664e-02 9.3528816199405160e-03 " - "-2.7501515672069238e-02" - << endl; - outfile << "57 -1.7980703138665951e-02 -2.0041585094997282e-02 " - "1.4030560841356713e-02" - << endl; - outfile << "58 -1.6968971591429328e-02 5.3087226038875824e-03 " - "1.4873355151351859e-02" - << endl; - outfile << "" << endl; - outfile << "Bonds" << endl; - outfile << "" << endl; - outfile << "1 1 5 6" << endl; - outfile << "2 1 6 7" << endl; - outfile << "3 1 7 8" << endl; - outfile << "4 1 9 10" << endl; - outfile << "5 1 8 9" << endl; - outfile << "6 1 10 11" << endl; - outfile << "7 1 13 14" << endl; - outfile << "8 1 14 15" << endl; - outfile << "9 1 11 12" << endl; - outfile << "10 1 12 13" << endl; - outfile << "11 1 15 16" << endl; - outfile << "12 1 16 17" << endl; - outfile << "13 1 17 18" << endl; - outfile << "14 1 18 19" << endl; - outfile << "15 1 19 20" << endl; - outfile << "16 1 20 21" << endl; - outfile << "17 1 22 23" << endl; - outfile << "18 1 23 24" << endl; - outfile << "19 1 21 22" << endl; - outfile << "20 1 1 2" << endl; - outfile << "21 1 3 4" << endl; - outfile << "22 1 4 5" << endl; - outfile << "23 1 2 3" << endl; - outfile << "24 1 24 25" << endl; - outfile << "25 1 25 26" << endl; - outfile << "26 1 26 27" << endl; - outfile << "27 1 27 28" << endl; - outfile << "28 1 28 29" << endl; - outfile << "29 1 30 31" << endl; - outfile << "30 1 31 32" << endl; - outfile << "31 1 29 30" << endl; - outfile << "32 1 32 33" << endl; - outfile << "33 1 33 34" << endl; - outfile << "34 1 34 35" << endl; - outfile << "35 1 35 36" << endl; - outfile << "36 1 36 37" << endl; - outfile << "37 1 37 38" << endl; - outfile << "38 1 77 78" << endl; - outfile << "39 1 82 83" << endl; - outfile << "40 1 83 84" << endl; - outfile << "41 1 81 82" << endl; - outfile << "42 1 84 85" << endl; - outfile << "43 1 80 81" << endl; - outfile << "44 1 85 86" << endl; - outfile << "45 1 87 88" << endl; - outfile << "46 1 86 87" << endl; - outfile << "47 1 79 80" << endl; - outfile << "48 1 38 39" << endl; - outfile << "49 1 46 47" << endl; - outfile << "50 1 43 44" << endl; - outfile << "51 1 45 46" << endl; - outfile << "52 1 44 45" << endl; - outfile << "53 1 68 69" << endl; - outfile << "54 1 98 99" << endl; - outfile << "55 1 99 100" << endl; - outfile << "56 1 39 40" << endl; - outfile << "57 1 40 41" << endl; - outfile << "58 1 42 43" << endl; - outfile << "59 1 41 42" << endl; - outfile << "60 1 70 71" << endl; - outfile << "61 1 69 70" << endl; - outfile << "62 1 71 72" << endl; - outfile << "63 1 73 74" << endl; - outfile << "64 1 74 75" << endl; - outfile << "65 1 72 73" << endl; - outfile << "66 1 75 76" << endl; - outfile << "67 1 76 77" << endl; - outfile << "68 1 89 90" << endl; - outfile << "69 1 88 89" << endl; - outfile << "70 1 90 91" << endl; - outfile << "71 1 91 92" << endl; - outfile << "72 1 92 93" << endl; - outfile << "73 1 97 98" << endl; - outfile << "74 1 96 97" << endl; - outfile << "75 1 94 95" << endl; - outfile << "76 1 93 94" << endl; - outfile << "77 1 95 96" << endl; - outfile << "78 1 78 79" << endl; - outfile << "79 1 52 53" << endl; - outfile << "80 1 51 52" << endl; - outfile << "81 1 53 54" << endl; - outfile << "82 1 59 60" << endl; - outfile << "83 1 60 61" << endl; - outfile << "84 1 47 48" << endl; - outfile << "85 1 49 50" << endl; - outfile << "86 1 48 49" << endl; - outfile << "87 1 50 51" << endl; - outfile << "88 1 62 63" << endl; - outfile << "89 1 63 64" << endl; - outfile << "90 1 64 65" << endl; - outfile << "91 1 65 66" << endl; - outfile << "92 1 66 67" << endl; - outfile << "93 1 67 68" << endl; - outfile << "94 1 61 62" << endl; - outfile << "95 1 54 55" << endl; - outfile << "96 1 55 56" << endl; - outfile << "97 1 56 57" << endl; - outfile << "98 1 57 58" << endl; - outfile << "99 1 58 59" << endl; - outfile << "" << endl; - outfile << "Angles" << endl; - outfile << "" << endl; - outfile << "1 1 4 5 6" << endl; - outfile << "2 1 5 6 7" << endl; - outfile << "3 1 6 7 8" << endl; - outfile << "4 1 8 9 10" << endl; - outfile << "5 1 7 8 9" << endl; - outfile << "6 1 9 10 11" << endl; - outfile << "7 1 12 13 14" << endl; - outfile << "8 1 13 14 15" << endl; - outfile << "9 1 10 11 12" << endl; - outfile << "10 1 11 12 13" << endl; - outfile << "11 1 14 15 16" << endl; - outfile << "12 1 15 16 17" << endl; - outfile << "13 1 16 17 18" << endl; - outfile << "14 1 17 18 19" << endl; - outfile << "15 1 18 19 20" << endl; - outfile << "16 1 19 20 21" << endl; - outfile << "17 1 21 22 23" << endl; - outfile << "18 1 22 23 24" << endl; - outfile << "19 1 20 21 22" << endl; - outfile << "20 1 2 3 4" << endl; - outfile << "21 1 3 4 5" << endl; - outfile << "22 1 1 2 3" << endl; - outfile << "23 1 23 24 25" << endl; - outfile << "24 1 24 25 26" << endl; - outfile << "25 1 25 26 27" << endl; - outfile << "26 1 26 27 28" << endl; - outfile << "27 1 27 28 29" << endl; - outfile << "28 1 29 30 31" << endl; - outfile << "29 1 30 31 32" << endl; - outfile << "30 1 28 29 30" << endl; - outfile << "31 1 31 32 33" << endl; - outfile << "32 1 32 33 34" << endl; - outfile << "33 1 33 34 35" << endl; - outfile << "34 1 34 35 36" << endl; - outfile << "35 1 35 36 37" << endl; - outfile << "36 1 36 37 38" << endl; - outfile << "37 1 76 77 78" << endl; - outfile << "38 1 81 82 83" << endl; - outfile << "39 1 82 83 84" << endl; - outfile << "40 1 80 81 82" << endl; - outfile << "41 1 83 84 85" << endl; - outfile << "42 1 79 80 81" << endl; - outfile << "43 1 84 85 86" << endl; - outfile << "44 1 86 87 88" << endl; - outfile << "45 1 85 86 87" << endl; - outfile << "46 1 78 79 80" << endl; - outfile << "47 1 37 38 39" << endl; - outfile << "48 1 45 46 47" << endl; - outfile << "49 1 42 43 44" << endl; - outfile << "50 1 44 45 46" << endl; - outfile << "51 1 43 44 45" << endl; - outfile << "52 1 67 68 69" << endl; - outfile << "53 1 97 98 99" << endl; - outfile << "54 1 98 99 100" << endl; - outfile << "55 1 38 39 40" << endl; - outfile << "56 1 39 40 41" << endl; - outfile << "57 1 41 42 43" << endl; - outfile << "58 1 40 41 42" << endl; - outfile << "59 1 69 70 71" << endl; - outfile << "60 1 68 69 70" << endl; - outfile << "61 1 70 71 72" << endl; - outfile << "62 1 72 73 74" << endl; - outfile << "63 1 73 74 75" << endl; - outfile << "64 1 71 72 73" << endl; - outfile << "65 1 74 75 76" << endl; - outfile << "66 1 75 76 77" << endl; - outfile << "67 1 88 89 90" << endl; - outfile << "68 1 87 88 89" << endl; - outfile << "69 1 89 90 91" << endl; - outfile << "70 1 90 91 92" << endl; - outfile << "71 1 91 92 93" << endl; - outfile << "72 1 96 97 98" << endl; - outfile << "73 1 95 96 97" << endl; - outfile << "74 1 93 94 95" << endl; - outfile << "75 1 92 93 94" << endl; - outfile << "76 1 94 95 96" << endl; - outfile << "77 1 77 78 79" << endl; - outfile << "78 1 51 52 53" << endl; - outfile << "79 1 50 51 52" << endl; - outfile << "80 1 52 53 54" << endl; - outfile << "81 1 58 59 60" << endl; - outfile << "82 1 59 60 61" << endl; - outfile << "83 1 46 47 48" << endl; - outfile << "84 1 48 49 50" << endl; - outfile << "85 1 47 48 49" << endl; - outfile << "86 1 49 50 51" << endl; - outfile << "87 1 61 62 63" << endl; - outfile << "88 1 62 63 64" << endl; - outfile << "89 1 63 64 65" << endl; - outfile << "90 1 64 65 66" << endl; - outfile << "91 1 65 66 67" << endl; - outfile << "92 1 66 67 68" << endl; - outfile << "93 1 60 61 62" << endl; - outfile << "94 1 53 54 55" << endl; - outfile << "95 1 54 55 56" << endl; - outfile << "96 1 55 56 57" << endl; - outfile << "97 1 56 57 58" << endl; - outfile << "98 1 57 58 59" << endl; - outfile << "" << endl; - outfile << "Dihedrals" << endl; - outfile << "" << endl; - outfile << "1 1 4 5 6 7" << endl; - outfile << "2 1 5 6 7 8" << endl; - outfile << "3 1 6 7 8 9" << endl; - outfile << "4 1 8 9 10 11" << endl; - outfile << "5 1 7 8 9 10" << endl; - outfile << "6 1 9 10 11 12" << endl; - outfile << "7 1 12 13 14 15" << endl; - outfile << "8 1 13 14 15 16" << endl; - outfile << "9 1 10 11 12 13" << endl; - outfile << "10 1 11 12 13 14" << endl; - outfile << "11 1 14 15 16 17" << endl; - outfile << "12 1 15 16 17 18" << endl; - outfile << "13 1 16 17 18 19" << endl; - outfile << "14 1 17 18 19 20" << endl; - outfile << "15 1 18 19 20 21" << endl; - outfile << "16 1 19 20 21 22" << endl; - outfile << "17 1 21 22 23 24" << endl; - outfile << "18 1 22 23 24 25" << endl; - outfile << "19 1 20 21 22 23" << endl; - outfile << "20 1 2 3 4 5" << endl; - outfile << "21 1 3 4 5 6" << endl; - outfile << "22 1 1 2 3 4" << endl; - outfile << "23 1 23 24 25 26" << endl; - outfile << "24 1 24 25 26 27" << endl; - outfile << "25 1 25 26 27 28" << endl; - outfile << "26 1 26 27 28 29" << endl; - outfile << "27 1 27 28 29 30" << endl; - outfile << "28 1 29 30 31 32" << endl; - outfile << "29 1 30 31 32 33" << endl; - outfile << "30 1 28 29 30 31" << endl; - outfile << "31 1 31 32 33 34" << endl; - outfile << "32 1 32 33 34 35" << endl; - outfile << "33 1 33 34 35 36" << endl; - outfile << "34 1 34 35 36 37" << endl; - outfile << "35 1 35 36 37 38" << endl; - outfile << "36 1 36 37 38 39" << endl; - outfile << "37 1 76 77 78 79" << endl; - outfile << "38 1 81 82 83 84" << endl; - outfile << "39 1 82 83 84 85" << endl; - outfile << "40 1 80 81 82 83" << endl; - outfile << "41 1 83 84 85 86" << endl; - outfile << "42 1 79 80 81 82" << endl; - outfile << "43 1 84 85 86 87" << endl; - outfile << "44 1 86 87 88 89" << endl; - outfile << "45 1 85 86 87 88" << endl; - outfile << "46 1 78 79 80 81" << endl; - outfile << "47 1 37 38 39 40" << endl; - outfile << "48 1 45 46 47 48" << endl; - outfile << "49 1 42 43 44 45" << endl; - outfile << "50 1 44 45 46 47" << endl; - outfile << "51 1 43 44 45 46" << endl; - outfile << "52 1 67 68 69 70" << endl; - outfile << "53 1 97 98 99 100" << endl; - outfile << "54 1 38 39 40 41" << endl; - outfile << "55 1 39 40 41 42" << endl; - outfile << "56 1 41 42 43 44" << endl; - outfile << "57 1 40 41 42 43" << endl; - outfile << "58 1 69 70 71 72" << endl; - outfile << "59 1 68 69 70 71" << endl; - outfile << "60 1 70 71 72 73" << endl; - outfile << "61 1 72 73 74 75" << endl; - outfile << "62 1 73 74 75 76" << endl; - outfile << "63 1 71 72 73 74" << endl; - outfile << "64 1 74 75 76 77" << endl; - outfile << "65 1 75 76 77 78" << endl; - outfile << "66 1 88 89 90 91" << endl; - outfile << "67 1 87 88 89 90" << endl; - outfile << "68 1 89 90 91 92" << endl; - outfile << "69 1 90 91 92 93" << endl; - outfile << "70 1 91 92 93 94" << endl; - outfile << "71 1 96 97 98 99" << endl; - outfile << "72 1 95 96 97 98" << endl; - outfile << "73 1 93 94 95 96" << endl; - outfile << "74 1 92 93 94 95" << endl; - outfile << "75 1 94 95 96 97" << endl; - outfile << "76 1 77 78 79 80" << endl; - outfile << "77 1 51 52 53 54" << endl; - outfile << "78 1 50 51 52 53" << endl; - outfile << "79 1 52 53 54 55" << endl; - outfile << "80 1 58 59 60 61" << endl; - outfile << "81 1 59 60 61 62" << endl; - outfile << "82 1 46 47 48 49" << endl; - outfile << "83 1 48 49 50 51" << endl; - outfile << "84 1 47 48 49 50" << endl; - outfile << "85 1 49 50 51 52" << endl; - outfile << "86 1 61 62 63 64" << endl; - outfile << "87 1 62 63 64 65" << endl; - outfile << "88 1 63 64 65 66" << endl; - outfile << "89 1 64 65 66 67" << endl; - outfile << "90 1 65 66 67 68" << endl; - outfile << "91 1 66 67 68 69" << endl; - outfile << "92 1 60 61 62 63" << endl; - outfile << "93 1 53 54 55 56" << endl; - outfile << "94 1 54 55 56 57" << endl; - outfile << "95 1 55 56 57 58" << endl; - outfile << "96 1 56 57 58 59" << endl; - outfile << "97 1 57 58 59 60" << endl; - outfile.close(); -} - -void printTestFile2_(const string filename) { - - ofstream outfile(filename); - outfile - << "LAMMPS data file via write_data, version 17 Nov 2015, timestep = 1010" - << endl; - outfile << "" << endl; - outfile << "100 atoms" << endl; - outfile << "1 atom types" << endl; - outfile << "99 bonds" << endl; - outfile << "1 bond types" << endl; - outfile << "98 angles" << endl; - outfile << "1 angle types" << endl; - outfile << "97 dihedrals" << endl; - outfile << "1 dihedral types" << endl; - outfile << "" << endl; - outfile << "0.0000000000000000e+00 1.5850000000000000e+02 xlo xhi" << endl; - outfile << "0.0000000000000000e+00 1.5850000000000000e+02 ylo yhi" << endl; - outfile << "0.0000000000000000e+00 1.0000000000000000e+02 zlo zhi" << endl; - outfile << "" << endl; - outfile << "Masses" << endl; - outfile << "" << endl; - outfile << "1 14.02" << endl; - outfile << "" << endl; - outfile << "Pair Coeffs # lj/cut" << endl; - outfile << "" << endl; - outfile << "1 0.112 4.01" << endl; - outfile << "" << endl; - outfile << "Bond Coeffs # harmonic" << endl; - outfile << "" << endl; - outfile << "1 350 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<< endl; - outfile << "85 1 61 62 63 64" << endl; - outfile << "86 1 63 64 65 66" << endl; - outfile << "87 1 64 65 66 67" << endl; - outfile << "88 1 62 63 64 65" << endl; - outfile << "89 1 65 66 67 68" << endl; - outfile << "90 1 66 67 68 69" << endl; - outfile << "91 1 41 42 43 44" << endl; - outfile << "92 1 40 41 42 43" << endl; - outfile << "93 1 68 69 70 71" << endl; - outfile << "94 1 69 70 71 72" << endl; - outfile << "95 1 67 68 69 70" << endl; - outfile << "96 1 71 72 73 74" << endl; - outfile << "97 1 70 71 72 73" << endl; - outfile << "" << endl; - outfile.close(); -} BOOST_AUTO_TEST_SUITE_END() diff --git a/src/tests/test_lammpsdumpreaderwriter.cc b/src/tests/test_lammpsdumpreaderwriter.cc index 7db1fd5d89..a8bab7a8b2 100644 --- a/src/tests/test_lammpsdumpreaderwriter.cc +++ b/src/tests/test_lammpsdumpreaderwriter.cc @@ -1,5 +1,5 @@ /* - * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org) + * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -36,12 +36,6 @@ using namespace std; using namespace votca::csg; using namespace votca::tools; -// Check if file exists -bool fexists(const string filename) { - std::ifstream ifile(filename); - return (bool)ifile; -} - BOOST_AUTO_TEST_SUITE(lammpsdumpreaderwriter_test) /** @@ -60,11 +54,8 @@ BOOST_AUTO_TEST_CASE(test_trajectoryreader) { // and read from it. Create a topology object with the same // molecule to enable the ability to read in the trajectory // file - string lammpsdumpfilename = "test_thiophene.dump"; - if (fexists(lammpsdumpfilename)) { - remove(lammpsdumpfilename.c_str()); - } - ofstream outfile(lammpsdumpfilename); + string lammpsdumpfilename = std::string(CSG_TEST_DATA_FOLDER) + + "/lammpsdumpreaderwriter/test_thiophene.dump"; // Atom Coordinates vector> atom_xyz_file = { @@ -92,50 +83,6 @@ BOOST_AUTO_TEST_CASE(test_trajectoryreader) { {0.1, 0.1, 0.1}, {0.1, 0.1, 0.1}, {0.1, 0.1, 0.1}, {0.1, 0.1, 0.1}, {0.1, 0.1, 0.1}, {0.1, 0.1, 0.1}, {0.1, 0.1, 0.1}, {0.1, 0.1, 0.1}}; - outfile << "ITEM: TIMESTEP" << endl; - outfile << "1" << endl; - outfile << "ITEM: NUMBER OF ATOMS" << endl; - outfile << "16" << endl; - outfile << "ITEM: BOX BOUNDS pp pp pp" << endl; - outfile << "0 0.000000" << endl; - outfile << "0 10.000000" << endl; - outfile << "0 10.000000" << endl; - outfile << "ITEM: ATOMS id type x y z fx fy fz" << endl; - outfile << "1 0 3.571663 -2.912328 0.627991 0.100000 0.100000 0.100000" - << endl; - outfile << "2 0 2.702771 -1.746477 0.724159 0.100000 0.100000 0.100000" - << endl; - outfile << "3 0 1.448135 -2.025836 0.308560 0.100000 0.100000 0.100000" - << endl; - outfile << "4 0 2.946939 -3.992905 0.161081 0.100000 0.100000 0.100000" - << endl; - outfile << "5 1 4.611604 -2.882320 0.919327 0.100000 0.100000 0.100000" - << endl; - outfile << "6 2 1.284820 -3.692216 -0.197094 0.100000 0.100000 0.100000" - << endl; - outfile << "7 1 3.374874 -4.971104 0.004941 0.100000 0.100000 0.100000" - << endl; - outfile << "8 1 3.082680 -0.806748 1.097073 0.100000 0.100000 0.100000" - << endl; - outfile << "9 0 0.244597 -1.159273 0.241620 0.100000 0.100000 0.100000" - << endl; - outfile << "10 2 -0.599083 -0.820914 -1.247944 0.100000 0.100000 0.100000" - << endl; - outfile << "11 0 -0.362405 -0.567118 1.284770 0.100000 0.100000 0.100000" - << endl; - outfile << "12 1 -0.017750 -0.642753 2.305544 0.100000 0.100000 0.100000" - << endl; - outfile << "13 0 -1.542466 0.201364 0.915934 0.100000 0.100000 0.100000" - << endl; - outfile << "14 0 -1.764805 0.138711 -0.400894 0.100000 0.100000 0.100000" - << endl; - outfile << "15 1 -2.563883 0.611988 -0.947270 0.100000 0.100000 0.100000" - << endl; - outfile << "16 1 -2.121735 0.732859 1.656506 0.100000 0.100000 0.100000" - << endl; - - outfile.close(); - Topology top; // Make square box @@ -337,9 +284,6 @@ BOOST_AUTO_TEST_CASE(test_trajectorywriter) { top.SetHasVel(true); string lammpsDumpFileName = "test_thiophene.dump"; - if (fexists(lammpsDumpFileName)) { - remove(lammpsDumpFileName.c_str()); - } // Write the topology object to a file TrajectoryWriter::RegisterPlugins(); diff --git a/src/tests/test_pdbreader.cc b/src/tests/test_pdbreader.cc index 5d95761ccd..a0544b10db 100644 --- a/src/tests/test_pdbreader.cc +++ b/src/tests/test_pdbreader.cc @@ -1,5 +1,5 @@ /* - * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org) + * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -34,66 +34,12 @@ BOOST_AUTO_TEST_SUITE(pdbreader_test) BOOST_AUTO_TEST_CASE(test_topologyreader) { - ////////////////////////////////////////////////////////////////////////// - // Create pdb test file - ////////////////////////////////////////////////////////////////////////// - ofstream outfile("Molecule1.pdb"); - outfile << "COMPND UNNAMED" << endl; - outfile << "AUTHOR GENERATED BY OPEN BABEL 2.4.1" << endl; - outfile << "HETATM 1 C UNL 1 -5.249 1.055 -0.000 1.00 " - "0.00 C" - << endl; - outfile << "HETATM 2 H UNL 1 -6.202 1.521 -0.141 1.00 " - "0.00 H" - << endl; - outfile << "HETATM 3 H UNL 1 -5.390 0.026 0.255 1.00 " - "0.00 H" - << endl; - outfile << "HETATM 4 H UNL 1 -4.682 1.124 -0.904 1.00 " - "0.00 H" - << endl; - outfile << "HETATM 5 H UNL 1 -4.724 1.550 0.790 1.00 " - "0.00 H" - << endl; - outfile << "HETATM 6 C UNL 2 -2.248 1.671 -0.000 1.00 " - "0.00 C" - << endl; - outfile << "HETATM 7 H UNL 2 -1.518 2.451 0.051 1.00 " - "0.00 H" - << endl; - outfile << "HETATM 8 H UNL 2 -3.153 1.999 0.467 1.00 " - "0.00 H" - << endl; - outfile << "HETATM 9 H UNL 2 -2.442 1.430 -1.024 1.00 " - "0.00 H" - << endl; - outfile << "HETATM 10 H UNL 2 -1.880 0.804 0.507 1.00 " - "0.00 H" - << endl; - outfile << "CONECT 1 2 3 4 5" << endl; - outfile << "CONECT 2 1" << endl; - outfile << "CONECT 3 1" << endl; - outfile << "CONECT 4 1" << endl; - outfile << "CONECT 5 1" << endl; - outfile << "CONECT 6 7 8 9 10" << endl; - outfile << "CONECT 7 6" << endl; - outfile << "CONECT 8 6" << endl; - outfile << "CONECT 9 6" << endl; - outfile << "CONECT 10 6" << endl; - outfile << "MASTER 0 0 0 0 0 0 0 0 10 0 " - "10 0" - << endl; - outfile << "END" << endl; - outfile.close(); - ////////////////////////////////////////////////////////////////////////// - votca::tools::Elements ele; Topology top; TopologyReader::RegisterPlugins(); - TopologyReader *reader; - string str = "Molecule1.pdb"; - reader = TopReaderFactory().Create(str); + string str = std::string(CSG_TEST_DATA_FOLDER) + "/pdbreader/Molecule1.pdb"; + auto reader = std::unique_ptr(TopReaderFactory().Create(str)); reader->ReadTopology(str, top); BOOST_CHECK_EQUAL(reader != nullptr, true); BOOST_CHECK_EQUAL(top.BeadCount(), 10);