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[Cdk-commits] CVS: cdk/src/org/openscience/cdk/test/modeling/forcefield ForceFieldTests.java,1.22,1.23 TestPotentialFunction.java,1.7,1.8
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From: labarta <la...@us...> - 2005-03-27 17:45:52
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Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/test/modeling/forcefield In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv4938/src/org/openscience/cdk/test/modeling/forcefield Modified Files: ForceFieldTests.java TestPotentialFunction.java Log Message: forcefield: bond angle from radian to degrees and small changes Index: ForceFieldTests.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/test/modeling/forcefield/ForceFieldTests.java,v retrieving revision 1.22 retrieving revision 1.23 diff -u -r1.22 -r1.23 --- ForceFieldTests.java 24 Mar 2005 13:40:18 -0000 1.22 +++ ForceFieldTests.java 27 Mar 2005 17:45:42 -0000 1.23 @@ -96,6 +96,7 @@ } } + /** * A unit test for JUnit (MMFF94EnergyFunction minimization with Steepest Descents Method) */ @@ -113,10 +114,34 @@ gm.steepestDescentsMinimization(acCoordinates, mmff94EF); System.out.println("gm.getSteepestDescentsMinimum() : " + gm.getSteepestDescentsMinimum()); + /*for (int i = 0; i < acCoordinates.getSize(); i++) { + assertEquals(testResult3C[i], gm.getSteepestDescentsMinimum().getElement(i), 0.1); + }*/ } - + /** + * A unit test for JUnit (MMFF94EnergyFunction minimization with Conjugate Gradient Method) + */ + public void testMMFF94EnergyFunctionMinimizationWithConjugateGradientMethod() throws Exception { + System.out.println("\n\nFORCEFIELDTESTS: MMFF94EnergyFunction minimization with Conjugate Gradient Method"); + + createTestMoleculeAndSetMMFF94Parameters(); + + System.out.println("Molecule created:"+ac.getAtomCount()+" Size Table:"+mmff94Tables.size()); + MMFF94EnergyFunction mmff94EF = new MMFF94EnergyFunction(ac,mmff94Tables); + System.out.println("EnergyFunction is set"); + + gm.setConvergenceParametersForCGM(5, 0.001); + System.out.println("CGM Parameters are set"); + gm.conjugateGradientMinimization(acCoordinates, mmff94EF); + + System.out.println("gm.getConjugateGradientMinimum() : " + gm.getConjugateGradientMinimum()); + /*for (int i = 0; i < acCoordinates.getSize(); i++) { + assertEquals(testResult3C[i], gm.getConjugateGradientMinimum().getElement(i), 0.1); + }*/ + } + /** * A unit test for JUnit (Conjugate Gradient Method minimization) @@ -168,7 +193,7 @@ a.setPoint3d(atomCoordinate0); ac.setAtomAt(0, a); a = ac.getAtomAt(1); - Point3d atomCoordinate1 = new Point3d(10, 0, 0); + Point3d atomCoordinate1 = new Point3d(2, 0, 0); a.setPoint3d(atomCoordinate1); ac.setAtomAt(1, a); AtomTools at = new AtomTools(); @@ -300,128 +325,110 @@ //System.out.println(""); //System.out.println("FORCEFIELDTESTS with Angle Bending"); - double testResult_SumEA = 2.5626995828317845E8; - double[] testResult_gradientSumEA = {-460695.4430488355, -1.1641532182693481E-10, 6.984919309616089E-10, 460695.4430488365, - -1.1641532182693481E-10, -4.817608823842778E-10, 153565.1476829451, 51188.382560981845, -1.1641532182693481E-10, - 153565.14768294524, -25594.191280490835, -44330.439676446666, 153565.14768294513, -25594.19128049095, - 44330.43967644649, -153565.14768294542, 51188.3825609818, -5.820766091346741E-11, -153565.14768294568, - -25594.19128049095, 44330.439676446724, -153565.14768294545, -25594.191280490835, -44330.439676446666}; - double[] testResult_hessianSumEA = {3700746.0072377375, 9549159.616507957, 1.5122498239088112E7, 1.5122498239088112E7, - 1.0287335116940476E7,5452171.9947928395, 4257343.448739336, 2972132.569563469, 1776630.3041617107, 543048.3017491314, - -665729.841304185, -1884226.60131351, -3156562.060085164, -4423470.387677092, -5495293.725397054, -5495293.725397054, - -4579411.437830878, -3663529.1502647027, -3663529.1502647027,-2747646.862698527, -1831764.5751323511,-1831764.5751323514, - -915882.2875661755, 4.6566128730773926E-10, 5848413.609270222,1.0402462602184748E7,1.5925459008227788E7,1.109029588608015E7, - 8295030.885432094, 3459867.763284457, 2171881.35751756, 1754923.5347738175, 559421.2693720589, -647969.1103857418, - -1800023.722602844, -2772486.5248701903, -4038007.0891666035,-5277256.9781916225,-6544772.057116449, -5640330.173539949, - -5636516.7055433905,-4720634.417977215, -3799031.928416202, -3276199.4965547845,-2060661.4704867117,-1139058.9809256983, - -616226.5490642814, -2.561137080192566E-9, - 5573338.622580152,1.1096335028623192E7,1.6173555682385229E7,1.1338392560237592E7,6503229.438089955, 3707964.437441901, - 2512462.172040142, 1316959.9066383836, 36133.400340718246, -1179959.683131894, -2152422.4853992397,-3046933.3094552164, - -4121160.32371189, -5388675.402636715, -6544772.057116446, -5628889.76955027, -4713007.481984095, -4017168.7288343916, - -3111194.1217528316,-1895656.0956847589,-1718836.3063999144,-793046.3383491231, -176819.7892848443, - 5.820766091346741E-10, - 4.661961783586849E-10, -4835163.122147637, -9670326.244295275, -5969580.237057531, -469947.73501898116,5103390.887561175, - 5103390.887561175, 6019273.175127351, 6935155.462693526, 6935155.462693526, 7851037.750259702, 8766920.037825879, - 8766920.037825879, 9682802.325392054, 1.059868461295823E7,9403856.066904724, 8298062.415277073, 7102560.149875315, - 5868978.147462735, 4686751.759712535, 3468254.9997032094, 2195919.540931555, 1071823.3377199671, - 5.471520125865936E-9, - -4835163.122147633,-7630428.122795684, -1.246559124494332E7,-6965958.742904768, -2411909.7499902416,3413139.955275491, - 4340462.646831342, 4344276.1148279, 5260158.402394076, 6170320.487965414, 6693152.919826832, 7309379.468891111, - 8219541.55446245, 8742373.986323867, 9957912.01239194, 8854893.887355322, 8437936.064611578, 7242433.79920982, - 6058819.648164105, 4906765.0359470025, 3488223.307410832, 2362739.340903728, 1123489.4518787074, 1.5541445463895798E-8, - -4835163.122147623,-9670326.244295262, -1.2465591244943317E7,-6892252.622363162, -1067202.91709743, 4010017.7366646053, - 4925900.024230781, 5841782.311796957, 6537621.06494666, 7443595.67202822, 8059822.2210925, 8236642.010377345, - 9162431.978428137, 1.037797000449621E7,1.0554789793781053E7,9359287.528379295, 8163785.262977537, 6882958.756679872, - 5666865.67320726,4248323.944671088, 3353813.1206151107, 2279586.106358437, 1156096.6544797448, 1.3620592653751373E-8, - -1194828.546053491,-4305549.245842045, -7323785.805265459, -7323785.805265459, -6396463.113709608, -5480580.826143432, - -5056303.338299569, -4615866.979254789, -4008288.8812475703,-3623013.3521427503,-2751532.527548789, -2224082.0364153218, - -1838806.5073105018,-967325.6827165403, 1.2223608791828156E-8,1.2223608791828156E-8,1.2223608791828156E-8,1.2223608791828156E-8, - 1.2223608791828156E-8,1.2223608791828156E-8,1.2223608791828156E-8,1.2223608791828156E-8,1.2223608791828156E-8,1.2223608791828156E-8, - -3107945.1731975097, -3524902.9959412524,-6543139.5553646665,-5627257.267798491, -5623443.799801933, -4707561.512235757, - -4267125.153190977, -3936709.2902230932,-3329131.1922158743,-2453317.9289225917,-2411953.683032941, -1737878.1280384455, - -862064.8647451622, -820700.6188555118, 1.210719347000122E-8,1.210719347000122E-8,1.210719347000122E-8, - 1.210719347000122E-8, 1.210719347000122E-8,1.210719347000122E-8,1.210719347000122E-8,1.210719347000122E-8, - 1.210719347000122E-8,1.210719347000122E-8, - -3018236.559423402,-6036473.118846816, -7317299.625144481, -6401417.337578305, -5485535.050012129, -4789696.296862426, - -4182118.198855208, -3574540.100847989, -3250253.757058193, -2720301.9312754245,-2053730.380228832, -1923379.675549749, - -958555.3274824977, -130350.70467907062,1.2456439435482025E-8,1.2456439435482025E-8,1.2456439435482025E-8, - 1.2456439435482025E-8, 1.2456439435482025E-8,1.2456439435482025E-8,1.2456439435482025E-8,1.2456439435482025E-8, - 1.2456439435482025E-8,1.2456439435482025E-8, - -1233582.0024125667, -4263706.676192022, -7302534.053686289, -7302534.053686289, -6392371.968114951, -5486397.36103339, - -5101121.831928571, -4225308.568635288, -3695356.7428525193,-3232325.798649581, -2483046.646622532, -1630035.123566904, - -1244759.594462084, -749889.4215742992, 1.1175870895385742E-8,1.1175870895385742E-8,1.1175870895385742E-8, - 1.1175870895385742E-8, 1.1175870895385742E-8,1.1175870895385742E-8,1.1175870895385742E-8,1.1175870895385742E-8, - 1.1175870895385742E-8,1.1175870895385742E-8, - -3031512.43707496,-4183567.049292062, -6978764.145581063, -6062881.858014887, -5540049.42615347, -4923822.87708919, - -4052342.052495229, -4010977.806605579, -3344406.255558986, -2595127.103531937, -2182113.1031397013,-1420854.1958605333, - -925984.0229727486, -751140.0888989496, 1.1408701539039612E-8,1.1408701539039612E-8,1.1408701539039612E-8, - 1.1408701539039612E-8, 1.1408701539039612E-8,1.1408701539039612E-8,1.1408701539039612E-8,1.1408701539039612E-8, - 1.1408701539039612E-8,1.1408701539039612E-8, - -3041231.054030969,-5836428.150319969, -6730938.9743759455,-5815056.68680977, -5198830.13774549, -5022010.348460645, - -4494559.857327178, -3820484.302332683, -3690133.5976536, -2837122.0745979724,-2075863.1673188047,-1485393.8537216892, - -740507.1014459806, 3128.9835050774273, 1.1635342009543199E-8,1.1635342009543199E-8,1.1635342009543199E-8, - 1.1635342009543199E-8, 1.1635342009543199E-8,1.1635342009543199E-8,1.1635342009543199E-8,1.1635342009543199E-8, - 1.1635342009543199E-8,1.1635342009543199E-8, - -1272335.458771642,-4360590.31708971, -7257551.625368041, -7257551.625368041, -6347389.539796703, -5421599.571745912, - -5036324.042641092, -4160510.7793478086,-3195686.431280557, -2810410.902175737, -2315540.729287952, -1570653.977012244, - -1068869.5764502306, -261460.23988456847, 9.691575542092323E-9, 9.691575542092323E-9, 9.691575542092323E-9, - 9.691575542092323E-9, 9.691575542092323E-9, 9.691575542092323E-9, 9.691575542092323E-9, 9.691575542092323E-9, - 9.691575542092323E-9, 9.691575542092323E-9, - -3089642.6216135737, -4328892.510638593, -7419141.883585074, -6503259.596018898, -5980427.164157481, -4764889.138089408, - -3893408.3134954465, -3852044.0676057963,-3023839.4448023695,-2528969.2719145846,-2354125.3378407857,-1610489.2528897277, - -803079.9163240656, -302870.6391239119, 1.0739313438534737E-8,1.0739313438534737E-8, 1.0739313438534737E-8, - 1.0739313438534737E-8, 1.0739313438534737E-8, 1.0739313438534737E-8,1.0739313438534737E-8, 1.0739313438534737E-8, - 1.0739313438534737E-8, 1.0739313438534737E-8, - -2894557.6317416066, -5984807.004688088, -7140903.659167819, -6225021.371601643, -5009483.34553357, -4832663.556248725, - -3865337.8735321728, -3044637.254676649, -2914286.549997566, -2164397.1284232554,-1413257.039524294, -1416386.0230293598, - -1154925.7831447818,-852055.144020859, 9.89530235528946E-9, 9.89530235528946E-9, 9.89530235528946E-9, - 9.89530235528946E-9, 9.89530235528946E-9,9.89530235528946E-9, 9.89530235528946E-9,9.89530235528946E-9, - 9.89530235528946E-9,9.89530235528946E-9, - 9.818048734772133E-9, 904441.8835765106, 1820324.1711426864, 625495.6250891807, -2300256.7939690943,-5318493.353392509, - -5318493.353392509, -5318493.353392509, -5318493.353392509, -5318493.353392509, -5318493.353392509, -5318493.353392509, - -5318493.353392509, -5318493.353392509, -5318493.353392509, -4894215.865548644, -4119496.028578987, - -3511917.930571768, -3126642.4014669475, -2503347.0522108893,-1975896.5610774218,-1590621.031972601, - -967325.682716542, 1.0593794286251068E-8, - 915882.2875661865,919695.7555627448, 1835578.0431289207, -1092949.9025203863,-1509907.7252641283,-4528144.284687542, - -4528144.284687542, -4528144.284687542, -4528144.284687542, -4528144.284687542, -4528144.284687542, -4528144.284687542, - -4528144.284687542, -4528144.284687542, -4528144.284687542, -3753424.447717885, -3423008.5847500013, - -2815430.4867427824, -2196467.576186046, -2155103.330296396, -1334402.7114408722,-715439.800884135, - -674075.5549944845, 1.1757947504520416E-8, - 915882.2875661876,1831764.5751323635, 2527603.3282820666, -490633.231141348, -3508869.7905647624,-4789696.296862427, - -4789696.296862427, -4789696.296862427, -4789696.296862427, -4789696.296862427, -4789696.296862427, -4789696.296862427, - -4789696.296862427, -4789696.296862427, -4789696.296862427, -4182118.1988552087,-3574540.10084799, - -3250253.757058194, -2720301.9312754255, -1892097.3084719987,-1761746.603792916, -796922.2557256644, - -130350.70467907097,1.1976226232945919E-8, - 1.1956912827816588E-8, 921602.4895610255, 1827577.096642586, 593995.0942300055, -2412353.350837366, -5451180.728331635, - -5451180.728331635, -5451180.728331635, -5451180.728331635, -5451180.728331635, -5451180.728331635, -5451180.728331635, - -5451180.728331635, -5451180.728331635, -5451180.728331635, -5065905.199226814, -4446942.288670078, - -3916990.4628873095, -3453959.5186843704,-2988082.474696983, -2135070.951641355, -1749795.4225365347, - -749889.4215743, 1.0826624929904938E-8, - 915882.2875661869,1438714.7194276042, 2654252.745495677, -350707.9362761788, -1502762.5484932812,-4744038.571051108, - -4744038.571051108, -4744038.571051108, -4744038.571051108, -4744038.571051108, -4744038.571051108, -4744038.571051108, - -4744038.571051108, -4744038.571051108, -4744038.571051108, -4120743.2217950495,-4079378.975905399, - -3251174.353101972, -2785297.3091145847, -2372283.308722349, -1918386.0199870798, -918480.0190248451, - -743636.084951046, 1.1990778148174286E-8, - 915882.287566188,2131420.313634261, 2308240.1029191054, -732990.9511118752, -3974266.9736697017,-4868777.797725678, - -4868777.797725678, -4868777.797725678, -4868777.797725678, -4868777.797725678, -4868777.797725678, -4868777.797725678, - -4868777.797725678, -4868777.797725678, -4868777.797725678, -4341327.306592211, -3520626.6877366873, - -3390275.9830576046, -2537264.460001976, -2083367.171266707, -1492897.8576695914,-748011.1053938826, - 3128.9835050785914, 1.2973589341266566E-8, - 1.2954275936137235E-8, 921602.4895610263, 1847392.4576118176, 575056.9988401625, -2373161.261688598, -5270122.569966928, - -5270122.569966928, -5270122.569966928, -5270122.569966928, -5270122.569966928, -5270122.569966928, -5270122.569966928, - -5270122.569966928, -5270122.569966928, -5270122.569966928, -4884847.040862108, -4265884.13030537, - -3301059.782238119, -2915784.2531332984,-1915878.2521710638,-1170991.4998953552,-669207.0993333411, - -261460.23988456576,1.2660166248679161E-8, - 915882.2875661886,1438714.7194276056, 2054941.2684918842, -891889.2287413607, -2131139.1177663812,-5077362.863666729, - -5077362.863666729, -5077362.863666729, -5077362.863666729, -5077362.863666729, -5077362.863666729, -5077362.863666729, - -5077362.863666729, -5077362.863666729, -5077362.863666729, -4454067.51441067, -4412703.268521019, - -3746131.717474426, -2746225.7165121916, -2571381.7824383928,-1820241.693539431, -1412494.8340906557, - -912285.5568905018, 1.30385160446167E-8, - 915882.287566189,1532108.8366304678, 1708928.625915313, -1185629.005826305, -4131852.7517266525,-5287949.406206385, - -5287949.406206385, -5287949.406206385, -5287949.406206385, -5287949.406206385, -5287949.406206385, -5287949.406206385, - -5287949.406206385, -5287949.406206385, -5287949.406206385, -4320623.723489832, -3646548.168495336, - -3516197.463816253, -2766308.042241942, -2022671.957290884, -2025800.94079595, -1764340.7009113717, - -852055.1440208568, 1.257285475730896E-8}; + double testResult_SumEA = 2473.158312247272; + double[] testResult_gradientSumEA = {-1253.45470761264,-1.4210854715202004E-12,-2.2168933355715126E-12, + 1253.4547076126391,-2.2510882047299674E-12,3.5314503535469013E-12,417.81823587087973, + 139.2727452902932,1.8323120798413584E-12,417.8182358708807,-69.63637264514672,-120.61373547619371, + 417.81823587087973,-69.63637264514504,120.61373547619431,-417.81823587087933,139.27274529029293, + -2.741917803916749E-12,-417.8182358708808,-69.63637264514671,120.61373547619367,-417.8182358708794, + -69.63637264514416,-120.61373547619459}; + double[] testResult_hessianSumEA = {1568.8626742584759, 3906.165743403598, 6243.895379734757, 6243.895379734757, + 3023.680810562986, -196.53375860878458, -719.5480795303931, -671.5310330601114, -987.2941765121353, + -1510.2484012649602, -2007.8114954249556, -2638.4613903167074, -3161.3555189007498, -3658.8284688075746, + -3659.8609952463735, -3659.8609952463735, -3049.8841627053116, -2439.9073301642497, -2439.9073301642497, + -1829.9304976231876, -1219.9536650821256, -1219.9536650821256, -609.9768325410635, -1.3642420526593924E-12, + 2337.30306914512, 5508.940790537674, 7846.748494082077, 4626.533924910307, 1515.6999508848735, -1704.5146182868968, + -2030.203681659631, -2179.803575315665, -2495.5667187676827, -2806.2767580061704, -3186.4525601569794, -3368.7803719178787, + -3679.400266903195, -4059.4408526742423, -4508.873529457143, -4206.637693789036, -4104.057361498051, -3494.0805289569894, + -2730.23319797945, -2357.0170970195577, -1590.7886305851607, -826.9412996076209, -453.7251986477287, -1.5916157281026244E-12, + 2337.7296363311575, 4675.53733987556, 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-28.01123588171919, -28.01123588171919, -28.01123588171919, -28.01123588171919, + -28.01123588171919, -28.01123588171919, -28.01123588171919, -19.259738696240564, -23.72223447915482, -43.65350716948425, + -63.85499257549885, -36.45025831852825, -12.629523079339972, -172.28029994995808, -29.01058593949459, -2.9023450309750842E-12}; createTestMoleculeAndSetMMFF94Parameters(); @@ -460,13 +467,14 @@ //System.out.println(""); //System.out.println("FORCEFIELDTESTS with StretchBendInteraction"); - double testResult_SumEBA = 384.0621424329229; - double[] testResult_gradientSumEBA = {-61985.71873683456, -61985.71873683456, -61985.71873683456, -61985.71873683456, - -61985.71873683456, -61985.71873683456, -61985.71873683456, -61985.71873683456, - -61985.71873683456, -61985.71873683456, -61985.71873683456, -61985.71873683456, - -61985.71873683456, -61985.71873683456, -61985.71873683456, -61985.71873683456, - -61985.71873683456, -61985.71873683456, -61985.71873683456, -61985.71873683456, - -61985.71873683456, -61985.71873683456, -61985.71873683456, -61985.71873683456}; + double testResult_SumEBA = 241.0516463157123; + double[] testResult_gradientSumEBA = {-424.4366745401653,-424.4366745401653,-424.4366745401653, + -424.4366745401653,-424.4366745401653,-424.4366745401653,-424.4366745401653, + -424.4366745401653,-424.4366745401653,-424.4366745401653,-424.4366745401653, + -424.4366745401653,-424.4366745401653,-424.4366745401653,-424.4366745401653, + -424.4366745401653,-424.4366745401653,-424.4366745401653,-424.4366745401653, + -424.4366745401653,-424.4366745401653,-424.4366745401653,-424.4366745401653, + -424.4366745401653}; createTestMoleculeAndSetMMFF94Parameters(); @@ -477,7 +485,7 @@ assertEquals(testResult_SumEBA, sbi.functionMMFF94SumEBA(acCoordinates), 0.00001); sbi.setGradientMMFF94SumEBA(acCoordinates); - //System.out.println("sbi.getGradientMMFF94SumEBA(acCoordinates) = " + sbi.getGradientMMFF94SumEBA(acCoordinates)); + //System.out.println("sbi.getGradientMMFF94SumEBA() = " + sbi.getGradientMMFF94SumEBA()); for (int i = 0; i < testResult_gradientSumEBA.length; i++) { assertEquals(testResult_gradientSumEBA[i], sbi.getGradientMMFF94SumEBA().getElement(i), 0.00001); } Index: TestPotentialFunction.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/test/modeling/forcefield/TestPotentialFunction.java,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- TestPotentialFunction.java 17 Mar 2005 09:25:54 -0000 1.7 +++ TestPotentialFunction.java 27 Mar 2005 17:45:42 -0000 1.8 @@ -18,7 +18,7 @@ public class TestPotentialFunction implements PotentialFunction { String functionShape = " f(X,Y) = X2 + 2 Y2 "; String gradientShape = " g = ( 2x , 4y )"; - double energyFunction = 0; + double energy = 0; GVector energyGradient = new GVector(3); GMatrix energyHessian = null; @@ -35,19 +35,11 @@ * Evaluate the potential energy function in a given point * *@param point Current molecule coordinates. - */ - public void setEnergyFunction(GVector point) { - energyFunction = ((point.getElement(0)) * (point.getElement(0))) + (2 * (point.getElement(1)) * (point.getElement(1))); - } - - - /** - * Get the potential energy function in a given point - * *@return Function value */ - public double getEnergyFunction() { - return energyFunction; + public double energyFunction(GVector point) { + energy = ((point.getElement(0)) * (point.getElement(0))) + (2 * (point.getElement(1)) * (point.getElement(1))); + return energy; } |