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Commit 6cc49dbe authored by Andy Simmonett's avatar Andy Simmonett
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Initial reference implementation of LJPME.

parent 1e5b258c
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tests/TestNonbondedForce.h
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...@@ -35,10 +35,12 @@ ...@@ -35,10 +35,12 @@
#include "openmm/HarmonicBondForce.h" #include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h" #include "openmm/NonbondedForce.h"
#include "openmm/System.h" #include "openmm/System.h"
#include "openmm/Units.h"
#include "openmm/VerletIntegrator.h" #include "openmm/VerletIntegrator.h"
#include "SimTKOpenMMRealType.h" #include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h" #include "sfmt/SFMT.h"
#include <iostream> #include <iostream>
#include <iomanip>
#include <vector> #include <vector>
using namespace OpenMM; using namespace OpenMM;
...@@ -46,6 +48,762 @@ using namespace std; ...@@ -46,6 +48,762 @@ using namespace std;
const double TOL = 1e-5; const double TOL = 1e-5;
void make_waterbox(int natoms, double boxEdgeLength, NonbondedForce *forceField, vector<Vec3> &positions, vector<double>& eps, vector<double>& sig,
vector<pair<int, int> >& bonds, System &system, bool do_electrostatics) {
const int RESSIZE = 3;
const double masses[RESSIZE] = { 8.0, 1.0, 1.0 };
const double charges[RESSIZE] = { -0.834, 0.417, 0.417 };
// Values from the CHARMM force field, in AKMA units
const double epsilons[RESSIZE] = { -0.1521, -0.046, -0.046 };
const double halfrmins[RESSIZE] = { 1.7682, 0.2245, 0.2245 };
positions.clear();
if(natoms == 6){
const double coords[6][3] = {
{ 2.000000, 2.000000, 2.000000},
{ 2.500000, 2.000000, 3.000000},
{ 1.500000, 2.000000, 3.000000},
{ 0.000000, 0.000000, 0.000000},
{ 0.500000, 0.000000, 1.000000},
{ -0.500000, 0.000000, 1.000000}
};
for(int atom = 0; atom < natoms; ++atom)
positions.push_back(Vec3(coords[atom][0], coords[atom][1], coords[atom][2])*OpenMM::NmPerAngstrom);
}else if(natoms == 375){
const double coords[375][3] = {
{ -6.227577, -6.257691, -6.242372 },
{ -5.323856, -6.038433, -6.004096 },
{ -6.756728, -5.564157, -5.841659 },
{ -3.045385, -6.233543, -6.190951 },
{ -3.526738, -5.554781, -5.712262 },
{ -3.599325, -6.431115, -6.949685 },
{ 0.021426, -6.231744, -6.149739 },
{ -0.875209, -5.976613, -6.378901 },
{ 0.535110, -6.037842, -6.937199 },
{ 3.100433, -6.203101, -6.272233 },
{ 3.874100, -6.357529, -5.725284 },
{ 2.378191, -6.111572, -5.646492 },
{ 6.186877, -6.143892, -6.207648 },
{ 6.463778, -6.660529, -5.447403 },
{ 6.262846, -6.748390, -6.949519 },
{ -6.215886, -3.157497, -6.242725 },
{ -6.237827, -3.077604, -5.286327 },
{ -6.028329, -2.268904, -6.553829 },
{ -3.143522, -3.072478, -6.164691 },
{ -3.384628, -3.637034, -6.902733 },
{ -2.183705, -3.058977, -6.176044 },
{ -0.001261, -3.162923, -6.234377 },
{ -0.032904, -2.309579, -6.672970 },
{ 0.052913, -2.950816, -5.299691 },
{ 3.087208, -3.110696, -6.143281 },
{ 2.657287, -2.555869, -6.798183 },
{ 3.804920, -3.533514, -6.620435 },
{ 6.169768, -3.141467, -6.167741 },
{ 7.044757, -3.328081, -6.515780 },
{ 5.953438, -2.272871, -6.514589 },
{ -6.207742, -0.041917, -6.155951 },
{ -5.438834, 0.329527, -6.594553 },
{ -6.956596, 0.335819, -6.622957 },
{ -3.102424, -0.064365, -6.193126 },
{ -3.759220, 0.421493, -6.697232 },
{ -2.461457, 0.600160, -5.930203 },
{ 0.057084, -0.011721, -6.176128 },
{ -0.107739, 0.025184, -7.121132 },
{ -0.798344, 0.160864, -5.776104 },
{ 3.038705, 0.009068, -6.198274 },
{ 3.541849, 0.080397, -7.012718 },
{ 3.690240, -0.224328, -5.533000 },
{ 6.176831, 0.057180, -6.193629 },
{ 5.789021, -0.734630, -6.573369 },
{ 7.097056, -0.172982, -6.046071 },
{ -6.202562, 3.152015, -6.250632 },
{ -6.598511, 3.181133, -5.376596 },
{ -5.879135, 2.252396, -6.338049 },
{ -3.097153, 3.045646, -6.175594 },
{ -3.888514, 3.580848, -6.269758 },
{ -2.415842, 3.541069, -6.635956 },
{ 0.004020, 3.065952, -6.260601 },
{ -0.714153, 3.647384, -6.000359 },
{ 0.650339, 3.152212, -5.556049 },
{ 3.148082, 3.065474, -6.236447 },
{ 3.111314, 3.313051, -5.309670 },
{ 2.384648, 3.494128, -6.630129 },
{ 6.195396, 3.144020, -6.257042 },
{ 6.825505, 3.254686, -5.541307 },
{ 5.765894, 2.305751, -6.071584 },
{ -6.224762, 6.269436, -6.199499 },
{ -6.227138, 5.744470, -7.003219 },
{ -5.898129, 5.671700, -5.523050 },
{ -3.049795, 6.244848, -6.205918 },
{ -3.087748, 5.286175, -6.173255 },
{ -3.968304, 6.520275, -6.251129 },
{ -0.053210, 6.218043, -6.169688 },
{ 0.825799, 6.589399, -6.064810 },
{ 0.018791, 5.642523, -6.934642 },
{ 3.109156, 6.250395, -6.157883 },
{ 3.646142, 5.470269, -6.314764 },
{ 2.467680, 6.248139, -6.872071 },
{ 6.221542, 6.201019, -6.270430 },
{ 5.372468, 6.425629, -5.882893 },
{ 6.803922, 6.076521, -5.517505 },
{ -6.192636, -6.150665, -3.134919 },
{ -6.377934, -7.011364, -3.517572 },
{ -6.257279, -6.290045, -2.187314 },
{ -3.109530, -6.270465, -3.117828 },
{ -2.298394, -5.772194, -2.993950 },
{ -3.809490, -5.627637, -2.982220 },
{ -0.038820, -6.182503, -3.150607 },
{ -0.071984, -7.054630, -2.750788 },
{ 0.688173, -5.741421, -2.705086 },
{ 3.102774, -6.145922, -3.077989 },
{ 2.352681, -6.724399, -3.233832 },
{ 3.862449, -6.652292, -3.374712 },
{ 6.221089, -6.201529, -3.167266 },
{ 6.825244, -6.363707, -2.439079 },
{ 5.358331, -6.130338, -2.752367 },
{ -6.262103, -3.132226, -3.123586 },
{ -6.166340, -2.275929, -2.700331 },
{ -5.366218, -3.471706, -3.184445 },
{ -3.111137, -3.051004, -3.142406 },
{ -3.311768, -3.968529, -3.341042 },
{ -2.770611, -3.068346, -2.245019 },
{ 0.005724, -3.130303, -3.163012 },
{ 0.482202, -2.374690, -2.811473 },
{ -0.573062, -3.403472, -2.447507 },
{ 3.095078, -3.099676, -3.168462 },
{ 2.417453, -3.190640, -2.494584 },
{ 3.919837, -3.073655, -2.677893 },
{ 6.196105, -3.040136, -3.088337 },
{ 5.640465, -3.619831, -3.614436 },
{ 6.939673, -3.589544, -2.829842 },
{ -6.182065, -0.003400, -3.042390 },
{ -6.005810, -0.591008, -3.780776 },
{ -6.797182, 0.644978, -3.392815 },
{ -3.055877, -0.038021, -3.078205 },
{ -2.957574, 0.804401, -3.527898 },
{ -4.001938, -0.200904, -3.077218 },
{ -0.034735, 0.036962, -3.061441 },
{ -0.339387, -0.376429, -3.872525 },
{ 0.890739, -0.210258, -2.998671 },
{ 3.137299, -0.056306, -3.103061 },
{ 3.449365, 0.817518, -3.349247 },
{ 2.217754, 0.076224, -2.861330 },
{ 6.202733, -0.057422, -3.135143 },
{ 6.891866, 0.607339, -3.204067 },
{ 5.583070, 0.304112, -2.497277 },
{ -6.235328, 3.091028, -3.161196 },
{ -5.620224, 3.796590, -2.948140 },
{ -6.337344, 2.604974, -2.339669 },
{ -3.100761, 3.085670, -3.040001 },
{ -3.841514, 3.471502, -3.513266 },
{ -2.405567, 3.015122, -3.698249 },
{ 0.017686, 3.040997, -3.114710 },
{ -0.562190, 3.593571, -3.643829 },
{ 0.281457, 3.602138, -2.381834 },
{ 3.040493, 3.118625, -3.091261 },
{ 3.497428, 2.301545, -2.878768 },
{ 3.706278, 3.661985, -3.519106 },
{ 6.153747, 3.141770, -3.110452 },
{ 6.524448, 2.527782, -3.748544 },
{ 6.728033, 3.068367, -2.344704 },
{ -6.228412, 6.153262, -3.134991 },
{ -5.497842, 6.211200, -2.514933 },
{ -6.569498, 7.048988, -3.188810 },
{ -3.114261, 6.247531, -3.052990 },
{ -3.763440, 5.838093, -3.629608 },
{ -2.269351, 5.925773, -3.375729 },
{ 0.033856, 6.255675, -3.075505 },
{ 0.340270, 5.631131, -3.737032 },
{ -0.877663, 6.003468, -2.910926 },
{ 3.072932, 6.151993, -3.082847 },
{ 3.294846, 6.929869, -2.565910 },
{ 3.393954, 6.350465, -3.965522 },
{ 6.229389, 6.147520, -3.121044 },
{ 5.797138, 6.388219, -2.298375 },
{ 6.254689, 6.963103, -3.626757 },
{ -6.218080, -6.208893, -0.064724 },
{ -5.793234, -6.874918, 0.480691 },
{ -6.438098, -5.502241, 0.546665 },
{ -3.161793, -6.216735, -0.028339 },
{ -2.502753, -6.872853, 0.209857 },
{ -2.775567, -5.379832, 0.239959 },
{ -0.002532, -6.140991, -0.003478 },
{ 0.689039, -6.720671, -0.330985 },
{ -0.648843, -6.734293, 0.386184 },
{ 3.039844, -6.205646, -0.017228 },
{ 3.777609, -6.569800, -0.511855 },
{ 3.436401, -5.858902, 0.785313 },
{ 6.257004, -6.165220, -0.008551 },
{ 5.368434, -6.091008, -0.364215 },
{ 6.245060, -6.979374, 0.499948 },
{ -6.246883, -3.055033, -0.019337 },
{ -6.350454, -3.640127, 0.734652 },
{ -5.423699, -3.332793, -0.427723 },
{ -3.094331, -3.063472, 0.051555 },
{ -2.443051, -3.620051, -0.381590 },
{ -3.906094, -3.218919, -0.436745 },
{ 0.059986, -3.108175, 0.026527 },
{ -0.319331, -2.356822, -0.435152 },
{ -0.632825, -3.772569, 0.014099 },
{ 3.056825, -3.094971, -0.045775 },
{ 3.286789, -3.903484, 0.417890 },
{ 3.657675, -2.435504, 0.308690 },
{ 6.204418, -3.046271, -0.032672 },
{ 5.666837, -3.316225, 0.715455 },
{ 6.781360, -3.795765, -0.196864 },
{ -6.187331, 0.042326, -0.046499 },
{ -6.739113, -0.736038, -0.152558 },
{ -5.980298, 0.064208, 0.890635 },
{ -3.111868, -0.045870, -0.046351 },
{ -3.369378, -0.088582, 0.877460 },
{ -2.701406, 0.816674, -0.141741 },
{ -0.028600, -0.027927, -0.052228 },
{ -0.450128, 0.284536, 0.751664 },
{ 0.904097, 0.158746, 0.077351 },
{ 3.043640, 0.022778, -0.015695 },
{ 3.263633, -0.820206, 0.387469 },
{ 3.890123, 0.458652, -0.138341 },
{ 6.198501, 0.054145, -0.036443 },
{ 5.524424, -0.562672, 0.258040 },
{ 7.017693, -0.296767, 0.320414 },
{ -6.142883, 3.087172, 0.001701 },
{ -6.832739, 2.822585, 0.614608 },
{ -6.592184, 3.640199, -0.641611 },
{ -3.054590, 3.097169, -0.043753 },
{ -3.795838, 2.503772, 0.097642 },
{ -3.184109, 3.800316, 0.596849 },
{ 0.025258, 3.140300, 0.048161 },
{ -0.898451, 3.040556, -0.193447 },
{ 0.497539, 2.578923, -0.571006 },
{ 3.142639, 3.155831, 0.004528 },
{ 3.281734, 2.283294, 0.379885 },
{ 2.300622, 3.089671, -0.451752 },
{ 6.271003, 3.089878, -0.000229 },
{ 5.555786, 2.545332, -0.337120 },
{ 5.835504, 3.874496, 0.340762 },
{ -6.186874, 6.153181, -0.032864 },
{ -6.458269, 6.211097, 0.886130 },
{ -6.268404, 7.050370, -0.364476 },
{ -3.063571, 6.194209, -0.050917 },
{ -2.845329, 6.642761, 0.769286 },
{ -3.992058, 5.967481, 0.038907 },
{ -0.005511, 6.203833, 0.065479 },
{ -0.675428, 5.996461, -0.590089 },
{ 0.762902, 6.461025, -0.449259 },
{ 3.107182, 6.260055, -0.038149 },
{ 3.570052, 6.091314, 0.785768 },
{ 2.575104, 5.473755, -0.180227 },
{ 6.264803, 6.186329, 0.022994 },
{ 5.538470, 5.646253, -0.296882 },
{ 5.951245, 7.089071, -0.068103 },
{ -6.267283, -6.211735, 3.078419 },
{ -5.985306, -6.384271, 3.979686 },
{ -5.465039, -5.947785, 2.622023 },
{ -3.107839, -6.241119, 3.047498 },
{ -2.699991, -6.510712, 3.873658 },
{ -3.434740, -5.354930, 3.218863 },
{ -0.033434, -6.169301, 3.060705 },
{ 0.838698, -6.005633, 3.426984 },
{ -0.308002, -6.999962, 3.455898 },
{ 3.150365, -6.250863, 3.115724 },
{ 2.771880, -5.609654, 3.721663 },
{ 2.687846, -6.101322, 2.287910 },
{ 6.204347, -6.213550, 3.168674 },
{ 5.750267, -6.738865, 2.505789 },
{ 6.699059, -5.564375, 2.663310 },
{ -6.172325, -3.107328, 3.047333 },
{ -6.828965, -2.449862, 3.288422 },
{ -6.128632, -3.692984, 3.806714 },
{ -3.080296, -3.042262, 3.111628 },
{ -3.599745, -3.563632, 3.727994 },
{ -2.972174, -3.611996, 2.346596 },
{ 0.018427, -3.040709, 3.111508 },
{ -0.861291, -3.412145, 3.209954 },
{ 0.568794, -3.788138, 2.866545 },
{ 3.076991, -3.074154, 3.156063 },
{ 3.816301, -3.685968, 3.130285 },
{ 2.808084, -2.983447, 2.238990 },
{ 6.202874, -3.044570, 3.132656 },
{ 5.483336, -3.645941, 2.927282 },
{ 6.989368, -3.493060, 2.813525 },
{ -6.185279, -0.059803, 3.120451 },
{ -6.419455, 0.669043, 3.699681 },
{ -6.332522, 0.280211, 2.234860 },
{ -3.050408, 0.039017, 3.105488 },
{ -3.468427, -0.425632, 3.834133 },
{ -3.577897, -0.193686, 2.337916 },
{ 0.036504, -0.020609, 3.153990 },
{ 0.239664, -0.086591, 2.218077 },
{ -0.819081, 0.413707, 3.184104 },
{ 3.091492, 0.008311, 3.039147 },
{ 2.481020, -0.295977, 3.714642 },
{ 3.913193, 0.164051, 3.510436 },
{ 6.191365, -0.063471, 3.111335 },
{ 6.055864, 0.479518, 2.331358 },
{ 6.599523, 0.527950, 3.747880 },
{ -6.205614, 3.054919, 3.058779 },
{ -6.876203, 3.731733, 3.176233 },
{ -5.553000, 3.242989, 3.737223 },
{ -3.118412, 3.069232, 3.157498 },
{ -3.646030, 3.741133, 2.719629 },
{ -2.320885, 3.006400, 2.626871 },
{ 0.024980, 3.055432, 3.065769 },
{ -0.877220, 3.144581, 3.381441 },
{ 0.480709, 3.822007, 3.421065 },
{ 3.070975, 3.105245, 3.160550 },
{ 3.950017, 3.440960, 2.970440 },
{ 2.769856, 2.734952, 2.327620 },
{ 6.198446, 3.079479, 3.164063 },
{ 7.022878, 3.306229, 2.727648 },
{ 5.520109, 3.278660, 2.514642 },
{ -6.193602, 6.242270, 3.157025 },
{ -5.567869, 5.886374, 2.521920 },
{ -7.052009, 5.960994, 2.832091 },
{ -3.103387, 6.145098, 3.080057 },
{ -2.343780, 6.698458, 3.275890 },
{ -3.861615, 6.691317, 3.299822 },
{ -0.045554, 6.242642, 3.134180 },
{ 0.637737, 6.548568, 2.533277 },
{ 0.085332, 5.292898, 3.183344 },
{ 3.128530, 6.249892, 3.145938 },
{ 3.572612, 5.823157, 2.409562 },
{ 2.233691, 5.903232, 3.120423 },
{ 6.255670, 6.195132, 3.061028 },
{ 5.552429, 5.596136, 3.322210 },
{ 6.082243, 6.999450, 3.555555 },
{ -6.208072, -6.163006, 6.157412 },
{ -6.293854, -5.991009, 7.097954 },
{ -6.096342, -7.114505, 6.096361 },
{ -3.093215, -6.194828, 6.270532 },
{ -2.561298, -5.900834, 5.527435 },
{ -3.805554, -6.699586, 5.871339 },
{ 0.028309, -6.255582, 6.240192 },
{ -0.704628, -5.700497, 6.516318 },
{ 0.255286, -5.935581, 5.364040 },
{ 3.112376, -6.185324, 6.145057 },
{ 3.768593, -6.549569, 6.743611 },
{ 2.294122, -6.201701, 6.646808 },
{ 6.221282, -6.173949, 6.151454 },
{ 6.616602, -6.986255, 6.476173 },
{ 5.563911, -5.945569, 6.812716 },
{ -6.214945, -3.105559, 6.141418 },
{ -6.767312, -2.662372, 6.789520 },
{ -5.513791, -3.508545, 6.658668 },
{ -3.134984, -3.050634, 6.183218 },
{ -2.194062, -3.145360, 6.348303 },
{ -3.509793, -3.897382, 6.436395 },
{ 0.019709, -3.066046, 6.156136 },
{ -0.062167, -2.811154, 7.078030 },
{ -0.250671, -3.986954, 6.136538 },
{ 3.047052, -3.093053, 6.174132 },
{ 3.846770, -3.511425, 5.847060 },
{ 3.252831, -2.858011, 7.081861 },
{ 6.264526, -3.131008, 6.192287 },
{ 6.014957, -2.208761, 6.098811 },
{ 5.479151, -3.558207, 6.541928 },
{ -6.202784, 0.012060, 6.271161 },
{ -5.794767, -0.706266, 5.782190 },
{ -6.679360, 0.514844, 5.606597 },
{ -3.132137, 0.011406, 6.148615 },
{ -3.531033, -0.354855, 6.941266 },
{ -2.218018, 0.173816, 6.392684 },
{ -0.048817, -0.044068, 6.207411 },
{ 0.264785, 0.472342, 5.461397 },
{ 0.510082, 0.227141, 6.939285 },
{ 3.104615, -0.056762, 6.239817 },
{ 2.334121, 0.441331, 5.957323 },
{ 3.851786, 0.459650, 5.928986 },
{ 6.191962, -0.011674, 6.269664 },
{ 7.056171, 0.162434, 5.889678 },
{ 5.589740, 0.022864, 5.522872 },
{ -6.227582, 3.048278, 6.177333 },
{ -5.456950, 3.575652, 5.954701 },
{ -6.623561, 3.504488, 6.923412 },
{ -3.095950, 3.167462, 6.219110 },
{ -3.718176, 2.753599, 5.616521 },
{ -2.605272, 2.434738, 6.598467 },
{ -0.028196, 3.102085, 6.266027 },
{ 0.892169, 3.276065, 6.055742 },
{ -0.444613, 2.949998, 5.414541 },
{ 3.122055, 3.044925, 6.230400 },
{ 2.318548, 3.530579, 6.430594 },
{ 3.590528, 3.602778, 5.605184 },
{ 6.235943, 3.056340, 6.242112 },
{ 5.925321, 3.913199, 6.543556 },
{ 6.022471, 3.038970, 5.306329 },
{ -6.152078, 6.212531, 6.242895 },
{ -6.277517, 6.463813, 5.324917 },
{ -7.001466, 5.855602, 6.512529 },
{ -3.075211, 6.151648, 6.229296 },
{ -3.984620, 6.273567, 5.947033 },
{ -2.668015, 7.012240, 6.106276 },
{ 0.047399, 6.200405, 6.251791 },
{ -0.389422, 5.502373, 5.758333 },
{ -0.362937, 7.009521, 5.937917 },
{ 3.121019, 6.156392, 6.245211 },
{ 3.669300, 6.880502, 5.934383 },
{ 2.256232, 6.330001, 5.866310 },
{ 6.204797, 6.271399, 6.195395 },
{ 5.469074, 5.654753, 6.199970 },
{ 6.973096, 5.730251, 6.391449 }
};
for(int atom = 0; atom < natoms; ++atom)
positions.push_back(Vec3(coords[atom][0], coords[atom][1], coords[atom][2])*OpenMM::NmPerAngstrom);
}else{
throw exception();
}
system.setDefaultPeriodicBoxVectors(Vec3(boxEdgeLength, 0, 0),
Vec3(0, boxEdgeLength, 0),
Vec3(0, 0, boxEdgeLength));
sig.clear();
eps.clear();
bonds.clear();
for(int atom = 0; atom < natoms; ++atom){
system.addParticle(masses[atom%RESSIZE]);
double sigma = 2.0*pow(2.0, -1.0/6.0)*halfrmins[atom%RESSIZE]*OpenMM::NmPerAngstrom;
double epsilon = fabs(epsilons[atom%RESSIZE])*OpenMM::KJPerKcal;
sig.push_back(0.5*sigma);
eps.push_back(2.0*sqrt(epsilon));
if(atom%RESSIZE == 0){
bonds.push_back(pair<int, int>(atom, atom+1));
bonds.push_back(pair<int, int>(atom, atom+2));
}
double charge = do_electrostatics ? charges[atom] : 0;
forceField->addParticle(charge, sigma, epsilon);
}
}
void print_forces(const vector<Vec3>& forces){
// Print the forces in AKMA units, to compare against other codes.
std::cout << "Forces:" << std::endl;
for(int n = 0; n < forces.size(); ++ n){
std::cout << setw(3)<< n+1
<< setw(16) << setprecision(10) << -forces[n][0]*OpenMM::NmPerAngstrom*OpenMM::KcalPerKJ
<< setw(16) << setprecision(10) << -forces[n][1]*OpenMM::NmPerAngstrom*OpenMM::KcalPerKJ
<< setw(16) << setprecision(10) << -forces[n][2]*OpenMM::NmPerAngstrom*OpenMM::KcalPerKJ << std::endl;
}
}
void test_water2_dpme_energies_forces_no_exclusions() {
const double cutoff = 7.0*OpenMM::NmPerAngstrom;
const double alpha = 0.45*OpenMM::AngstromsPerNm;
const double dalpha = 0.45*OpenMM::AngstromsPerNm;
const int grid = 32;
NonbondedForce* forceField = new NonbondedForce();
vector<Vec3> positions;
vector<double> epsvals;
vector<double> sigvals;
vector<pair<int, int> > bonds;
System system;
const int NATOMS = 6;
double boxEdgeLength = 25*OpenMM::NmPerAngstrom;
make_waterbox(NATOMS, boxEdgeLength, forceField, positions, epsvals, sigvals, bonds, system, false);
forceField->setNonbondedMethod(OpenMM::NonbondedForce::LJPME);
forceField->setPMEParameters(alpha, grid, grid, grid);
forceField->setLJPMEParameters(dalpha, grid, grid, grid);
forceField->setCutoffDistance(cutoff);
forceField->setReactionFieldDielectric(1.0);
system.addForce(forceField);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
double refenergy = 322.193557*OpenMM::KJPerKcal;
vector<Vec3> refforces(6);
refforces[0] = Vec3( -0.0075112601, 0.0001181820, 1598.8884050404 )*-OpenMM::AngstromsPerNm*OpenMM::KJPerKcal;
refforces[1] = Vec3( -399.7221412167, 0.0009078954, -799.4541619659 )*-OpenMM::AngstromsPerNm*OpenMM::KJPerKcal;
refforces[2] = Vec3( 399.7249891850, 0.0022847756, -799.4520972788 )*-OpenMM::AngstromsPerNm*OpenMM::KJPerKcal;
refforces[3] = Vec3( 0.0425828202, 0.0422389115, 1598.9516906516 )*-OpenMM::AngstromsPerNm*OpenMM::KJPerKcal;
refforces[4] = Vec3( -399.7517916369, -0.0380211838, -799.4745351713 )*-OpenMM::AngstromsPerNm*OpenMM::KJPerKcal;
refforces[5] = Vec3( 399.7138981618, -0.0075023610, -799.4592751266 )*-OpenMM::AngstromsPerNm*OpenMM::KJPerKcal;
State state = context.getState(State::Forces | State::Energy);
double energy = state.getPotentialEnergy();
// std::cout << "Energy " << energy*OpenMM::KcalPerKJ << std::endl;
const vector<Vec3>& forces = state.getForces();
// print_forces(forces);
ASSERT_EQUAL_TOL(refenergy, energy, 1E-8);
for(int n = 0; n < NATOMS; ++n)
ASSERT_EQUAL_VEC(refforces[n], forces[n], 1E-8);
}
void test_water2_dpme_energies_forces_with_exclusions() {
const double cutoff = 7.0*OpenMM::NmPerAngstrom;
const double alpha = 0.45*OpenMM::AngstromsPerNm;
const double dalpha = 0.45*OpenMM::AngstromsPerNm;
const int grid = 32;
NonbondedForce* forceField = new NonbondedForce();
vector<Vec3> positions;
vector<double> epsvals;
vector<double> sigvals;
vector<pair<int, int> > bonds;
System system;
const int NATOMS = 6;
double boxEdgeLength = 25*OpenMM::NmPerAngstrom;
make_waterbox(NATOMS, boxEdgeLength, forceField, positions, epsvals, sigvals, bonds, system, false);
forceField->setNonbondedMethod(OpenMM::NonbondedForce::LJPME);
forceField->createExceptionsFromBonds(bonds, 1.0, 1.0);
forceField->setPMEParameters(alpha, grid, grid, grid);
forceField->setLJPMEParameters(dalpha, grid, grid, grid);
forceField->setCutoffDistance(cutoff);
forceField->setReactionFieldDielectric(1.0);
system.addForce(forceField);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
double refenergy = -0.186059064*OpenMM::KJPerKcal;
vector<Vec3> refforces(6);
refforces[0] = Vec3( -0.0075112601, 0.0001181820, -0.0226423064 )*-OpenMM::AngstromsPerNm*OpenMM::KJPerKcal;
refforces[1] = Vec3( 0.0011347776, 0.0009078954, 0.0013617075 )*-OpenMM::AngstromsPerNm*OpenMM::KJPerKcal;
refforces[2] = Vec3( 0.0017131906, 0.0022847756, 0.0034263946 )*-OpenMM::AngstromsPerNm*OpenMM::KJPerKcal;
refforces[3] = Vec3( 0.0425828202, 0.0422389115, 0.0406433048 )*-OpenMM::AngstromsPerNm*OpenMM::KJPerKcal;
refforces[4] = Vec3( -0.0285156425, -0.0380211838, -0.0190114979 )*-OpenMM::AngstromsPerNm*OpenMM::KJPerKcal;
refforces[5] = Vec3( -0.0093778326, -0.0075023610, -0.0037514532 )*-OpenMM::AngstromsPerNm*OpenMM::KJPerKcal;
State state = context.getState(State::Forces | State::Energy);
double energy = state.getPotentialEnergy();
// std::cout << "Energy " << energy*OpenMM::KcalPerKJ << std::endl;
const vector<Vec3>& forces = state.getForces();
// print_forces(forces);
ASSERT_EQUAL_TOL(refenergy, energy, 1E-8);
for(int n = 0; n < NATOMS; ++n)
ASSERT_EQUAL_VEC(refforces[n], forces[n], 1E-8);
}
void test_water125_dpme_vs_long_cutoff_no_exclusions() {
const double cutoff = 8.5*OpenMM::NmPerAngstrom;
const double alpha = 0.45*OpenMM::AngstromsPerNm;
const double dalpha = 0.45*OpenMM::AngstromsPerNm;
const int grid = 32;
NonbondedForce* forceField = new NonbondedForce();
vector<Vec3> positions;
vector<double> epsvals;
vector<double> sigvals;
vector<pair<int, int> > bonds;
System system;
const int NATOMS = 375;
double boxEdgeLength = 17.01*OpenMM::NmPerAngstrom;
make_waterbox(NATOMS, boxEdgeLength, forceField, positions, epsvals, sigvals, bonds, system, false);
forceField->setNonbondedMethod(OpenMM::NonbondedForce::LJPME);
forceField->setPMEParameters(alpha, grid, grid, grid);
forceField->setLJPMEParameters(dalpha, grid, grid, grid);
forceField->setCutoffDistance(cutoff);
forceField->setReactionFieldDielectric(1.0);
system.addForce(forceField);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
double energy = state.getPotentialEnergy();
// std::cout << "Energy " << energy*OpenMM::KcalPerKJ << std::endl;
const vector<Vec3>& forces = state.getForces();
// print_forces(forces);
const double longcutoff = 30.0*OpenMM::NmPerAngstrom;
const double longcutoff2 = longcutoff*longcutoff;
const double cutoff2 = cutoff*cutoff;
const double cutoff6inv = 1.0 / (cutoff2*cutoff2*cutoff2);
const int nboxes = ceil(longcutoff/boxEdgeLength);
double refenergy = 0.0;
// Loop over home box first...
for(int i = 0; i < NATOMS; ++ i){
for(int j = i+1; j < NATOMS; ++j){
Vec3 dR = positions[i] - positions[j];
double R2 = dR[0]*dR[0] + dR[1]*dR[1] + dR[2]*dR[2];
double sig2 = (sigvals[i] + sigvals[j])*(sigvals[i] + sigvals[j]) / R2;
double sig6 = sig2*sig2*sig2;
double eps = epsvals[i]*epsvals[j];
refenergy += 2.0*eps*(sig6-1.0)*sig6;
if(R2 < cutoff2){
// Add a shift term for direct space parts withing t
refenergy += 2.0*eps*(pow(sigvals[i]+sigvals[j], 6) - 64.0*pow(sigvals[i]*sigvals[j], 3))*cutoff6inv;
}
}
}
// ... and now add in the image box terms
for(int bx = -nboxes; bx <= nboxes; ++bx){
for(int by = -nboxes; by <= nboxes; ++by){
for(int bz = -nboxes; bz <= nboxes; ++bz){
if(bx==0 && by==0 && bz==0) continue;
Vec3 offset(bx*boxEdgeLength, by*boxEdgeLength, bz*boxEdgeLength);
for(int i = 0; i < NATOMS; ++ i){
for(int j = 0; j < NATOMS; ++j){
Vec3 dR = positions[i] - positions[j] + offset;
double R2 = dR[0]*dR[0] + dR[1]*dR[1] + dR[2]*dR[2];
if(R2 > longcutoff2) continue;
double sig2 = (sigvals[i] + sigvals[j])*(sigvals[i] + sigvals[j]) / R2;
double sig6 = sig2*sig2*sig2;
double eps = epsvals[i]*epsvals[j];
refenergy += eps*(sig6-1.0)*sig6;
if(R2 < cutoff2){
// Add a shift term for direct space parts withing teh
refenergy += eps*(pow(sigvals[i]+sigvals[j], 6) - 64.0*pow(sigvals[i]*sigvals[j], 3))*cutoff6inv;
}
}
}
}
}
}
refenergy *= 0.5;
// For this test the reference energy is 545636 kJ/mol, while the difference between DPME and 30A cutoffs
// is just 1.062 kJ/mol. The difference is due to the fact that arithmetic mean combination rules are used
// up to the cutoff, while the reciprocal space uses the geometric mean. See DOI: 10.1021/acs.jctc.5b00726
ASSERT_EQUAL_TOL(refenergy, energy, 5E-6);
}
void test_water125_dpme_vs_long_cutoff_with_exclusions() {
const double cutoff = 8.5*OpenMM::NmPerAngstrom;
const double alpha = 0.45*OpenMM::AngstromsPerNm;
const double dalpha = 0.45*OpenMM::AngstromsPerNm;
const int grid = 32;
NonbondedForce* forceField = new NonbondedForce();
vector<Vec3> positions;
vector<double> epsvals;
vector<double> sigvals;
vector<pair<int, int> > bonds;
System system;
const int NATOMS = 375;
double boxEdgeLength = 17.01*OpenMM::NmPerAngstrom;
make_waterbox(NATOMS, boxEdgeLength, forceField, positions, epsvals, sigvals, bonds, system, false);
forceField->setNonbondedMethod(OpenMM::NonbondedForce::LJPME);
forceField->createExceptionsFromBonds(bonds, 1.0, 1.0);
forceField->setPMEParameters(alpha, grid, grid, grid);
forceField->setLJPMEParameters(dalpha, grid, grid, grid);
forceField->setCutoffDistance(cutoff);
forceField->setReactionFieldDielectric(1.0);
system.addForce(forceField);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
double energy = state.getPotentialEnergy();
// std::cout << "Energy " << energy*OpenMM::KcalPerKJ << std::endl;
const vector<Vec3>& forces = state.getForces();
// print_forces(forces);
// Find the exclusion information
vector<set<int> > exclusions(NATOMS);
for (int i = 0; i < forceField->getNumExceptions(); i++) {
int particle1, particle2;
double chargeProd, sigma, epsilon;
forceField->getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
exclusions[particle1].insert(particle2);
exclusions[particle2].insert(particle1);
}
const double longcutoff = 35.0*OpenMM::NmPerAngstrom;
const double longcutoff2 = longcutoff*longcutoff;
const double cutoff2 = cutoff*cutoff;
const double cutoff6inv = 1.0 / (cutoff2*cutoff2*cutoff2);
const int nboxes = ceil(longcutoff/boxEdgeLength);
double refenergy = 0.0;
// Loop over home box first...
for(int i = 0; i < NATOMS; ++ i){
for(int j = i+1; j < NATOMS; ++j){
Vec3 dR = positions[i] - positions[j];
double R2 = dR[0]*dR[0] + dR[1]*dR[1] + dR[2]*dR[2];
double sig2 = (sigvals[i] + sigvals[j])*(sigvals[i] + sigvals[j]) / R2;
double sig6 = sig2*sig2*sig2;
double eps = epsvals[i]*epsvals[j];
refenergy += 2.0*eps*(sig6-1.0)*sig6;
if(R2 < cutoff2){
// Add a shift term for direct space parts withing t
refenergy += 2.0*eps*(pow(sigvals[i]+sigvals[j], 6) - 64.0*pow(sigvals[i]*sigvals[j], 3))*cutoff6inv;
}
}
}
// ... back out exclusions
for (int ii = 0; ii < NATOMS; ii++){
for (set<int>::const_iterator iter = exclusions[ii].begin(); iter != exclusions[ii].end(); ++iter) {
if (*iter > ii) {
int i = ii;
int j = *iter;
Vec3 dR = positions[i] - positions[j];
double R2 = dR[0]*dR[0] + dR[1]*dR[1] + dR[2]*dR[2];
double sig2 = (sigvals[i] + sigvals[j])*(sigvals[i] + sigvals[j]) / R2;
double sig6 = sig2*sig2*sig2;
double eps = epsvals[i]*epsvals[j];
refenergy -= 2.0*eps*(sig6-1.0)*sig6;
if(R2 < cutoff2){
// Add a shift term for direct space parts withing t
refenergy -= 2.0*eps*(pow(sigvals[i]+sigvals[j], 6) - 64.0*pow(sigvals[i]*sigvals[j], 3))*cutoff6inv;
}
}
}
}
// ... and now add in the image box terms
for(int bx = -nboxes; bx <= nboxes; ++bx){
for(int by = -nboxes; by <= nboxes; ++by){
for(int bz = -nboxes; bz <= nboxes; ++bz){
if(bx==0 && by==0 && bz==0) continue;
Vec3 offset(bx*boxEdgeLength, by*boxEdgeLength, bz*boxEdgeLength);
for(int i = 0; i < NATOMS; ++ i){
for(int j = 0; j < NATOMS; ++j){
Vec3 dR = positions[i] - positions[j] + offset;
double R2 = dR[0]*dR[0] + dR[1]*dR[1] + dR[2]*dR[2];
if(R2 > longcutoff2) continue;
double sig2 = (sigvals[i] + sigvals[j])*(sigvals[i] + sigvals[j]) / R2;
double sig6 = sig2*sig2*sig2;
double eps = epsvals[i]*epsvals[j];
refenergy += eps*(sig6-1.0)*sig6;
if(R2 < cutoff2){
// Add a shift term for direct space parts withing teh
refenergy += eps*(pow(sigvals[i]+sigvals[j], 6) - 64.0*pow(sigvals[i]*sigvals[j], 3))*cutoff6inv;
}
}
}
}
}
}
refenergy *= 0.5;
// For this test the reference energy is -294.078 kJ/mol, while the difference between DPME and 30A cutoffs
// is just 0.064 kJ/mol. The difference is due to the fact that arithmetic mean combination rules are used
// up to the cutoff, while the reciprocal space uses the geometric mean. See DOI: 10.1021/acs.jctc.5b00726
ASSERT_EQUAL_TOL(refenergy, energy, 5E-3);
}
void testCoulomb() { void testCoulomb() {
System system; System system;
system.addParticle(1.0); system.addParticle(1.0);
...@@ -689,6 +1447,10 @@ void runPlatformTests(); ...@@ -689,6 +1447,10 @@ void runPlatformTests();
int main(int argc, char* argv[]) { int main(int argc, char* argv[]) {
try { try {
initializeTests(argc, argv); initializeTests(argc, argv);
test_water2_dpme_energies_forces_no_exclusions();
test_water2_dpme_energies_forces_with_exclusions();
test_water125_dpme_vs_long_cutoff_no_exclusions();
test_water125_dpme_vs_long_cutoff_with_exclusions();
testCoulomb(); testCoulomb();
testLJ(); testLJ();
testExclusionsAnd14(); testExclusionsAnd14();
......
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