use of ffx.potential.nonbonded.ParticleMeshEwaldCart in project ffx by mjschnie.
the class ExtendedVariableTest method testEndStates.
/**
* Verify that a lys-lys system with two ESVs can exactly reproduce the
* energy yielded by vanilla energy() calls on mutated PDB files.
*/
public void testEndStates() {
ExtendedSystemConfig esvConfig = activateAll();
MolecularAssembly mola = openResource(stateFilenames[3], true);
ExtendedSystem esvSystem = (esvConfig != null) ? new ExtendedSystem(mola, esvConfig) : new ExtendedSystem(mola);
esvSystem.setConstantPh(7.4);
esvSystem.populate(esvResidueIDs);
mola.getPotentialEnergy().attachExtendedSystem(esvSystem);
ForceFieldEnergy ffe = mola.getPotentialEnergy();
if (resultsOnly) {
utils.setSilentPotential(true);
}
ParticleMeshEwaldQI esvPme = ffe.getPmeQiNode();
final double[] totalEsv = new double[4];
final double[] vdwEsv = new double[4];
final double[] permEsv = new double[4], permRealEsv = new double[4], permSelfEsv = new double[4], permRecipEsv = new double[4];
final double[] directEsv = new double[4];
final double[] mutualEsv = new double[4], indRealEsv = new double[4], indSelfEsv = new double[4], indRecipEsv = new double[4];
final String[] esvStateNames = new String[4];
final double[] decompPolarStateEsv = (decompPolarState == Polarization.MUTUAL) ? mutualEsv : directEsv;
final double[] decompPolarCompEsv = (decompPolarComplement == Polarization.MUTUAL) ? mutualEsv : directEsv;
esvSystem.setLambda(0, 0.0);
esvSystem.setLambda(1, 0.0);
esvStateNames[0] = format("L=%1.0f,%1.0f", esvSystem.getLambda(0), esvSystem.getLambda(1));
esvPme.setPolarization(decompPolarState);
ffe.energy(true, false);
totalEsv[0] = ffe.getTotalEnergy() - esvSystem.getBiasEnergy();
vdwEsv[0] = ffe.getVanDerWaalsEnergy();
permEsv[0] = esvPme.getPermanentEnergy();
permRealEsv[0] = esvPme.getPermRealEnergy();
permSelfEsv[0] = esvPme.getPermSelfEnergy();
permRecipEsv[0] = esvPme.getPermRecipEnergy();
decompPolarStateEsv[0] = esvPme.getPolarizationEnergy();
indRealEsv[0] = esvPme.getIndRealEnergy();
indSelfEsv[0] = esvPme.getIndSelfEnergy();
indRecipEsv[0] = esvPme.getIndRecipEnergy();
ffe.getPmeNode().setPolarization(decompPolarComplement);
ffe.energy(true, false);
decompPolarCompEsv[0] = ffe.getPolarizationEnergy();
ffe.getPmeNode().setPolarization(decompPolarState);
esvSystem.setLambda(0, 0.0);
esvSystem.setLambda(1, 1.0);
esvStateNames[1] = format("L=%1.0f,%1.0f", esvSystem.getLambda(0), esvSystem.getLambda(1));
esvPme.setPolarization(decompPolarState);
ffe.energy(true, false);
totalEsv[1] = ffe.getTotalEnergy() - esvSystem.getBiasEnergy();
vdwEsv[1] = ffe.getVanDerWaalsEnergy();
permEsv[1] = esvPme.getPermanentEnergy();
permRealEsv[1] = esvPme.getPermRealEnergy();
permSelfEsv[1] = esvPme.getPermSelfEnergy();
permRecipEsv[1] = esvPme.getPermRecipEnergy();
decompPolarStateEsv[1] = esvPme.getPolarizationEnergy();
indRealEsv[1] = esvPme.getIndRealEnergy();
indSelfEsv[1] = esvPme.getIndSelfEnergy();
indRecipEsv[1] = esvPme.getIndRecipEnergy();
ffe.getPmeNode().setPolarization(decompPolarComplement);
ffe.energy(true, false);
decompPolarCompEsv[1] = ffe.getPolarizationEnergy();
ffe.getPmeNode().setPolarization(decompPolarState);
esvSystem.setLambda(0, 1.0);
esvSystem.setLambda(1, 0.0);
esvStateNames[2] = format("L=%1.0f,%1.0f", esvSystem.getLambda(0), esvSystem.getLambda(1));
esvPme.setPolarization(decompPolarState);
ffe.energy(true, false);
totalEsv[2] = ffe.getTotalEnergy() - esvSystem.getBiasEnergy();
vdwEsv[2] = ffe.getVanDerWaalsEnergy();
permEsv[2] = esvPme.getPermanentEnergy();
permRealEsv[2] = esvPme.getPermRealEnergy();
permSelfEsv[2] = esvPme.getPermSelfEnergy();
permRecipEsv[2] = esvPme.getPermRecipEnergy();
decompPolarStateEsv[2] = esvPme.getPolarizationEnergy();
indRealEsv[2] = esvPme.getIndRealEnergy();
indSelfEsv[2] = esvPme.getIndSelfEnergy();
indRecipEsv[2] = esvPme.getIndRecipEnergy();
ffe.getPmeNode().setPolarization(decompPolarComplement);
ffe.energy(true, false);
decompPolarCompEsv[2] = ffe.getPolarizationEnergy();
ffe.getPmeNode().setPolarization(decompPolarState);
esvSystem.setLambda(0, 1.0);
esvSystem.setLambda(1, 1.0);
esvStateNames[3] = format("L=%1.0f,%1.0f", esvSystem.getLambda(0), esvSystem.getLambda(1));
esvPme.setPolarization(decompPolarState);
ffe.energy(true, false);
totalEsv[3] = ffe.getTotalEnergy() - esvSystem.getBiasEnergy();
vdwEsv[3] = ffe.getVanDerWaalsEnergy();
permEsv[3] = esvPme.getPermanentEnergy();
permRealEsv[3] = esvPme.getPermRealEnergy();
permSelfEsv[3] = esvPme.getPermSelfEnergy();
permRecipEsv[3] = esvPme.getPermRecipEnergy();
decompPolarStateEsv[3] = esvPme.getPolarizationEnergy();
indRealEsv[3] = esvPme.getIndRealEnergy();
indSelfEsv[3] = esvPme.getIndSelfEnergy();
indRecipEsv[3] = esvPme.getIndRecipEnergy();
ffe.getPmeNode().setPolarization(decompPolarComplement);
ffe.energy(true, false);
decompPolarCompEsv[3] = ffe.getPolarizationEnergy();
ffe.getPmeNode().setPolarization(decompPolarState);
/* Open vanilla end states. */
MolecularAssembly qiMola, cartMola;
ForceFieldEnergy qiPot, cartPot;
final int numStates = stateFilenames.length;
final double[] totalQi = new double[numStates], totalCart = new double[numStates];
final double[] vdwQi = new double[numStates], vdwCart = new double[numStates];
final double[] permQi = new double[numStates], permCart = new double[numStates];
final double[] permRealQi = new double[numStates], permRealCart = new double[numStates];
final double[] permSelfQi = new double[numStates], permSelfCart = new double[numStates];
final double[] permRecipQi = new double[numStates], permRecipCart = new double[numStates];
final double[] mutualQi = new double[numStates], mutualCart = new double[numStates];
final double[] directQi = new double[numStates], directCart = new double[numStates];
final double[] indRealQi = new double[numStates], indRealCart = new double[numStates];
final double[] indSelfQi = new double[numStates], indSelfCart = new double[numStates];
final double[] indRecipQi = new double[numStates], indRecipCart = new double[numStates];
final double[] decompPolarStateQi = (decompPolarState == Polarization.MUTUAL) ? mutualQi : directQi;
final double[] decompPolarCompQi = (decompPolarComplement == Polarization.MUTUAL) ? mutualQi : directQi;
final double[] decompPolarStateCart = (decompPolarState == Polarization.MUTUAL) ? mutualCart : directCart;
final double[] decompPolarCompCart = (decompPolarComplement == Polarization.MUTUAL) ? mutualCart : directCart;
// Get manual (no ESVs) end state energy components from both vanilla-qi and cartesian PME.
for (int i = 0; i < stateFilenames.length; i++) {
String state = stateFilenames[i];
setProp("pme.qi", true);
qiMola = openResource(stateFilenames[i], true);
qiPot = qiMola.getPotentialEnergy();
ParticleMeshEwaldQI qiPme = qiPot.getPmeQiNode();
qiPme.setPolarization(decompPolarState);
qiPot.energy(true, false);
totalQi[i] = qiPot.getTotalEnergy();
vdwQi[i] = qiPot.getVanDerWaalsEnergy();
permQi[i] = qiPme.getPermanentEnergy();
permRealQi[i] = qiPme.getPermRealEnergy();
permSelfQi[i] = qiPme.getPermSelfEnergy();
permRecipQi[i] = qiPme.getPermRecipEnergy();
decompPolarStateQi[i] = qiPme.getPolarizationEnergy();
indRealQi[i] = qiPme.getIndRealEnergy();
indSelfQi[i] = qiPme.getIndSelfEnergy();
indRecipQi[i] = qiPme.getIndRecipEnergy();
qiPme.setPolarization(decompPolarComplement);
qiPot.energy(true, false);
decompPolarCompQi[i] = qiPme.getPolarizationEnergy();
utils.close(qiMola);
setProp("pme.qi", false);
cartMola = openResource(stateFilenames[i], true);
cartPot = cartMola.getPotentialEnergy();
ParticleMeshEwaldCart cartPme = (ParticleMeshEwaldCart) cartPot.getPmeNode();
cartPme.setPolarization(decompPolarState);
cartPot.energy(true, false);
totalCart[i] = cartPot.getTotalEnergy();
vdwCart[i] = cartPot.getVanDerWaalsEnergy();
permCart[i] = cartPme.getPermanentEnergy();
permRealCart[i] = cartPme.getPermRealEnergy();
permSelfCart[i] = cartPme.getPermSelfEnergy();
permRecipCart[i] = cartPme.getPermRecipEnergy();
decompPolarStateCart[i] = cartPme.getPolarizationEnergy();
indRealCart[i] = cartPme.getIndRealEnergy();
indSelfCart[i] = cartPme.getIndSelfEnergy();
indRecipCart[i] = cartPme.getIndRecipEnergy();
cartPme.setPolarization(decompPolarComplement);
cartPot.energy(true, false);
decompPolarCompCart[i] = cartPme.getPolarizationEnergy();
utils.close(cartMola);
if (assertions) {
assertEquals("Total" + i, totalCart[i], totalEsv[i], tolerance);
assertEquals("VanDerWaals" + i, vdwCart[i], vdwEsv[i], tolerance);
assertEquals("Permanent" + i, permCart[i], permEsv[i], tolerance);
assertEquals("Ind.Direct" + i, directCart[i], directEsv[i], tolerance);
assertEquals("Ind.Mutual" + i, mutualCart[i], mutualEsv[i], tolerance);
assertEquals("PermReal" + i, permRealCart[i], permRealEsv[i], tolerance);
assertEquals("PermSelf" + i, permSelfCart[i], permSelfEsv[i], tolerance);
assertEquals("PermRecip" + i, permRecipCart[i], permRecipEsv[i], tolerance);
assertEquals("IndReal" + i, indRealCart[i], indRealEsv[i], tolerance);
assertEquals("IndSelf" + i, indSelfCart[i], indSelfEsv[i], tolerance);
assertEquals("IndRecip" + i, indRecipCart[i], indRecipEsv[i], tolerance);
}
}
sb.append(format(" Two-site End State Analysis \n"));
sb.append(format(" ***************************** \n"));
if (includeManualQiEndStates) {
sb.append(format(" %-27s %-22s %-22s %-22s\n", "Extended System (1 File, QI)", "Manual (4 Files, QI)", "Manual (4 Files, Cart)", "Error (Cart-ESV)"));
} else {
sb.append(format(" %-27s %-22s %-22s\n", "Extended System (1 File, QI)", "Manual (4 Files, Cart)", "Error (Cart-ESV)"));
}
double[][] esvResult = new double[][] { totalEsv, vdwEsv, permEsv, directEsv, mutualEsv, permRealEsv, permSelfEsv, permRecipEsv, indRealEsv, indSelfEsv, indRecipEsv };
double[][] qiResult = new double[][] { totalQi, vdwQi, permQi, directQi, mutualQi, permRealQi, permSelfQi, permRecipQi, indRealQi, indSelfQi, indRecipQi };
double[][] cartResult = new double[][] { totalCart, vdwCart, permCart, directCart, mutualCart, permRealCart, permSelfCart, permRecipCart, indRealCart, indSelfCart, indRecipCart };
String[] names = new String[] { "Total", "VanWaals", "Permanent", "Direct", "Mutual", "PermReal", "PermSelf", "PermRecip", "IndReal", "IndSelf", "IndRecip" };
for (int component = 0; component < names.length; component++) {
for (int state = 0; state < numStates; state++) {
String name = (state == 0) ? names[component] : "";
sb.append(format(" %-27s", format("%-9s %-7.7s %10.5f", name, esvStateNames[state], esvResult[component][state])));
if (includeManualQiEndStates) {
sb.append(format(" %-22s", format("%-7.7s %12.6f", stateFilenames[state], qiResult[component][state])));
}
sb.append(format(" %-22s", format("%-7.7s %12.6f", stateFilenames[state], cartResult[component][state])));
final double error = Math.abs(cartResult[component][state] - esvResult[component][state]);
final String errorStr = (error < errorThreshold) ? format("< %.1e", errorThreshold) : format("%+g", error);
sb.append(format(" %16s\n", errorStr));
}
}
utils.setSilentPotential(false);
logger.info(sb.toString());
}
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