--- trunk/OOPSE/libmdtools/SimSetup.cpp 2003/11/10 21:50:36 859 +++ trunk/OOPSE/libmdtools/SimSetup.cpp 2004/01/26 21:52:56 984 @@ -30,6 +30,30 @@ using namespace std; using namespace std; +/** + * Check whether dividend is divisble by divisor or not + */ +bool isDivisible(double dividend, double divisor){ + double tolerance = 0.000001; + double quotient; + double diff; + int intQuotient; + + quotient = dividend / divisor; + + if (quotient < 0) + quotient = -quotient; + + intQuotient = int (quotient + tolerance); + + diff = fabs(fabs(dividend) - intQuotient * fabs(divisor)); + + if (diff <= tolerance) + return true; + else + return false; +} + SimSetup::SimSetup(){ initSuspend = false; @@ -150,7 +174,6 @@ void SimSetup::makeMolecules(void){ bend_set* theBends; torsion_set* theTorsions; - //init the forceField paramters the_ff->readParams(); @@ -158,6 +181,9 @@ void SimSetup::makeMolecules(void){ // init the atoms + double phi, theta, psi; + double sux, suy, suz; + double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz; double ux, uy, uz, u, uSqr; for (k = 0; k < nInfo; k++){ @@ -194,10 +220,34 @@ void SimSetup::makeMolecules(void){ info[k].n_oriented++; molInfo.myAtoms[j] = dAtom; - ux = currentAtom->getOrntX(); - uy = currentAtom->getOrntY(); - uz = currentAtom->getOrntZ(); + // Directional Atoms have standard unit vectors which are oriented + // in space using the three Euler angles. We assume the standard + // unit vector was originally along the z axis below. + phi = currentAtom->getEulerPhi() * M_PI / 180.0; + theta = currentAtom->getEulerTheta() * M_PI / 180.0; + psi = currentAtom->getEulerPsi()* M_PI / 180.0; + + Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); + Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); + Axz = sin(theta) * sin(psi); + + Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); + Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); + Ayz = sin(theta) * cos(psi); + + Azx = sin(phi) * sin(theta); + Azy = -cos(phi) * sin(theta); + Azz = cos(theta); + + sux = 0.0; + suy = 0.0; + suz = 1.0; + + ux = (Axx * sux) + (Ayx * suy) + (Azx * suz); + uy = (Axy * sux) + (Ayy * suy) + (Azy * suz); + uz = (Axz * sux) + (Ayz * suy) + (Azz * suz); + uSqr = (ux * ux) + (uy * uy) + (uz * uz); u = sqrt(uSqr); @@ -613,8 +663,8 @@ void SimSetup::gatherInfo(void){ } else{ sprintf(painCave.errMsg, - "SimSetup Warning. Unrecognized Ensemble -> %s, " - "reverting to NVE for this simulation.\n", + "SimSetup Warning. Unrecognized Ensemble -> %s \n" + "\treverting to NVE for this simulation.\n", ensemble); painCave.isFatal = 0; simError(); @@ -646,8 +696,8 @@ void SimSetup::gatherInfo(void){ if (!the_components[i]->haveNMol()){ // we have a problem sprintf(painCave.errMsg, - "SimSetup Error. No global NMol or component NMol" - " given. Cannot calculate the number of atoms.\n"); + "SimSetup Error. No global NMol or component NMol given.\n" + "\tCannot calculate the number of atoms.\n"); painCave.isFatal = 1; simError(); } @@ -667,6 +717,47 @@ void SimSetup::gatherInfo(void){ simError(); } + //check whether sample time, status time, thermal time and reset time are divisble by dt + if (!isDivisible(globals->getSampleTime(), globals->getDt())){ + sprintf(painCave.errMsg, + "Sample time is not divisible by dt.\n" + "\tThis will result in samples that are not uniformly\n" + "\tdistributed in time. If this is a problem, change\n" + "\tyour sampleTime variable.\n"); + painCave.isFatal = 0; + simError(); + } + + if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ + sprintf(painCave.errMsg, + "Status time is not divisible by dt.\n" + "\tThis will result in status reports that are not uniformly\n" + "\tdistributed in time. If this is a problem, change \n" + "\tyour statusTime variable.\n"); + painCave.isFatal = 0; + simError(); + } + + if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){ + sprintf(painCave.errMsg, + "Thermal time is not divisible by dt.\n" + "\tThis will result in thermalizations that are not uniformly\n" + "\tdistributed in time. If this is a problem, change \n" + "\tyour thermalTime variable.\n"); + painCave.isFatal = 0; + simError(); + } + + if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){ + sprintf(painCave.errMsg, + "Reset time is not divisible by dt.\n" + "\tThis will result in integrator resets that are not uniformly\n" + "\tdistributed in time. If this is a problem, change\n" + "\tyour resetTime variable.\n"); + painCave.isFatal = 0; + simError(); + } + // set the status, sample, and thermal kick times for (i = 0; i < nInfo; i++){ @@ -781,8 +872,9 @@ void SimSetup::finalInfoCheck(void){ if (!globals->haveECR()){ sprintf(painCave.errMsg, - "SimSetup Warning: using default value of 15.0 angstroms" - "box length for the electrostaticCutoffRadius.\n"); + "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" + "\tOOPSE will use a default value of 15.0 angstroms" + "\tfor the electrostaticCutoffRadius.\n"); painCave.isFatal = 0; simError(); theEcr = 15.0; @@ -793,8 +885,10 @@ void SimSetup::finalInfoCheck(void){ if (!globals->haveEST()){ sprintf(painCave.errMsg, - "SimSetup Warning: using default value of 0.05 * the " - "electrostaticCutoffRadius for the electrostaticSkinThickness\n"); + "SimSetup Warning: No value was set for electrostaticSkinThickness.\n" + "\tOOPSE will use a default value of\n" + "\t0.05 * electrostaticCutoffRadius\n" + "\tfor the electrostaticSkinThickness\n"); painCave.isFatal = 0; simError(); theEst = 0.05 * theEcr; @@ -807,8 +901,9 @@ void SimSetup::finalInfoCheck(void){ if (!globals->haveDielectric()){ sprintf(painCave.errMsg, - "SimSetup Error: You are trying to use Reaction Field without" - "setting a dielectric constant!\n"); + "SimSetup Error: No Dielectric constant was set.\n" + "\tYou are trying to use Reaction Field without" + "\tsetting a dielectric constant!\n"); painCave.isFatal = 1; simError(); } @@ -818,8 +913,9 @@ void SimSetup::finalInfoCheck(void){ if (usesDipoles){ if (!globals->haveECR()){ sprintf(painCave.errMsg, - "SimSetup Warning: using default value of 15.0 angstroms" - "box length for the electrostaticCutoffRadius.\n"); + "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" + "\tOOPSE will use a default value of 15.0 angstroms" + "\tfor the electrostaticCutoffRadius.\n"); painCave.isFatal = 0; simError(); theEcr = 15.0; @@ -830,9 +926,10 @@ void SimSetup::finalInfoCheck(void){ if (!globals->haveEST()){ sprintf(painCave.errMsg, - "SimSetup Warning: using default value of 0.05 * the " - "electrostaticCutoffRadius for the " - "electrostaticSkinThickness\n"); + "SimSetup Warning: No value was set for electrostaticSkinThickness.\n" + "\tOOPSE will use a default value of\n" + "\t0.05 * electrostaticCutoffRadius\n" + "\tfor the electrostaticSkinThickness\n"); painCave.isFatal = 0; simError(); theEst = 0.05 * theEcr; @@ -1181,8 +1278,8 @@ void SimSetup::mpiMolDivide(void){ if (local_atoms != info[0].n_atoms){ sprintf(painCave.errMsg, - "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" - " localAtom (%d) are not equal.\n", + "SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" + "\tlocalAtom (%d) are not equal.\n", info[0].n_atoms, local_atoms); painCave.isFatal = 1; simError(); @@ -1324,7 +1421,7 @@ void SimSetup::makeIntegrator(void){ else{ sprintf(painCave.errMsg, "SimSetup error: If you use the NVT\n" - " ensemble, you must set tauThermostat.\n"); + "\tensemble, you must set tauThermostat.\n"); painCave.isFatal = 1; simError(); } @@ -1347,7 +1444,7 @@ void SimSetup::makeIntegrator(void){ else{ sprintf(painCave.errMsg, "SimSetup error: If you use a constant pressure\n" - " ensemble, you must set targetPressure in the BASS file.\n"); + "\tensemble, you must set targetPressure in the BASS file.\n"); painCave.isFatal = 1; simError(); } @@ -1357,7 +1454,7 @@ void SimSetup::makeIntegrator(void){ else{ sprintf(painCave.errMsg, "SimSetup error: If you use an NPT\n" - " ensemble, you must set tauThermostat.\n"); + "\tensemble, you must set tauThermostat.\n"); painCave.isFatal = 1; simError(); } @@ -1367,7 +1464,7 @@ void SimSetup::makeIntegrator(void){ else{ sprintf(painCave.errMsg, "SimSetup error: If you use an NPT\n" - " ensemble, you must set tauBarostat.\n"); + "\tensemble, you must set tauBarostat.\n"); painCave.isFatal = 1; simError(); } @@ -1390,7 +1487,7 @@ void SimSetup::makeIntegrator(void){ else{ sprintf(painCave.errMsg, "SimSetup error: If you use a constant pressure\n" - " ensemble, you must set targetPressure in the BASS file.\n"); + "\tensemble, you must set targetPressure in the BASS file.\n"); painCave.isFatal = 1; simError(); } @@ -1401,7 +1498,7 @@ void SimSetup::makeIntegrator(void){ else{ sprintf(painCave.errMsg, "SimSetup error: If you use an NPT\n" - " ensemble, you must set tauThermostat.\n"); + "\tensemble, you must set tauThermostat.\n"); painCave.isFatal = 1; simError(); } @@ -1412,7 +1509,7 @@ void SimSetup::makeIntegrator(void){ else{ sprintf(painCave.errMsg, "SimSetup error: If you use an NPT\n" - " ensemble, you must set tauBarostat.\n"); + "\tensemble, you must set tauBarostat.\n"); painCave.isFatal = 1; simError(); } @@ -1435,7 +1532,7 @@ void SimSetup::makeIntegrator(void){ else{ sprintf(painCave.errMsg, "SimSetup error: If you use a constant pressure\n" - " ensemble, you must set targetPressure in the BASS file.\n"); + "\tensemble, you must set targetPressure in the BASS file.\n"); painCave.isFatal = 1; simError(); } @@ -1445,7 +1542,7 @@ void SimSetup::makeIntegrator(void){ else{ sprintf(painCave.errMsg, "SimSetup error: If you use an NPT\n" - " ensemble, you must set tauThermostat.\n"); + "\tensemble, you must set tauThermostat.\n"); painCave.isFatal = 1; simError(); } @@ -1455,7 +1552,7 @@ void SimSetup::makeIntegrator(void){ else{ sprintf(painCave.errMsg, "SimSetup error: If you use an NPT\n" - " ensemble, you must set tauBarostat.\n"); + "\tensemble, you must set tauBarostat.\n"); painCave.isFatal = 1; simError(); } @@ -1508,8 +1605,8 @@ void SimSetup::setupZConstraint(SimInfo& theInfo){ } else{ sprintf(painCave.errMsg, - "ZConstraint error: If you use an ZConstraint\n" - " , you must set sample time.\n"); + "ZConstraint error: If you use a ZConstraint,\n" + "\tyou must set zconsTime.\n"); painCave.isFatal = 1; simError(); } @@ -1524,8 +1621,9 @@ void SimSetup::setupZConstraint(SimInfo& theInfo){ else{ double defaultZConsTol = 0.01; sprintf(painCave.errMsg, - "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" - " , default value %f is used.\n", + "ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" + "\tOOPSE will use a default value of %f.\n" + "\tTo set the tolerance, use the zconsTol variable.\n", defaultZConsTol); painCave.isFatal = 0; simError(); @@ -1543,8 +1641,9 @@ void SimSetup::setupZConstraint(SimInfo& theInfo){ } else{ sprintf(painCave.errMsg, - "ZConstraint Warning: User does not set force Subtraction policy, " - "PolicyByMass is used\n"); + "ZConstraint Warning: No force subtraction policy was set.\n" + "\tOOPSE will use PolicyByMass.\n" + "\tTo set the policy, use the zconsForcePolicy variable.\n"); painCave.isFatal = 0; simError(); zconsForcePolicy->setData("BYMASS"); @@ -1588,7 +1687,7 @@ void SimSetup::setupZConstraint(SimInfo& theInfo){ //check the uniqueness of index if(!zconsParaData->isIndexUnique()){ sprintf(painCave.errMsg, - "ZConstraint Error: molIndex is not unique\n"); + "ZConstraint Error: molIndex is not unique!\n"); painCave.isFatal = 1; simError(); }