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// Thermodynamic integration is not multiprocessor friendly right now |
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|
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#include <iostream> |
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#include <stdlib.h> |
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#include <cstdio> |
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using namespace std; |
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|
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< |
#include "Restraints.hpp" |
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< |
#include "SimInfo.hpp" |
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< |
#include "simError.h" |
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> |
#include "restraints/Restraints.hpp" |
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> |
#include "brains/SimInfo.hpp" |
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> |
#include "utils/simError.h" |
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> |
#include "io/basic_ifstrstream.hpp" |
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|
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#ifdef IS_MPI |
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#include<mpi.h> |
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#include "brains/mpiSimulation.hpp" |
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#endif // is_mpi |
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|
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#define PI 3.14159265359 |
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#define TWO_PI 6.28318530718 |
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|
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Restraints::Restraints(double lambdaVal, double lambdaExp){ |
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lambdaValue = lambdaVal; |
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lambdaK = lambdaExp; |
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|
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vector<double> resConsts; |
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const char *jolt = " \t\n;,"; |
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|
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#ifdef IS_MPI |
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|
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if (!springs) { |
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sprintf(painCave.errMsg, |
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"In Restraints: Unable to open HarmSpringConsts.txt for reading.\n" |
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"\tDefault spring constants will be loaded. If you want to specify\n" |
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"\tspring constants, include a three line HarmSpringConsts.txt file\n" |
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"\tin the current directory.\n"); |
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"Unable to open HarmSpringConsts.txt for reading, so the\n" |
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"\tdefault spring constants will be loaded. If you want\n" |
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"\tto specify spring constants, include a three line\n" |
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"\tHarmSpringConsts.txt file in the execution directory.\n"); |
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painCave.severity = OOPSE_WARNING; |
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painCave.isFatal = 0; |
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simError(); |
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} else { |
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|
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springs.getline(inLine,999,'\n'); |
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// the file is blank! |
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if (springs.eof()){ |
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sprintf(painCave.errMsg, |
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"HarmSpringConsts.txt file is not valid.\n" |
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"\tThe file should contain four rows, the last three containing\n" |
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"\ta label and the spring constant value. They should be listed\n" |
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"\tin the following order: kDist (positional restrant), kTheta\n" |
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"\t(rot. restraint: deflection of z-axis), and kOmega (rot.\n" |
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"\trestraint: rotation about the z-axis).\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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// read in spring constants and check to make sure it is a valid file |
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springs.getline(inLine,999,'\n'); |
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token = strtok(inLine,jolt); |
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token = strtok(NULL,jolt); |
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strcpy(inValue,token); |
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kDist = (atof(inValue)); |
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springs.getline(inLine,999,'\n'); |
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token = strtok(inLine,jolt); |
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token = strtok(NULL,jolt); |
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strcpy(inValue,token); |
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kTheta = (atof(inValue)); |
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springs.getline(inLine,999,'\n'); |
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token = strtok(inLine,jolt); |
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token = strtok(NULL,jolt); |
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strcpy(inValue,token); |
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kOmega = (atof(inValue)); |
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springs.close(); |
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while (!springs.eof()){ |
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if (NULL != inLine){ |
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token = strtok(inLine,jolt); |
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token = strtok(NULL,jolt); |
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if (NULL != token){ |
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strcpy(inValue,token); |
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resConsts.push_back(atof(inValue)); |
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} |
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} |
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springs.getline(inLine,999,'\n'); |
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} |
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if (resConsts.size() == 3){ |
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kDist = resConsts[0]; |
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kTheta = resConsts[1]; |
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kOmega = resConsts[2]; |
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} |
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else { |
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sprintf(painCave.errMsg, |
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"HarmSpringConsts.txt file is not valid.\n" |
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"\tThe file should contain four rows, the last three containing\n" |
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"\ta label and the spring constant value. They should be listed\n" |
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"\tin the following order: kDist (positional restrant), kTheta\n" |
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"\t(rot. restraint: deflection of z-axis), and kOmega (rot.\n" |
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"\trestraint: rotation about the z-axis).\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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#ifdef IS_MPI |
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} |
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Restraints::~Restraints(){ |
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} |
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|
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void Restraints::Calc_rVal(double position[3], int currentMol){ |
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delRx = position[0] - cofmPosX[currentMol]; |
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delRy = position[1] - cofmPosY[currentMol]; |
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delRz = position[2] - cofmPosZ[currentMol]; |
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void Restraints::Calc_rVal(double position[3], double refPosition[3]){ |
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delRx = position[0] - refPosition[0]; |
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delRy = position[1] - refPosition[1]; |
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delRz = position[2] - refPosition[2]; |
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|
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return; |
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} |
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|
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void Restraints::Calc_body_thetaVal(double matrix[3][3], int currentMol){ |
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ub0x = matrix[0][0]*uX0[currentMol] + matrix[0][1]*uY0[currentMol] |
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+ matrix[0][2]*uZ0[currentMol]; |
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ub0y = matrix[1][0]*uX0[currentMol] + matrix[1][1]*uY0[currentMol] |
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+ matrix[1][2]*uZ0[currentMol]; |
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ub0z = matrix[2][0]*uX0[currentMol] + matrix[2][1]*uY0[currentMol] |
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+ matrix[2][2]*uZ0[currentMol]; |
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void Restraints::Calc_body_thetaVal(double matrix[3][3], double refUnit[3]){ |
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ub0x = matrix[0][0]*refUnit[0] + matrix[0][1]*refUnit[1] |
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+ matrix[0][2]*refUnit[2]; |
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ub0y = matrix[1][0]*refUnit[0] + matrix[1][1]*refUnit[1] |
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+ matrix[1][2]*refUnit[2]; |
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ub0z = matrix[2][0]*refUnit[0] + matrix[2][1]*refUnit[1] |
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+ matrix[2][2]*refUnit[2]; |
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|
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normalize = sqrt(ub0x*ub0x + ub0y*ub0y + ub0z*ub0z); |
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ub0x = ub0x/normalize; |
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double Restraints::Calc_Restraint_Forces(vector<StuntDouble*> vecParticles){ |
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double pos[3]; |
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double A[3][3]; |
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double refPos[3]; |
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double refVec[3]; |
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double tolerance; |
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double tempPotent; |
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double factor; |
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double spaceTrq[3]; |
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double omegaPass; |
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GenericData* data; |
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DoubleGenericData* doubleData; |
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|
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tolerance = 5.72957795131e-7; |
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factor = 1 - pow(lambdaValue, lambdaK); |
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for (i=0; i<vecParticles.size(); i++){ |
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// obtain the current and reference positions |
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vecParticles[i]->getPos(pos); |
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|
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data = vecParticles[i]->getProperty("refPosX"); |
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if (data){ |
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doubleData = dynamic_cast<DoubleGenericData*>(data); |
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if (!doubleData){ |
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cerr << "Can't obtain refPosX from StuntDouble\n"; |
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return 0.0; |
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} |
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else refPos[0] = doubleData->getData(); |
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} |
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data = vecParticles[i]->getProperty("refPosY"); |
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if (data){ |
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doubleData = dynamic_cast<DoubleGenericData*>(data); |
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if (!doubleData){ |
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cerr << "Can't obtain refPosY from StuntDouble\n"; |
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return 0.0; |
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} |
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else refPos[1] = doubleData->getData(); |
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} |
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data = vecParticles[i]->getProperty("refPosZ"); |
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if (data){ |
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doubleData = dynamic_cast<DoubleGenericData*>(data); |
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if (!doubleData){ |
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cerr << "Can't obtain refPosZ from StuntDouble\n"; |
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return 0.0; |
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} |
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else refPos[2] = doubleData->getData(); |
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} |
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|
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// calculate the displacement |
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Calc_rVal( pos, refPos ); |
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|
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// calculate the derivatives |
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dVdrx = -kDist*delRx; |
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dVdry = -kDist*delRy; |
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dVdrz = -kDist*delRz; |
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|
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// next we calculate the restraint forces |
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restraintFrc[0] = dVdrx; |
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restraintFrc[1] = dVdry; |
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restraintFrc[2] = dVdrz; |
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tempPotent = 0.5*kDist*(delRx*delRx + delRy*delRy + delRz*delRz); |
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|
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// apply the lambda scaling factor to the forces |
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for (j = 0; j < 3; j++) restraintFrc[j] *= factor; |
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|
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// and add the temporary force to the total force |
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vecParticles[i]->addFrc(restraintFrc); |
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|
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// if the particle is directional, we accumulate the rot. restraints |
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if (vecParticles[i]->isDirectional()){ |
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< |
vecParticles[i]->getPos(pos); |
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> |
|
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> |
// get the current rotation matrix and reference vector |
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vecParticles[i]->getA(A); |
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< |
Calc_rVal( pos, i ); |
| 271 |
< |
Calc_body_thetaVal( A, i ); |
| 270 |
> |
|
| 271 |
> |
data = vecParticles[i]->getProperty("refVectorX"); |
| 272 |
> |
if (data){ |
| 273 |
> |
doubleData = dynamic_cast<DoubleGenericData*>(data); |
| 274 |
> |
if (!doubleData){ |
| 275 |
> |
cerr << "Can't obtain refVectorX from StuntDouble\n"; |
| 276 |
> |
return 0.0; |
| 277 |
> |
} |
| 278 |
> |
else refVec[0] = doubleData->getData(); |
| 279 |
> |
} |
| 280 |
> |
data = vecParticles[i]->getProperty("refVectorY"); |
| 281 |
> |
if (data){ |
| 282 |
> |
doubleData = dynamic_cast<DoubleGenericData*>(data); |
| 283 |
> |
if (!doubleData){ |
| 284 |
> |
cerr << "Can't obtain refVectorY from StuntDouble\n"; |
| 285 |
> |
return 0.0; |
| 286 |
> |
} |
| 287 |
> |
else refVec[1] = doubleData->getData(); |
| 288 |
> |
} |
| 289 |
> |
data = vecParticles[i]->getProperty("refVectorZ"); |
| 290 |
> |
if (data){ |
| 291 |
> |
doubleData = dynamic_cast<DoubleGenericData*>(data); |
| 292 |
> |
if (!doubleData){ |
| 293 |
> |
cerr << "Can't obtain refVectorZ from StuntDouble\n"; |
| 294 |
> |
return 0.0; |
| 295 |
> |
} |
| 296 |
> |
else refVec[2] = doubleData->getData(); |
| 297 |
> |
} |
| 298 |
> |
|
| 299 |
> |
// calculate the theta and omega displacements |
| 300 |
> |
Calc_body_thetaVal( A, refVec ); |
| 301 |
|
omegaPass = vecParticles[i]->getZangle(); |
| 302 |
|
Calc_body_omegaVal( A, omegaPass ); |
| 303 |
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|
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– |
if (omega > PI || omega < -PI) |
| 184 |
– |
cout << "oops... " << omega << "\n"; |
| 185 |
– |
|
| 186 |
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// first we calculate the derivatives |
| 187 |
– |
dVdrx = -kDist*delRx; |
| 188 |
– |
dVdry = -kDist*delRy; |
| 189 |
– |
dVdrz = -kDist*delRz; |
| 190 |
– |
|
| 304 |
|
// uTx... and vTx... are the body-fixed z and y unit vectors |
| 305 |
|
uTx = 0.0; |
| 306 |
|
uTy = 0.0; |
| 309 |
|
vTy = 1.0; |
| 310 |
|
vTz = 0.0; |
| 311 |
|
|
| 312 |
< |
dVdux = 0; |
| 313 |
< |
dVduy = 0; |
| 314 |
< |
dVduz = 0; |
| 315 |
< |
dVdvx = 0; |
| 316 |
< |
dVdvy = 0; |
| 317 |
< |
dVdvz = 0; |
| 312 |
> |
dVdux = 0.0; |
| 313 |
> |
dVduy = 0.0; |
| 314 |
> |
dVduz = 0.0; |
| 315 |
> |
dVdvx = 0.0; |
| 316 |
> |
dVdvy = 0.0; |
| 317 |
> |
dVdvz = 0.0; |
| 318 |
|
|
| 319 |
|
if (fabs(theta) > tolerance) { |
| 320 |
|
dVdux = -(kTheta*theta/sin(theta))*ub0x; |
| 328 |
|
dVdvz = -(kOmega*omega/sin(omega))*vb0z; |
| 329 |
|
} |
| 330 |
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|
| 331 |
< |
// next we calculate the restraint forces and torques |
| 219 |
< |
restraintFrc[0] = dVdrx; |
| 220 |
< |
restraintFrc[1] = dVdry; |
| 221 |
< |
restraintFrc[2] = dVdrz; |
| 222 |
< |
tempPotent = 0.5*kDist*(delRx*delRx + delRy*delRy + delRz*delRz); |
| 223 |
< |
|
| 331 |
> |
// next we calculate the restraint torques |
| 332 |
|
restraintTrq[0] = 0.0; |
| 333 |
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restraintTrq[1] = 0.0; |
| 334 |
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restraintTrq[2] = 0.0; |
| 346 |
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tempPotent += 0.5*(kTheta*theta*theta); |
| 347 |
|
} |
| 348 |
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|
| 349 |
< |
for (j = 0; j < 3; j++) { |
| 350 |
< |
restraintFrc[j] *= factor; |
| 243 |
< |
restraintTrq[j] *= factor; |
| 244 |
< |
} |
| 349 |
> |
// apply the lambda scaling factor to these torques |
| 350 |
> |
for (j = 0; j < 3; j++) restraintTrq[j] *= factor; |
| 351 |
|
|
| 246 |
– |
harmPotent += tempPotent; |
| 247 |
– |
|
| 352 |
|
// now we need to convert from body-fixed torques to space-fixed torques |
| 353 |
|
spaceTrq[0] = A[0][0]*restraintTrq[0] + A[1][0]*restraintTrq[1] |
| 354 |
|
+ A[2][0]*restraintTrq[2]; |
| 357 |
|
spaceTrq[2] = A[0][2]*restraintTrq[0] + A[1][2]*restraintTrq[1] |
| 358 |
|
+ A[2][2]*restraintTrq[2]; |
| 359 |
|
|
| 360 |
< |
// now it's time to pass these temporary forces and torques |
| 257 |
< |
// to the total forces and torques |
| 258 |
< |
vecParticles[i]->addFrc(restraintFrc); |
| 360 |
> |
// now pass this temporary torque vector to the total torque |
| 361 |
|
vecParticles[i]->addTrq(spaceTrq); |
| 362 |
|
} |
| 261 |
– |
} |
| 363 |
|
|
| 364 |
< |
// and we can return the appropriately scaled potential energy |
| 364 |
> |
// update the total harmonic potential with this object's contribution |
| 365 |
> |
harmPotent += tempPotent; |
| 366 |
> |
} |
| 367 |
> |
|
| 368 |
> |
// we can finish by returning the appropriately scaled potential energy |
| 369 |
|
tempPotent = harmPotent * factor; |
| 370 |
|
return tempPotent; |
| 371 |
|
} |
| 372 |
|
|
| 373 |
< |
void Restraints::Store_Init_Info(vector<StuntDouble*> vecParticles){ |
| 374 |
< |
double pos[3]; |
| 375 |
< |
double A[3][3]; |
| 271 |
< |
double RfromQ[3][3]; |
| 272 |
< |
double quat0, quat1, quat2, quat3; |
| 273 |
< |
double dot; |
| 274 |
< |
// char *token; |
| 275 |
< |
// char fileName[200]; |
| 276 |
< |
// char angleName[200]; |
| 277 |
< |
// char inLine[1000]; |
| 278 |
< |
// char inValue[200]; |
| 279 |
< |
const char *delimit = " \t\n;,"; |
| 373 |
> |
void Restraints::Write_zAngle_File(vector<StuntDouble*> vecParticles, |
| 374 |
> |
int currTime, |
| 375 |
> |
int nIntObj){ |
| 376 |
|
|
| 377 |
< |
//open the idealCrystal.in file and zAngle.ang file |
| 282 |
< |
strcpy(fileName, "idealCrystal.in"); |
| 283 |
< |
strcpy(angleName, "zAngle.ang"); |
| 284 |
< |
|
| 285 |
< |
ifstream crystalIn(fileName); |
| 286 |
< |
ifstream angleIn(angleName); |
| 377 |
> |
char zOutName[200]; |
| 378 |
|
|
| 379 |
< |
if (!crystalIn) { |
| 289 |
< |
sprintf(painCave.errMsg, |
| 290 |
< |
"Restraints Error: Unable to open idealCrystal.in for reading.\n" |
| 291 |
< |
"\tMake sure a reference crystal file is in the current directory.\n"); |
| 292 |
< |
painCave.isFatal = 1; |
| 293 |
< |
simError(); |
| 294 |
< |
|
| 295 |
< |
return; |
| 296 |
< |
} |
| 379 |
> |
std::cerr << nIntObj << " is the number of integrable objects\n"; |
| 380 |
|
|
| 381 |
< |
if (!angleIn) { |
| 299 |
< |
sprintf(painCave.errMsg, |
| 300 |
< |
"Restraints Warning: The lack of a zAngle.ang file is mildly\n" |
| 301 |
< |
"\tunsettling... This means the simulation is starting from the\n" |
| 302 |
< |
"\tidealCrystal.in reference configuration, so the omega values\n" |
| 303 |
< |
"\twill all be set to zero. If this is not the case, you should\n" |
| 304 |
< |
"\tquestion your results.\n"); |
| 305 |
< |
painCave.isFatal = 0; |
| 306 |
< |
simError(); |
| 307 |
< |
} |
| 308 |
< |
|
| 309 |
< |
// A rather specific reader for OOPSE .eor files... |
| 310 |
< |
// Let's read in the perfect crystal file |
| 311 |
< |
crystalIn.getline(inLine,999,'\n'); |
| 312 |
< |
crystalIn.getline(inLine,999,'\n'); |
| 381 |
> |
//#ifndef IS_MPI |
| 382 |
|
|
| 314 |
– |
for (i=0; i<vecParticles.size(); i++) { |
| 315 |
– |
crystalIn.getline(inLine,999,'\n'); |
| 316 |
– |
token = strtok(inLine,delimit); |
| 317 |
– |
token = strtok(NULL,delimit); |
| 318 |
– |
strcpy(inValue,token); |
| 319 |
– |
cofmPosX.push_back(atof(inValue)); |
| 320 |
– |
token = strtok(NULL,delimit); |
| 321 |
– |
strcpy(inValue,token); |
| 322 |
– |
cofmPosY.push_back(atof(inValue)); |
| 323 |
– |
token = strtok(NULL,delimit); |
| 324 |
– |
strcpy(inValue,token); |
| 325 |
– |
cofmPosZ.push_back(atof(inValue)); |
| 326 |
– |
token = strtok(NULL,delimit); |
| 327 |
– |
token = strtok(NULL,delimit); |
| 328 |
– |
token = strtok(NULL,delimit); |
| 329 |
– |
token = strtok(NULL,delimit); |
| 330 |
– |
strcpy(inValue,token); |
| 331 |
– |
quat0 = atof(inValue); |
| 332 |
– |
token = strtok(NULL,delimit); |
| 333 |
– |
strcpy(inValue,token); |
| 334 |
– |
quat1 = atof(inValue); |
| 335 |
– |
token = strtok(NULL,delimit); |
| 336 |
– |
strcpy(inValue,token); |
| 337 |
– |
quat2 = atof(inValue); |
| 338 |
– |
token = strtok(NULL,delimit); |
| 339 |
– |
strcpy(inValue,token); |
| 340 |
– |
quat3 = atof(inValue); |
| 341 |
– |
|
| 342 |
– |
// now build the rotation matrix and find the unit vectors |
| 343 |
– |
RfromQ[0][0] = quat0*quat0 + quat1*quat1 - quat2*quat2 - quat3*quat3; |
| 344 |
– |
RfromQ[0][1] = 2*(quat1*quat2 + quat0*quat3); |
| 345 |
– |
RfromQ[0][2] = 2*(quat1*quat3 - quat0*quat2); |
| 346 |
– |
RfromQ[1][0] = 2*(quat1*quat2 - quat0*quat3); |
| 347 |
– |
RfromQ[1][1] = quat0*quat0 - quat1*quat1 + quat2*quat2 - quat3*quat3; |
| 348 |
– |
RfromQ[1][2] = 2*(quat2*quat3 + quat0*quat1); |
| 349 |
– |
RfromQ[2][0] = 2*(quat1*quat3 + quat0*quat2); |
| 350 |
– |
RfromQ[2][1] = 2*(quat2*quat3 - quat0*quat1); |
| 351 |
– |
RfromQ[2][2] = quat0*quat0 - quat1*quat1 - quat2*quat2 + quat3*quat3; |
| 352 |
– |
|
| 353 |
– |
normalize = sqrt(RfromQ[2][0]*RfromQ[2][0] + RfromQ[2][1]*RfromQ[2][1] |
| 354 |
– |
+ RfromQ[2][2]*RfromQ[2][2]); |
| 355 |
– |
uX0.push_back(RfromQ[2][0]/normalize); |
| 356 |
– |
uY0.push_back(RfromQ[2][1]/normalize); |
| 357 |
– |
uZ0.push_back(RfromQ[2][2]/normalize); |
| 358 |
– |
|
| 359 |
– |
normalize = sqrt(RfromQ[1][0]*RfromQ[1][0] + RfromQ[1][1]*RfromQ[1][1] |
| 360 |
– |
+ RfromQ[1][2]*RfromQ[1][2]); |
| 361 |
– |
vX0.push_back(RfromQ[1][0]/normalize); |
| 362 |
– |
vY0.push_back(RfromQ[1][1]/normalize); |
| 363 |
– |
vZ0.push_back(RfromQ[1][2]/normalize); |
| 364 |
– |
} |
| 365 |
– |
|
| 366 |
– |
// now we can read in the zAngle.ang file |
| 367 |
– |
if (angleIn){ |
| 368 |
– |
angleIn.getline(inLine,999,'\n'); |
| 369 |
– |
for (i=0; i<vecParticles.size(); i++) { |
| 370 |
– |
angleIn.getline(inLine,999,'\n'); |
| 371 |
– |
token = strtok(inLine,delimit); |
| 372 |
– |
strcpy(inValue,token); |
| 373 |
– |
vecParticles[i]->setZangle(atof(inValue)); |
| 374 |
– |
} |
| 375 |
– |
} |
| 376 |
– |
|
| 377 |
– |
return; |
| 378 |
– |
} |
| 379 |
– |
|
| 380 |
– |
void Restraints::Write_zAngle_File(vector<StuntDouble*> vecParticles){ |
| 381 |
– |
|
| 382 |
– |
char zOutName[200]; |
| 383 |
– |
|
| 383 |
|
strcpy(zOutName,"zAngle.ang"); |
| 384 |
< |
|
| 384 |
> |
|
| 385 |
|
ofstream angleOut(zOutName); |
| 386 |
< |
angleOut << "This file contains the omega values for the .eor file\n"; |
| 386 |
> |
angleOut << currTime << ": omega values at this time\n"; |
| 387 |
|
for (i=0; i<vecParticles.size(); i++) { |
| 388 |
|
angleOut << vecParticles[i]->getZangle() << "\n"; |
| 389 |
|
} |
| 390 |
+ |
|
| 391 |
|
return; |
| 392 |
|
} |
| 393 |
|
|
