| 1 |
// 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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#include <fstream> |
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#include <iomanip> |
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#include <string> |
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#include <cstring> |
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#include <math.h> |
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|
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using namespace std; |
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|
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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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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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if(worldRank == 0 ){ |
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#endif // is_mpi |
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|
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strcpy(springName, "HarmSpringConsts.txt"); |
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|
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ifstream springs(springName); |
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|
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if (!springs) { |
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sprintf(painCave.errMsg, |
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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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|
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// load default spring constants |
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kDist = 6; // spring constant in units of kcal/(mol*ang^2) |
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kTheta = 7.5; // in units of kcal/mol |
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kOmega = 13.5; // in units of kcal/mol |
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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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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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|
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MPI_Bcast(&kDist, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
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MPI_Bcast(&kTheta, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
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MPI_Bcast(&kOmega, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
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|
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sprintf( checkPointMsg, |
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"Sucessfully opened and read spring file.\n"); |
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MPIcheckPoint(); |
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|
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#endif // is_mpi |
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|
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sprintf(painCave.errMsg, |
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"The spring constants for thermodynamic integration are:\n" |
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"\tkDist = %lf\n" |
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"\tkTheta = %lf\n" |
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"\tkOmega = %lf\n", kDist, kTheta, kOmega); |
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painCave.severity = OOPSE_INFO; |
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painCave.isFatal = 0; |
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simError(); |
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} |
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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], 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], 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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ub0y = ub0y/normalize; |
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ub0z = ub0z/normalize; |
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|
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// Theta is the dot product of the reference and new z-axes |
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theta = acos(ub0z); |
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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_omegaVal(double matrix[3][3], double zAngle){ |
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double zRotator[3][3]; |
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double tempOmega; |
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double wholeTwoPis; |
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// Use the omega accumulated from the rotation propagation |
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omega = zAngle; |
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|
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// translate the omega into a range between -PI and PI |
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if (omega < -PI){ |
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tempOmega = omega / -TWO_PI; |
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wholeTwoPis = floor(tempOmega); |
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tempOmega = omega + TWO_PI*wholeTwoPis; |
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if (tempOmega < -PI) |
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omega = tempOmega + TWO_PI; |
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else |
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omega = tempOmega; |
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} |
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if (omega > PI){ |
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tempOmega = omega / TWO_PI; |
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wholeTwoPis = floor(tempOmega); |
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tempOmega = omega - TWO_PI*wholeTwoPis; |
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if (tempOmega > PI) |
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omega = tempOmega - TWO_PI; |
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else |
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omega = tempOmega; |
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} |
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|
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vb0x = sin(omega); |
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vb0y = cos(omega); |
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vb0z = 0.0; |
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|
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normalize = sqrt(vb0x*vb0x + vb0y*vb0y + vb0z*vb0z); |
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vb0x = vb0x/normalize; |
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vb0y = vb0y/normalize; |
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vb0z = vb0z/normalize; |
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|
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return; |
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} |
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|
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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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|
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harmPotent = 0.0; // zero out the global harmonic potential variable |
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|
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factor = 1 - pow(lambdaValue, lambdaK); |
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|
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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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|
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// get the current rotation matrix and reference vector |
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vecParticles[i]->getA(A); |
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|
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data = vecParticles[i]->getProperty("refVectorX"); |
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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 refVectorX from StuntDouble\n"; |
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return 0.0; |
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} |
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else refVec[0] = doubleData->getData(); |
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} |
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data = vecParticles[i]->getProperty("refVectorY"); |
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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 refVectorY from StuntDouble\n"; |
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return 0.0; |
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} |
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else refVec[1] = doubleData->getData(); |
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} |
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data = vecParticles[i]->getProperty("refVectorZ"); |
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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 refVectorZ from StuntDouble\n"; |
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return 0.0; |
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} |
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else refVec[2] = doubleData->getData(); |
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} |
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|
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// calculate the theta and omega displacements |
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Calc_body_thetaVal( A, refVec ); |
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omegaPass = vecParticles[i]->getZangle(); |
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Calc_body_omegaVal( A, omegaPass ); |
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|
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// uTx... and vTx... are the body-fixed z and y unit vectors |
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uTx = 0.0; |
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uTy = 0.0; |
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uTz = 1.0; |
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vTx = 0.0; |
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vTy = 1.0; |
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vTz = 0.0; |
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|
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dVdux = 0.0; |
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dVduy = 0.0; |
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dVduz = 0.0; |
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dVdvx = 0.0; |
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dVdvy = 0.0; |
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dVdvz = 0.0; |
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|
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if (fabs(theta) > tolerance) { |
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dVdux = -(kTheta*theta/sin(theta))*ub0x; |
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dVduy = -(kTheta*theta/sin(theta))*ub0y; |
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dVduz = -(kTheta*theta/sin(theta))*ub0z; |
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} |
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|
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if (fabs(omega) > tolerance) { |
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dVdvx = -(kOmega*omega/sin(omega))*vb0x; |
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dVdvy = -(kOmega*omega/sin(omega))*vb0y; |
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dVdvz = -(kOmega*omega/sin(omega))*vb0z; |
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} |
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|
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// next we calculate the restraint torques |
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restraintTrq[0] = 0.0; |
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restraintTrq[1] = 0.0; |
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restraintTrq[2] = 0.0; |
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|
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if (fabs(omega) > tolerance) { |
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restraintTrq[0] += 0.0; |
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restraintTrq[1] += 0.0; |
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restraintTrq[2] += vTy*dVdvx; |
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tempPotent += 0.5*(kOmega*omega*omega); |
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} |
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if (fabs(theta) > tolerance) { |
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restraintTrq[0] += (uTz*dVduy); |
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restraintTrq[1] += -(uTz*dVdux); |
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restraintTrq[2] += 0.0; |
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tempPotent += 0.5*(kTheta*theta*theta); |
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} |
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|
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// apply the lambda scaling factor to these torques |
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for (j = 0; j < 3; j++) restraintTrq[j] *= factor; |
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|
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// now we need to convert from body-fixed torques to space-fixed torques |
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spaceTrq[0] = A[0][0]*restraintTrq[0] + A[1][0]*restraintTrq[1] |
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+ A[2][0]*restraintTrq[2]; |
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spaceTrq[1] = A[0][1]*restraintTrq[0] + A[1][1]*restraintTrq[1] |
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+ A[2][1]*restraintTrq[2]; |
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spaceTrq[2] = A[0][2]*restraintTrq[0] + A[1][2]*restraintTrq[1] |
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+ A[2][2]*restraintTrq[2]; |
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|
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// now pass this temporary torque vector to the total torque |
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vecParticles[i]->addTrq(spaceTrq); |
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} |
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|
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// update the total harmonic potential with this object's contribution |
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harmPotent += tempPotent; |
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} |
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|
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// we can finish by returning the appropriately scaled potential energy |
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tempPotent = harmPotent * factor; |
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return tempPotent; |
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} |
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|
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void Restraints::Write_zAngle_File(vector<StuntDouble*> vecParticles, |
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int currTime, |
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int nIntObj){ |
| 376 |
|
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char zOutName[200]; |
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|
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std::cerr << nIntObj << " is the number of integrable objects\n"; |
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|
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//#ifndef IS_MPI |
| 382 |
|
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strcpy(zOutName,"zAngle.ang"); |
| 384 |
|
| 385 |
ofstream angleOut(zOutName); |
| 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 |
|
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return; |
| 392 |
} |
| 393 |
|
| 394 |
double Restraints::getVharm(){ |
| 395 |
return harmPotent; |
| 396 |
} |
| 397 |
|
