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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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|
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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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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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"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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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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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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} |
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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], 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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|
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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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|
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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 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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|
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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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if (vecParticles[i]->isDirectional()){ |
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vecParticles[i]->getPos(pos); |
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vecParticles[i]->getA(A); |
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Calc_rVal( pos, i ); |
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Calc_body_thetaVal( A, i ); |
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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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if (omega > PI || omega < -PI) |
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cout << "oops... " << omega << "\n"; |
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|
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// first we 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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// 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; |
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dVduy = 0; |
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dVduz = 0; |
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dVdvx = 0; |
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dVdvy = 0; |
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dVdvz = 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 forces and torques |
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restraintFrc[0] = dVdrx; |
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restraintFrc[1] = dVdry; |
| 221 |
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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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restraintTrq[0] = 0.0; |
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restraintTrq[1] = 0.0; |
| 226 |
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restraintTrq[2] = 0.0; |
| 227 |
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|
| 228 |
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if (fabs(omega) > tolerance) { |
| 229 |
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restraintTrq[0] += 0.0; |
| 230 |
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restraintTrq[1] += 0.0; |
| 231 |
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restraintTrq[2] += vTy*dVdvx; |
| 232 |
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tempPotent += 0.5*(kOmega*omega*omega); |
| 233 |
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} |
| 234 |
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if (fabs(theta) > tolerance) { |
| 235 |
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restraintTrq[0] += (uTz*dVduy); |
| 236 |
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restraintTrq[1] += -(uTz*dVdux); |
| 237 |
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restraintTrq[2] += 0.0; |
| 238 |
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tempPotent += 0.5*(kTheta*theta*theta); |
| 239 |
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} |
| 240 |
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|
| 241 |
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for (j = 0; j < 3; j++) { |
| 242 |
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restraintFrc[j] *= factor; |
| 243 |
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restraintTrq[j] *= factor; |
| 244 |
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} |
| 245 |
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|
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harmPotent += tempPotent; |
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|
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// now we need to convert from body-fixed torques to space-fixed torques |
| 249 |
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spaceTrq[0] = A[0][0]*restraintTrq[0] + A[1][0]*restraintTrq[1] |
| 250 |
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+ A[2][0]*restraintTrq[2]; |
| 251 |
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spaceTrq[1] = A[0][1]*restraintTrq[0] + A[1][1]*restraintTrq[1] |
| 252 |
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+ A[2][1]*restraintTrq[2]; |
| 253 |
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spaceTrq[2] = A[0][2]*restraintTrq[0] + A[1][2]*restraintTrq[1] |
| 254 |
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+ A[2][2]*restraintTrq[2]; |
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|
| 256 |
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// now it's time to pass these temporary forces and torques |
| 257 |
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// to the total forces and torques |
| 258 |
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vecParticles[i]->addFrc(restraintFrc); |
| 259 |
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vecParticles[i]->addTrq(spaceTrq); |
| 260 |
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} |
| 261 |
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} |
| 262 |
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|
| 263 |
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// and we can return the appropriately scaled potential energy |
| 264 |
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tempPotent = harmPotent * factor; |
| 265 |
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return tempPotent; |
| 266 |
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} |
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|
| 268 |
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void Restraints::Store_Init_Info(vector<StuntDouble*> vecParticles){ |
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double pos[3]; |
| 270 |
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double A[3][3]; |
| 271 |
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double RfromQ[3][3]; |
| 272 |
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double quat0, quat1, quat2, quat3; |
| 273 |
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double dot; |
| 274 |
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// char *token; |
| 275 |
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// char fileName[200]; |
| 276 |
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// char angleName[200]; |
| 277 |
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// char inLine[1000]; |
| 278 |
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// char inValue[200]; |
| 279 |
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const char *delimit = " \t\n;,"; |
| 280 |
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|
| 281 |
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//open the idealCrystal.in file and zAngle.ang file |
| 282 |
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strcpy(fileName, "idealCrystal.in"); |
| 283 |
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strcpy(angleName, "zAngle.ang"); |
| 284 |
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|
| 285 |
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ifstream crystalIn(fileName); |
| 286 |
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ifstream angleIn(angleName); |
| 287 |
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|
| 288 |
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if (!crystalIn) { |
| 289 |
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sprintf(painCave.errMsg, |
| 290 |
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"Restraints Error: Unable to open idealCrystal.in for reading.\n" |
| 291 |
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"\tMake sure a reference crystal file is in the current directory.\n"); |
| 292 |
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painCave.isFatal = 1; |
| 293 |
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simError(); |
| 294 |
< |
|
| 295 |
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return; |
| 296 |
< |
} |
| 297 |
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|
| 298 |
< |
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 |
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"\tidealCrystal.in reference configuration, so the omega values\n" |
| 303 |
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"\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'); |
| 313 |
< |
|
| 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 |
< |
|
| 384 |
< |
strcpy(zOutName,"zAngle.ang"); |
| 385 |
< |
|
| 386 |
< |
ofstream angleOut(zOutName); |
| 387 |
< |
angleOut << "This file contains the omega values for the .eor file\n"; |
| 388 |
< |
for (i=0; i<vecParticles.size(); i++) { |
| 389 |
< |
angleOut << vecParticles[i]->getZangle() << "\n"; |
| 390 |
< |
} |
| 391 |
< |
return; |
| 392 |
< |
} |
| 393 |
< |
|
| 394 |
< |
double Restraints::getVharm(){ |
| 395 |
< |
return harmPotent; |
| 396 |
< |
} |
| 397 |
< |
|
| 1 |
> |
// Thermodynamic integration is not multiprocessor friendly right now |
| 2 |
> |
|
| 3 |
> |
#include <iostream> |
| 4 |
> |
#include <stdlib.h> |
| 5 |
> |
#include <cstdio> |
| 6 |
> |
#include <fstream> |
| 7 |
> |
#include <iomanip> |
| 8 |
> |
#include <string> |
| 9 |
> |
#include <cstring> |
| 10 |
> |
#include <math.h> |
| 11 |
> |
|
| 12 |
> |
using namespace std; |
| 13 |
> |
|
| 14 |
> |
#include "restraints/Restraints.hpp" |
| 15 |
> |
#include "brains/SimInfo.hpp" |
| 16 |
> |
#include "utils/simError.h" |
| 17 |
> |
|
| 18 |
> |
#define PI 3.14159265359 |
| 19 |
> |
#define TWO_PI 6.28318530718 |
| 20 |
> |
|
| 21 |
> |
Restraints::Restraints(double lambdaVal, double lambdaExp){ |
| 22 |
> |
lambdaValue = lambdaVal; |
| 23 |
> |
lambdaK = lambdaExp; |
| 24 |
> |
vector<double> resConsts; |
| 25 |
> |
const char *jolt = " \t\n;,"; |
| 26 |
> |
|
| 27 |
> |
#ifdef IS_MPI |
| 28 |
> |
if(worldRank == 0 ){ |
| 29 |
> |
#endif // is_mpi |
| 30 |
> |
|
| 31 |
> |
strcpy(springName, "HarmSpringConsts.txt"); |
| 32 |
> |
|
| 33 |
> |
ifstream springs(springName); |
| 34 |
> |
|
| 35 |
> |
if (!springs) { |
| 36 |
> |
sprintf(painCave.errMsg, |
| 37 |
> |
"Unable to open HarmSpringConsts.txt for reading, so the\n" |
| 38 |
> |
"\tdefault spring constants will be loaded. If you want\n" |
| 39 |
> |
"\tto specify spring constants, include a three line\n" |
| 40 |
> |
"\tHarmSpringConsts.txt file in the execution directory.\n"); |
| 41 |
> |
painCave.severity = OOPSE_WARNING; |
| 42 |
> |
painCave.isFatal = 0; |
| 43 |
> |
simError(); |
| 44 |
> |
|
| 45 |
> |
// load default spring constants |
| 46 |
> |
kDist = 6; // spring constant in units of kcal/(mol*ang^2) |
| 47 |
> |
kTheta = 7.5; // in units of kcal/mol |
| 48 |
> |
kOmega = 13.5; // in units of kcal/mol |
| 49 |
> |
} else { |
| 50 |
> |
|
| 51 |
> |
springs.getline(inLine,999,'\n'); |
| 52 |
> |
// the file is blank! |
| 53 |
> |
if (springs.eof()){ |
| 54 |
> |
sprintf(painCave.errMsg, |
| 55 |
> |
"HarmSpringConsts.txt file is not valid.\n" |
| 56 |
> |
"\tThe file should contain four rows, the last three containing\n" |
| 57 |
> |
"\ta label and the spring constant value. They should be listed\n" |
| 58 |
> |
"\tin the following order: kDist (positional restrant), kTheta\n" |
| 59 |
> |
"\t(rot. restraint: deflection of z-axis), and kOmega (rot.\n" |
| 60 |
> |
"\trestraint: rotation about the z-axis).\n"); |
| 61 |
> |
painCave.severity = OOPSE_ERROR; |
| 62 |
> |
painCave.isFatal = 1; |
| 63 |
> |
simError(); |
| 64 |
> |
} |
| 65 |
> |
// read in spring constants and check to make sure it is a valid file |
| 66 |
> |
springs.getline(inLine,999,'\n'); |
| 67 |
> |
while (!springs.eof()){ |
| 68 |
> |
if (NULL != inLine){ |
| 69 |
> |
token = strtok(inLine,jolt); |
| 70 |
> |
token = strtok(NULL,jolt); |
| 71 |
> |
if (NULL != token){ |
| 72 |
> |
strcpy(inValue,token); |
| 73 |
> |
resConsts.push_back(atof(inValue)); |
| 74 |
> |
} |
| 75 |
> |
} |
| 76 |
> |
springs.getline(inLine,999,'\n'); |
| 77 |
> |
} |
| 78 |
> |
if (resConsts.size() == 3){ |
| 79 |
> |
kDist = resConsts[0]; |
| 80 |
> |
kTheta = resConsts[1]; |
| 81 |
> |
kOmega = resConsts[2]; |
| 82 |
> |
} |
| 83 |
> |
else { |
| 84 |
> |
sprintf(painCave.errMsg, |
| 85 |
> |
"HarmSpringConsts.txt file is not valid.\n" |
| 86 |
> |
"\tThe file should contain four rows, the last three containing\n" |
| 87 |
> |
"\ta label and the spring constant value. They should be listed\n" |
| 88 |
> |
"\tin the following order: kDist (positional restrant), kTheta\n" |
| 89 |
> |
"\t(rot. restraint: deflection of z-axis), and kOmega (rot.\n" |
| 90 |
> |
"\trestraint: rotation about the z-axis).\n"); |
| 91 |
> |
painCave.severity = OOPSE_ERROR; |
| 92 |
> |
painCave.isFatal = 1; |
| 93 |
> |
simError(); |
| 94 |
> |
} |
| 95 |
> |
} |
| 96 |
> |
#ifdef IS_MPI |
| 97 |
> |
} |
| 98 |
> |
|
| 99 |
> |
MPI_Bcast(&kDist, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
| 100 |
> |
MPI_Bcast(&kTheta, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
| 101 |
> |
MPI_Bcast(&kOmega, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
| 102 |
> |
|
| 103 |
> |
sprintf( checkPointMsg, |
| 104 |
> |
"Sucessfully opened and read spring file.\n"); |
| 105 |
> |
MPIcheckPoint(); |
| 106 |
> |
|
| 107 |
> |
#endif // is_mpi |
| 108 |
> |
|
| 109 |
> |
sprintf(painCave.errMsg, |
| 110 |
> |
"The spring constants for thermodynamic integration are:\n" |
| 111 |
> |
"\tkDist = %lf\n" |
| 112 |
> |
"\tkTheta = %lf\n" |
| 113 |
> |
"\tkOmega = %lf\n", kDist, kTheta, kOmega); |
| 114 |
> |
painCave.severity = OOPSE_INFO; |
| 115 |
> |
painCave.isFatal = 0; |
| 116 |
> |
simError(); |
| 117 |
> |
} |
| 118 |
> |
|
| 119 |
> |
Restraints::~Restraints(){ |
| 120 |
> |
} |
| 121 |
> |
|
| 122 |
> |
void Restraints::Calc_rVal(double position[3], int currentMol){ |
| 123 |
> |
delRx = position[0] - cofmPosX[currentMol]; |
| 124 |
> |
delRy = position[1] - cofmPosY[currentMol]; |
| 125 |
> |
delRz = position[2] - cofmPosZ[currentMol]; |
| 126 |
> |
|
| 127 |
> |
return; |
| 128 |
> |
} |
| 129 |
> |
|
| 130 |
> |
void Restraints::Calc_body_thetaVal(double matrix[3][3], int currentMol){ |
| 131 |
> |
ub0x = matrix[0][0]*uX0[currentMol] + matrix[0][1]*uY0[currentMol] |
| 132 |
> |
+ matrix[0][2]*uZ0[currentMol]; |
| 133 |
> |
ub0y = matrix[1][0]*uX0[currentMol] + matrix[1][1]*uY0[currentMol] |
| 134 |
> |
+ matrix[1][2]*uZ0[currentMol]; |
| 135 |
> |
ub0z = matrix[2][0]*uX0[currentMol] + matrix[2][1]*uY0[currentMol] |
| 136 |
> |
+ matrix[2][2]*uZ0[currentMol]; |
| 137 |
> |
|
| 138 |
> |
normalize = sqrt(ub0x*ub0x + ub0y*ub0y + ub0z*ub0z); |
| 139 |
> |
ub0x = ub0x/normalize; |
| 140 |
> |
ub0y = ub0y/normalize; |
| 141 |
> |
ub0z = ub0z/normalize; |
| 142 |
> |
|
| 143 |
> |
// Theta is the dot product of the reference and new z-axes |
| 144 |
> |
theta = acos(ub0z); |
| 145 |
> |
|
| 146 |
> |
return; |
| 147 |
> |
} |
| 148 |
> |
|
| 149 |
> |
void Restraints::Calc_body_omegaVal(double matrix[3][3], double zAngle){ |
| 150 |
> |
double zRotator[3][3]; |
| 151 |
> |
double tempOmega; |
| 152 |
> |
double wholeTwoPis; |
| 153 |
> |
// Use the omega accumulated from the rotation propagation |
| 154 |
> |
omega = zAngle; |
| 155 |
> |
|
| 156 |
> |
// translate the omega into a range between -PI and PI |
| 157 |
> |
if (omega < -PI){ |
| 158 |
> |
tempOmega = omega / -TWO_PI; |
| 159 |
> |
wholeTwoPis = floor(tempOmega); |
| 160 |
> |
tempOmega = omega + TWO_PI*wholeTwoPis; |
| 161 |
> |
if (tempOmega < -PI) |
| 162 |
> |
omega = tempOmega + TWO_PI; |
| 163 |
> |
else |
| 164 |
> |
omega = tempOmega; |
| 165 |
> |
} |
| 166 |
> |
if (omega > PI){ |
| 167 |
> |
tempOmega = omega / TWO_PI; |
| 168 |
> |
wholeTwoPis = floor(tempOmega); |
| 169 |
> |
tempOmega = omega - TWO_PI*wholeTwoPis; |
| 170 |
> |
if (tempOmega > PI) |
| 171 |
> |
omega = tempOmega - TWO_PI; |
| 172 |
> |
else |
| 173 |
> |
omega = tempOmega; |
| 174 |
> |
} |
| 175 |
> |
|
| 176 |
> |
vb0x = sin(omega); |
| 177 |
> |
vb0y = cos(omega); |
| 178 |
> |
vb0z = 0.0; |
| 179 |
> |
|
| 180 |
> |
normalize = sqrt(vb0x*vb0x + vb0y*vb0y + vb0z*vb0z); |
| 181 |
> |
vb0x = vb0x/normalize; |
| 182 |
> |
vb0y = vb0y/normalize; |
| 183 |
> |
vb0z = vb0z/normalize; |
| 184 |
> |
|
| 185 |
> |
return; |
| 186 |
> |
} |
| 187 |
> |
|
| 188 |
> |
double Restraints::Calc_Restraint_Forces(vector<StuntDouble*> vecParticles){ |
| 189 |
> |
double pos[3]; |
| 190 |
> |
double A[3][3]; |
| 191 |
> |
double tolerance; |
| 192 |
> |
double tempPotent; |
| 193 |
> |
double factor; |
| 194 |
> |
double spaceTrq[3]; |
| 195 |
> |
double omegaPass; |
| 196 |
> |
|
| 197 |
> |
tolerance = 5.72957795131e-7; |
| 198 |
> |
|
| 199 |
> |
harmPotent = 0.0; // zero out the global harmonic potential variable |
| 200 |
> |
|
| 201 |
> |
factor = 1 - pow(lambdaValue, lambdaK); |
| 202 |
> |
|
| 203 |
> |
for (i=0; i<vecParticles.size(); i++){ |
| 204 |
> |
if (vecParticles[i]->isDirectional()){ |
| 205 |
> |
pos = vecParticles[i]->getPos(); |
| 206 |
> |
vecParticles[i]->getA(A); |
| 207 |
> |
Calc_rVal( pos, i ); |
| 208 |
> |
Calc_body_thetaVal( A, i ); |
| 209 |
> |
omegaPass = vecParticles[i]->getZangle(); |
| 210 |
> |
Calc_body_omegaVal( A, omegaPass ); |
| 211 |
> |
|
| 212 |
> |
// first we calculate the derivatives |
| 213 |
> |
dVdrx = -kDist*delRx; |
| 214 |
> |
dVdry = -kDist*delRy; |
| 215 |
> |
dVdrz = -kDist*delRz; |
| 216 |
> |
|
| 217 |
> |
// uTx... and vTx... are the body-fixed z and y unit vectors |
| 218 |
> |
uTx = 0.0; |
| 219 |
> |
uTy = 0.0; |
| 220 |
> |
uTz = 1.0; |
| 221 |
> |
vTx = 0.0; |
| 222 |
> |
vTy = 1.0; |
| 223 |
> |
vTz = 0.0; |
| 224 |
> |
|
| 225 |
> |
dVdux = 0; |
| 226 |
> |
dVduy = 0; |
| 227 |
> |
dVduz = 0; |
| 228 |
> |
dVdvx = 0; |
| 229 |
> |
dVdvy = 0; |
| 230 |
> |
dVdvz = 0; |
| 231 |
> |
|
| 232 |
> |
if (fabs(theta) > tolerance) { |
| 233 |
> |
dVdux = -(kTheta*theta/sin(theta))*ub0x; |
| 234 |
> |
dVduy = -(kTheta*theta/sin(theta))*ub0y; |
| 235 |
> |
dVduz = -(kTheta*theta/sin(theta))*ub0z; |
| 236 |
> |
} |
| 237 |
> |
|
| 238 |
> |
if (fabs(omega) > tolerance) { |
| 239 |
> |
dVdvx = -(kOmega*omega/sin(omega))*vb0x; |
| 240 |
> |
dVdvy = -(kOmega*omega/sin(omega))*vb0y; |
| 241 |
> |
dVdvz = -(kOmega*omega/sin(omega))*vb0z; |
| 242 |
> |
} |
| 243 |
> |
|
| 244 |
> |
// next we calculate the restraint forces and torques |
| 245 |
> |
restraintFrc[0] = dVdrx; |
| 246 |
> |
restraintFrc[1] = dVdry; |
| 247 |
> |
restraintFrc[2] = dVdrz; |
| 248 |
> |
tempPotent = 0.5*kDist*(delRx*delRx + delRy*delRy + delRz*delRz); |
| 249 |
> |
|
| 250 |
> |
restraintTrq[0] = 0.0; |
| 251 |
> |
restraintTrq[1] = 0.0; |
| 252 |
> |
restraintTrq[2] = 0.0; |
| 253 |
> |
|
| 254 |
> |
if (fabs(omega) > tolerance) { |
| 255 |
> |
restraintTrq[0] += 0.0; |
| 256 |
> |
restraintTrq[1] += 0.0; |
| 257 |
> |
restraintTrq[2] += vTy*dVdvx; |
| 258 |
> |
tempPotent += 0.5*(kOmega*omega*omega); |
| 259 |
> |
} |
| 260 |
> |
if (fabs(theta) > tolerance) { |
| 261 |
> |
restraintTrq[0] += (uTz*dVduy); |
| 262 |
> |
restraintTrq[1] += -(uTz*dVdux); |
| 263 |
> |
restraintTrq[2] += 0.0; |
| 264 |
> |
tempPotent += 0.5*(kTheta*theta*theta); |
| 265 |
> |
} |
| 266 |
> |
|
| 267 |
> |
for (j = 0; j < 3; j++) { |
| 268 |
> |
restraintFrc[j] *= factor; |
| 269 |
> |
restraintTrq[j] *= factor; |
| 270 |
> |
} |
| 271 |
> |
|
| 272 |
> |
harmPotent += tempPotent; |
| 273 |
> |
|
| 274 |
> |
// now we need to convert from body-fixed torques to space-fixed torques |
| 275 |
> |
spaceTrq[0] = A[0][0]*restraintTrq[0] + A[1][0]*restraintTrq[1] |
| 276 |
> |
+ A[2][0]*restraintTrq[2]; |
| 277 |
> |
spaceTrq[1] = A[0][1]*restraintTrq[0] + A[1][1]*restraintTrq[1] |
| 278 |
> |
+ A[2][1]*restraintTrq[2]; |
| 279 |
> |
spaceTrq[2] = A[0][2]*restraintTrq[0] + A[1][2]*restraintTrq[1] |
| 280 |
> |
+ A[2][2]*restraintTrq[2]; |
| 281 |
> |
|
| 282 |
> |
// now it's time to pass these temporary forces and torques |
| 283 |
> |
// to the total forces and torques |
| 284 |
> |
vecParticles[i]->addFrc(restraintFrc); |
| 285 |
> |
vecParticles[i]->addTrq(spaceTrq); |
| 286 |
> |
} |
| 287 |
> |
} |
| 288 |
> |
|
| 289 |
> |
// and we can return the appropriately scaled potential energy |
| 290 |
> |
tempPotent = harmPotent * factor; |
| 291 |
> |
return tempPotent; |
| 292 |
> |
} |
| 293 |
> |
|
| 294 |
> |
void Restraints::Store_Init_Info(vector<StuntDouble*> vecParticles){ |
| 295 |
> |
int idealSize; |
| 296 |
> |
double pos[3]; |
| 297 |
> |
double A[3][3]; |
| 298 |
> |
double RfromQ[3][3]; |
| 299 |
> |
double quat0, quat1, quat2, quat3; |
| 300 |
> |
double dot; |
| 301 |
> |
vector<double> tempZangs; |
| 302 |
> |
const char *delimit = " \t\n;,"; |
| 303 |
> |
|
| 304 |
> |
//open the idealCrystal.in file and zAngle.ang file |
| 305 |
> |
strcpy(fileName, "idealCrystal.in"); |
| 306 |
> |
strcpy(angleName, "zAngle.ang"); |
| 307 |
> |
|
| 308 |
> |
ifstream crystalIn(fileName); |
| 309 |
> |
ifstream angleIn(angleName); |
| 310 |
> |
|
| 311 |
> |
// check to see if these files are present in the execution directory |
| 312 |
> |
if (!crystalIn) { |
| 313 |
> |
sprintf(painCave.errMsg, |
| 314 |
> |
"Restraints Error: Unable to open idealCrystal.in for reading.\n" |
| 315 |
> |
"\tMake sure a ref. crystal file is in the working directory.\n"); |
| 316 |
> |
painCave.severity = OOPSE_ERROR; |
| 317 |
> |
painCave.isFatal = 1; |
| 318 |
> |
simError(); |
| 319 |
> |
} |
| 320 |
> |
|
| 321 |
> |
// it's not fatal to lack a zAngle.ang file, it just means you're starting |
| 322 |
> |
// from the ideal crystal state |
| 323 |
> |
if (!angleIn) { |
| 324 |
> |
sprintf(painCave.errMsg, |
| 325 |
> |
"Restraints Warning: The lack of a zAngle.ang file is mildly\n" |
| 326 |
> |
"\tunsettling... This means the simulation is starting from the\n" |
| 327 |
> |
"\tidealCrystal.in reference configuration, so the omega values\n" |
| 328 |
> |
"\twill all be set to zero. If this is not the case, the energy\n" |
| 329 |
> |
"\tcalculations will be wrong.\n"); |
| 330 |
> |
painCave.severity = OOPSE_WARNING; |
| 331 |
> |
painCave.isFatal = 0; |
| 332 |
> |
simError(); |
| 333 |
> |
} |
| 334 |
> |
|
| 335 |
> |
// A rather specific reader for OOPSE .eor files... |
| 336 |
> |
// Let's read in the perfect crystal file |
| 337 |
> |
crystalIn.getline(inLine,999,'\n'); |
| 338 |
> |
// check to see if the crystal file is the same length as starting config. |
| 339 |
> |
token = strtok(inLine,delimit); |
| 340 |
> |
strcpy(inValue,token); |
| 341 |
> |
idealSize = atoi(inValue); |
| 342 |
> |
if (idealSize != vecParticles.size()) { |
| 343 |
> |
sprintf(painCave.errMsg, |
| 344 |
> |
"Restraints Error: Reference crystal file is not valid.\n" |
| 345 |
> |
"\tMake sure the idealCrystal.in file is the same size as the\n" |
| 346 |
> |
"\tstarting configuration. Using an incompatable crystal will\n" |
| 347 |
> |
"\tlead to energy calculation failures.\n"); |
| 348 |
> |
painCave.severity = OOPSE_ERROR; |
| 349 |
> |
painCave.isFatal = 1; |
| 350 |
> |
simError(); |
| 351 |
> |
} |
| 352 |
> |
// else, the file is okay... let's continue |
| 353 |
> |
crystalIn.getline(inLine,999,'\n'); |
| 354 |
> |
|
| 355 |
> |
for (i=0; i<vecParticles.size(); i++) { |
| 356 |
> |
crystalIn.getline(inLine,999,'\n'); |
| 357 |
> |
token = strtok(inLine,delimit); |
| 358 |
> |
token = strtok(NULL,delimit); |
| 359 |
> |
strcpy(inValue,token); |
| 360 |
> |
cofmPosX.push_back(atof(inValue)); |
| 361 |
> |
token = strtok(NULL,delimit); |
| 362 |
> |
strcpy(inValue,token); |
| 363 |
> |
cofmPosY.push_back(atof(inValue)); |
| 364 |
> |
token = strtok(NULL,delimit); |
| 365 |
> |
strcpy(inValue,token); |
| 366 |
> |
cofmPosZ.push_back(atof(inValue)); |
| 367 |
> |
token = strtok(NULL,delimit); |
| 368 |
> |
token = strtok(NULL,delimit); |
| 369 |
> |
token = strtok(NULL,delimit); |
| 370 |
> |
token = strtok(NULL,delimit); |
| 371 |
> |
strcpy(inValue,token); |
| 372 |
> |
quat0 = atof(inValue); |
| 373 |
> |
token = strtok(NULL,delimit); |
| 374 |
> |
strcpy(inValue,token); |
| 375 |
> |
quat1 = atof(inValue); |
| 376 |
> |
token = strtok(NULL,delimit); |
| 377 |
> |
strcpy(inValue,token); |
| 378 |
> |
quat2 = atof(inValue); |
| 379 |
> |
token = strtok(NULL,delimit); |
| 380 |
> |
strcpy(inValue,token); |
| 381 |
> |
quat3 = atof(inValue); |
| 382 |
> |
|
| 383 |
> |
// now build the rotation matrix and find the unit vectors |
| 384 |
> |
RfromQ[0][0] = quat0*quat0 + quat1*quat1 - quat2*quat2 - quat3*quat3; |
| 385 |
> |
RfromQ[0][1] = 2*(quat1*quat2 + quat0*quat3); |
| 386 |
> |
RfromQ[0][2] = 2*(quat1*quat3 - quat0*quat2); |
| 387 |
> |
RfromQ[1][0] = 2*(quat1*quat2 - quat0*quat3); |
| 388 |
> |
RfromQ[1][1] = quat0*quat0 - quat1*quat1 + quat2*quat2 - quat3*quat3; |
| 389 |
> |
RfromQ[1][2] = 2*(quat2*quat3 + quat0*quat1); |
| 390 |
> |
RfromQ[2][0] = 2*(quat1*quat3 + quat0*quat2); |
| 391 |
> |
RfromQ[2][1] = 2*(quat2*quat3 - quat0*quat1); |
| 392 |
> |
RfromQ[2][2] = quat0*quat0 - quat1*quat1 - quat2*quat2 + quat3*quat3; |
| 393 |
> |
|
| 394 |
> |
normalize = sqrt(RfromQ[2][0]*RfromQ[2][0] + RfromQ[2][1]*RfromQ[2][1] |
| 395 |
> |
+ RfromQ[2][2]*RfromQ[2][2]); |
| 396 |
> |
uX0.push_back(RfromQ[2][0]/normalize); |
| 397 |
> |
uY0.push_back(RfromQ[2][1]/normalize); |
| 398 |
> |
uZ0.push_back(RfromQ[2][2]/normalize); |
| 399 |
> |
|
| 400 |
> |
normalize = sqrt(RfromQ[1][0]*RfromQ[1][0] + RfromQ[1][1]*RfromQ[1][1] |
| 401 |
> |
+ RfromQ[1][2]*RfromQ[1][2]); |
| 402 |
> |
vX0.push_back(RfromQ[1][0]/normalize); |
| 403 |
> |
vY0.push_back(RfromQ[1][1]/normalize); |
| 404 |
> |
vZ0.push_back(RfromQ[1][2]/normalize); |
| 405 |
> |
} |
| 406 |
> |
crystalIn.close(); |
| 407 |
> |
|
| 408 |
> |
// now we read in the zAngle.ang file |
| 409 |
> |
if (angleIn){ |
| 410 |
> |
angleIn.getline(inLine,999,'\n'); |
| 411 |
> |
angleIn.getline(inLine,999,'\n'); |
| 412 |
> |
while (!angleIn.eof()) { |
| 413 |
> |
token = strtok(inLine,delimit); |
| 414 |
> |
strcpy(inValue,token); |
| 415 |
> |
tempZangs.push_back(atof(inValue)); |
| 416 |
> |
angleIn.getline(inLine,999,'\n'); |
| 417 |
> |
} |
| 418 |
> |
|
| 419 |
> |
// test to make sure the zAngle.ang file is the proper length |
| 420 |
> |
if (tempZangs.size() == vecParticles.size()) |
| 421 |
> |
for (i=0; i<vecParticles.size(); i++) |
| 422 |
> |
vecParticles[i]->setZangle(tempZangs[i]); |
| 423 |
> |
else { |
| 424 |
> |
sprintf(painCave.errMsg, |
| 425 |
> |
"Restraints Error: the supplied zAngle file is not valid.\n" |
| 426 |
> |
"\tMake sure the zAngle.ang file matches with the initial\n" |
| 427 |
> |
"\tconfiguration (i.e. they're the same length). Using the wrong\n" |
| 428 |
> |
"\tzAngle file will lead to errors in the energy calculations.\n"); |
| 429 |
> |
painCave.severity = OOPSE_ERROR; |
| 430 |
> |
painCave.isFatal = 1; |
| 431 |
> |
simError(); |
| 432 |
> |
} |
| 433 |
> |
} |
| 434 |
> |
angleIn.close(); |
| 435 |
> |
|
| 436 |
> |
return; |
| 437 |
> |
} |
| 438 |
> |
|
| 439 |
> |
void Restraints::Write_zAngle_File(vector<StuntDouble*> vecParticles){ |
| 440 |
> |
|
| 441 |
> |
char zOutName[200]; |
| 442 |
> |
|
| 443 |
> |
strcpy(zOutName,"zAngle.ang"); |
| 444 |
> |
|
| 445 |
> |
ofstream angleOut(zOutName); |
| 446 |
> |
angleOut << "This file contains the omega values for the .eor file\n"; |
| 447 |
> |
for (i=0; i<vecParticles.size(); i++) { |
| 448 |
> |
angleOut << vecParticles[i]->getZangle() << "\n"; |
| 449 |
> |
} |
| 450 |
> |
return; |
| 451 |
> |
} |
| 452 |
> |
|
| 453 |
> |
double Restraints::getVharm(){ |
| 454 |
> |
return harmPotent; |
| 455 |
> |
} |
| 456 |
> |
|
