| 1 |
tim |
1695 |
// Thermodynamic integration is not multiprocessor friendly right now
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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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using namespace std;
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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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#define PI 3.14159265359
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#define TWO_PI 6.28318530718
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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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#ifdef IS_MPI
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if(worldRank == 0 ){
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#endif // is_mpi
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strcpy(springName, "HarmSpringConsts.txt");
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ifstream springs(springName);
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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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// 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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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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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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sprintf( checkPointMsg,
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"Sucessfully opened and read spring file.\n");
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MPIcheckPoint();
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#endif // is_mpi
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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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Restraints::~Restraints(){
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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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return;
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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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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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// Theta is the dot product of the reference and new z-axes
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theta = acos(ub0z);
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return;
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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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// 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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vb0x = sin(omega);
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vb0y = cos(omega);
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vb0z = 0.0;
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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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return;
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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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tolerance = 5.72957795131e-7;
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harmPotent = 0.0; // zero out the global harmonic potential variable
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factor = 1 - pow(lambdaValue, lambdaK);
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for (i=0; i<vecParticles.size(); i++){
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if (vecParticles[i]->isDirectional()){
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pos = vecParticles[i]->getPos();
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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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// 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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// 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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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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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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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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// next we calculate the restraint forces and torques
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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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restraintTrq[0] = 0.0;
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restraintTrq[1] = 0.0;
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restraintTrq[2] = 0.0;
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| 254 |
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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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| 257 |
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restraintTrq[2] += vTy*dVdvx;
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| 258 |
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tempPotent += 0.5*(kOmega*omega*omega);
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}
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| 260 |
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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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| 267 |
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for (j = 0; j < 3; j++) {
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| 268 |
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restraintFrc[j] *= factor;
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restraintTrq[j] *= factor;
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| 270 |
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}
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| 271 |
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| 272 |
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harmPotent += tempPotent;
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| 273 |
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| 274 |
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// now we need to convert from body-fixed torques to space-fixed torques
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| 275 |
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spaceTrq[0] = A[0][0]*restraintTrq[0] + A[1][0]*restraintTrq[1]
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| 276 |
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+ A[2][0]*restraintTrq[2];
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| 277 |
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spaceTrq[1] = A[0][1]*restraintTrq[0] + A[1][1]*restraintTrq[1]
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| 278 |
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+ A[2][1]*restraintTrq[2];
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| 279 |
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spaceTrq[2] = A[0][2]*restraintTrq[0] + A[1][2]*restraintTrq[1]
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| 280 |
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+ A[2][2]*restraintTrq[2];
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| 281 |
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| 282 |
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// now it's time to pass these temporary forces and torques
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| 283 |
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// to the total forces and torques
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| 284 |
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vecParticles[i]->addFrc(restraintFrc);
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| 285 |
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vecParticles[i]->addTrq(spaceTrq);
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| 286 |
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}
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| 287 |
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}
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| 288 |
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| 289 |
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// and we can return the appropriately scaled potential energy
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| 290 |
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tempPotent = harmPotent * factor;
|
| 291 |
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return tempPotent;
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| 292 |
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}
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| 293 |
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| 294 |
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void Restraints::Store_Init_Info(vector<StuntDouble*> vecParticles){
|
| 295 |
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int idealSize;
|
| 296 |
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double pos[3];
|
| 297 |
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double A[3][3];
|
| 298 |
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double RfromQ[3][3];
|
| 299 |
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double quat0, quat1, quat2, quat3;
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| 300 |
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double dot;
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| 301 |
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vector<double> tempZangs;
|
| 302 |
|
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const char *delimit = " \t\n;,";
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| 303 |
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| 304 |
|
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//open the idealCrystal.in file and zAngle.ang file
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| 305 |
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strcpy(fileName, "idealCrystal.in");
|
| 306 |
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strcpy(angleName, "zAngle.ang");
|
| 307 |
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| 308 |
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ifstream crystalIn(fileName);
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| 309 |
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ifstream angleIn(angleName);
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| 310 |
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| 311 |
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// check to see if these files are present in the execution directory
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| 312 |
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if (!crystalIn) {
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| 313 |
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sprintf(painCave.errMsg,
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| 314 |
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"Restraints Error: Unable to open idealCrystal.in for reading.\n"
|
| 315 |
|
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"\tMake sure a ref. crystal file is in the working directory.\n");
|
| 316 |
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painCave.severity = OOPSE_ERROR;
|
| 317 |
|
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painCave.isFatal = 1;
|
| 318 |
|
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simError();
|
| 319 |
|
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}
|
| 320 |
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| 321 |
|
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// it's not fatal to lack a zAngle.ang file, it just means you're starting
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| 322 |
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// from the ideal crystal state
|
| 323 |
|
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if (!angleIn) {
|
| 324 |
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sprintf(painCave.errMsg,
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| 325 |
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"Restraints Warning: The lack of a zAngle.ang file is mildly\n"
|
| 326 |
|
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"\tunsettling... This means the simulation is starting from the\n"
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| 327 |
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"\tidealCrystal.in reference configuration, so the omega values\n"
|
| 328 |
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"\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 |
|
|
|
