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// Thermodynamic integration is not multiprocessor friendly right now |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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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 "primitives/Molecule.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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#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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namespace oopse { |
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|
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Restraints::Restraints(SimInfo* info, double lambdaVal, double lambdaExp){ |
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info_ = info; |
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Globals* simParam = info_->getSimParams(); |
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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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lambdaValue = lambdaVal; |
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lambdaK = lambdaExp; |
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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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if (simParam->getUseSolidThermInt()) { |
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if (simParam->haveThermIntDistSpringConst()) { |
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kDist = simParam->getThermIntDistSpringConst(); |
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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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else{ |
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kDist = 6.0; |
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sprintf(painCave.errMsg, |
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"ThermoIntegration Warning: the spring constant for the\n" |
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"\ttranslational restraint was not specified. OOPSE will use\n" |
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"\ta default value of %f. To set it to something else, use\n" |
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"\tthe thermIntDistSpringConst variable.\n", |
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kDist); |
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painCave.isFatal = 0; |
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simError(); |
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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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if (simParam->haveThermIntThetaSpringConst()) { |
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kTheta = simParam->getThermIntThetaSpringConst(); |
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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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else{ |
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kTheta = 7.5; |
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sprintf(painCave.errMsg, |
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"ThermoIntegration Warning: the spring constant for the\n" |
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"\tdeflection orientational restraint was not specified.\n" |
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"\tOOPSE will use a default value of %f. To set it to\n" |
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"\tsomething else, use the thermIntThetaSpringConst variable.\n", |
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kTheta); |
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painCave.isFatal = 0; |
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simError(); |
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} |
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if (simParam->haveThermIntOmegaSpringConst()) { |
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kOmega = simParam->getThermIntOmegaSpringConst(); |
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} |
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else{ |
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kOmega = 13.5; |
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sprintf(painCave.errMsg, |
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"ThermoIntegration Warning: the spring constant for the\n" |
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"\tspin orientational restraint was not specified. OOPSE\n" |
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"\twill use a default value of %f. To set it to something\n" |
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"\telse, use the thermIntOmegaSpringConst variable.\n", |
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kOmega); |
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painCave.isFatal = 0; |
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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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// build a RestReader and read in important information |
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|
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restRead_ = new RestReader(info_); |
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restRead_->readIdealCrystal(); |
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restRead_->readZangle(); |
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|
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delete restRead_; |
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restRead_ = NULL; |
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|
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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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Restraints::~Restraints(){ |
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} |
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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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void Restraints::Calc_rVal(Vector3d &position, double refPosition[3]){ |
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delRx = position.x() - refPosition[0]; |
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delRy = position.y() - refPosition[1]; |
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delRz = position.z() - refPosition[2]; |
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|
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return; |
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} |
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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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void Restraints::Calc_body_thetaVal(RotMat3x3d &matrix, 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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< |
if (omega > PI){ |
| 149 |
< |
tempOmega = omega / TWO_PI; |
| 150 |
< |
wholeTwoPis = floor(tempOmega); |
| 151 |
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tempOmega = omega - TWO_PI*wholeTwoPis; |
| 152 |
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if (tempOmega > PI) |
| 153 |
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omega = tempOmega - TWO_PI; |
| 154 |
< |
else |
| 155 |
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omega = tempOmega; |
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> |
|
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> |
void Restraints::Calc_body_omegaVal(double zAngle){ |
| 150 |
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double zRotator[3][3]; |
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double tempOmega; |
| 152 |
> |
double wholeTwoPis; |
| 153 |
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// Use the omega accumulated from the rotation propagation |
| 154 |
> |
omega = zAngle; |
| 155 |
> |
|
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> |
// 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 |
< |
vb0x = sin(omega); |
| 189 |
< |
vb0y = cos(omega); |
| 190 |
< |
vb0z = 0.0; |
| 191 |
< |
|
| 192 |
< |
normalize = sqrt(vb0x*vb0x + vb0y*vb0y + vb0z*vb0z); |
| 193 |
< |
vb0x = vb0x/normalize; |
| 194 |
< |
vb0y = vb0y/normalize; |
| 195 |
< |
vb0z = vb0z/normalize; |
| 196 |
< |
|
| 197 |
< |
return; |
| 198 |
< |
} |
| 199 |
< |
|
| 200 |
< |
double Restraints::Calc_Restraint_Forces(vector<StuntDouble*> vecParticles){ |
| 201 |
< |
double pos[3]; |
| 202 |
< |
double A[3][3]; |
| 203 |
< |
double tolerance; |
| 204 |
< |
double tempPotent; |
| 205 |
< |
double factor; |
| 206 |
< |
double spaceTrq[3]; |
| 207 |
< |
double omegaPass; |
| 208 |
< |
|
| 209 |
< |
tolerance = 5.72957795131e-7; |
| 210 |
< |
|
| 211 |
< |
harmPotent = 0.0; // zero out the global harmonic potential variable |
| 212 |
< |
|
| 213 |
< |
factor = 1 - pow(lambdaValue, lambdaK); |
| 214 |
< |
|
| 215 |
< |
for (i=0; i<vecParticles.size(); i++){ |
| 216 |
< |
if (vecParticles[i]->isDirectional()){ |
| 217 |
< |
vecParticles[i]->getPos(pos); |
| 218 |
< |
vecParticles[i]->getA(A); |
| 219 |
< |
Calc_rVal( pos, i ); |
| 220 |
< |
Calc_body_thetaVal( A, i ); |
| 221 |
< |
omegaPass = vecParticles[i]->getZangle(); |
| 222 |
< |
Calc_body_omegaVal( A, omegaPass ); |
| 223 |
< |
|
| 224 |
< |
// first we calculate the derivatives |
| 225 |
< |
dVdrx = -kDist*delRx; |
| 226 |
< |
dVdry = -kDist*delRy; |
| 227 |
< |
dVdrz = -kDist*delRz; |
| 228 |
< |
|
| 229 |
< |
// uTx... and vTx... are the body-fixed z and y unit vectors |
| 230 |
< |
uTx = 0.0; |
| 231 |
< |
uTy = 0.0; |
| 232 |
< |
uTz = 1.0; |
| 233 |
< |
vTx = 0.0; |
| 234 |
< |
vTy = 1.0; |
| 235 |
< |
vTz = 0.0; |
| 236 |
< |
|
| 237 |
< |
dVdux = 0; |
| 238 |
< |
dVduy = 0; |
| 239 |
< |
dVduz = 0; |
| 240 |
< |
dVdvx = 0; |
| 241 |
< |
dVdvy = 0; |
| 242 |
< |
dVdvz = 0; |
| 243 |
< |
|
| 244 |
< |
if (fabs(theta) > tolerance) { |
| 245 |
< |
dVdux = -(kTheta*theta/sin(theta))*ub0x; |
| 246 |
< |
dVduy = -(kTheta*theta/sin(theta))*ub0y; |
| 247 |
< |
dVduz = -(kTheta*theta/sin(theta))*ub0z; |
| 248 |
< |
} |
| 249 |
< |
|
| 250 |
< |
if (fabs(omega) > tolerance) { |
| 251 |
< |
dVdvx = -(kOmega*omega/sin(omega))*vb0x; |
| 252 |
< |
dVdvy = -(kOmega*omega/sin(omega))*vb0y; |
| 253 |
< |
dVdvz = -(kOmega*omega/sin(omega))*vb0z; |
| 187 |
> |
|
| 188 |
> |
double Restraints::Calc_Restraint_Forces(){ |
| 189 |
> |
SimInfo::MoleculeIterator mi; |
| 190 |
> |
Molecule* mol; |
| 191 |
> |
Molecule::IntegrableObjectIterator ii; |
| 192 |
> |
StuntDouble* integrableObject; |
| 193 |
> |
Vector3d pos; |
| 194 |
> |
RotMat3x3d A; |
| 195 |
> |
double refPos[3]; |
| 196 |
> |
double refVec[3]; |
| 197 |
> |
double tolerance; |
| 198 |
> |
double tempPotent; |
| 199 |
> |
double factor; |
| 200 |
> |
double spaceTrq[3]; |
| 201 |
> |
double omegaPass; |
| 202 |
> |
GenericData* data; |
| 203 |
> |
DoubleGenericData* doubleData; |
| 204 |
> |
|
| 205 |
> |
tolerance = 5.72957795131e-7; |
| 206 |
> |
|
| 207 |
> |
harmPotent = 0.0; // zero out the global harmonic potential variable |
| 208 |
> |
|
| 209 |
> |
factor = 1 - pow(lambdaValue, lambdaK); |
| 210 |
> |
|
| 211 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 212 |
> |
mol = info_->nextMolecule(mi)) { |
| 213 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); |
| 214 |
> |
integrableObject != NULL; |
| 215 |
> |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 216 |
> |
|
| 217 |
> |
// obtain the current and reference positions |
| 218 |
> |
pos = integrableObject->getPos(); |
| 219 |
> |
|
| 220 |
> |
data = integrableObject->getPropertyByName("refPosX"); |
| 221 |
> |
if (data){ |
| 222 |
> |
doubleData = dynamic_cast<DoubleGenericData*>(data); |
| 223 |
> |
if (!doubleData){ |
| 224 |
> |
cerr << "Can't obtain refPosX from StuntDouble\n"; |
| 225 |
> |
return 0.0; |
| 226 |
> |
} |
| 227 |
> |
else refPos[0] = doubleData->getData(); |
| 228 |
> |
} |
| 229 |
> |
data = integrableObject->getPropertyByName("refPosY"); |
| 230 |
> |
if (data){ |
| 231 |
> |
doubleData = dynamic_cast<DoubleGenericData*>(data); |
| 232 |
> |
if (!doubleData){ |
| 233 |
> |
cerr << "Can't obtain refPosY from StuntDouble\n"; |
| 234 |
> |
return 0.0; |
| 235 |
> |
} |
| 236 |
> |
else refPos[1] = doubleData->getData(); |
| 237 |
> |
} |
| 238 |
> |
data = integrableObject->getPropertyByName("refPosZ"); |
| 239 |
> |
if (data){ |
| 240 |
> |
doubleData = dynamic_cast<DoubleGenericData*>(data); |
| 241 |
> |
if (!doubleData){ |
| 242 |
> |
cerr << "Can't obtain refPosZ from StuntDouble\n"; |
| 243 |
> |
return 0.0; |
| 244 |
> |
} |
| 245 |
> |
else refPos[2] = doubleData->getData(); |
| 246 |
> |
} |
| 247 |
> |
|
| 248 |
> |
// calculate the displacement |
| 249 |
> |
Calc_rVal( pos, refPos ); |
| 250 |
> |
|
| 251 |
> |
// calculate the derivatives |
| 252 |
> |
dVdrx = -kDist*delRx; |
| 253 |
> |
dVdry = -kDist*delRy; |
| 254 |
> |
dVdrz = -kDist*delRz; |
| 255 |
> |
|
| 256 |
> |
// next we calculate the restraint forces |
| 257 |
> |
restraintFrc[0] = dVdrx; |
| 258 |
> |
restraintFrc[1] = dVdry; |
| 259 |
> |
restraintFrc[2] = dVdrz; |
| 260 |
> |
tempPotent = 0.5*kDist*(delRx*delRx + delRy*delRy + delRz*delRz); |
| 261 |
> |
|
| 262 |
> |
// apply the lambda scaling factor to the forces |
| 263 |
> |
for (j = 0; j < 3; j++) restraintFrc[j] *= factor; |
| 264 |
> |
|
| 265 |
> |
// and add the temporary force to the total force |
| 266 |
> |
integrableObject->addFrc(restraintFrc); |
| 267 |
> |
|
| 268 |
> |
// if the particle is directional, we accumulate the rot. restraints |
| 269 |
> |
if (integrableObject->isDirectional()){ |
| 270 |
> |
|
| 271 |
> |
// get the current rotation matrix and reference vector |
| 272 |
> |
A = integrableObject->getA(); |
| 273 |
> |
|
| 274 |
> |
data = integrableObject->getPropertyByName("refVectorX"); |
| 275 |
> |
if (data){ |
| 276 |
> |
doubleData = dynamic_cast<DoubleGenericData*>(data); |
| 277 |
> |
if (!doubleData){ |
| 278 |
> |
cerr << "Can't obtain refVectorX from StuntDouble\n"; |
| 279 |
> |
return 0.0; |
| 280 |
> |
} |
| 281 |
> |
else refVec[0] = doubleData->getData(); |
| 282 |
> |
} |
| 283 |
> |
data = integrableObject->getPropertyByName("refVectorY"); |
| 284 |
> |
if (data){ |
| 285 |
> |
doubleData = dynamic_cast<DoubleGenericData*>(data); |
| 286 |
> |
if (!doubleData){ |
| 287 |
> |
cerr << "Can't obtain refVectorY from StuntDouble\n"; |
| 288 |
> |
return 0.0; |
| 289 |
> |
} |
| 290 |
> |
else refVec[1] = doubleData->getData(); |
| 291 |
> |
} |
| 292 |
> |
data = integrableObject->getPropertyByName("refVectorZ"); |
| 293 |
> |
if (data){ |
| 294 |
> |
doubleData = dynamic_cast<DoubleGenericData*>(data); |
| 295 |
> |
if (!doubleData){ |
| 296 |
> |
cerr << "Can't obtain refVectorZ from StuntDouble\n"; |
| 297 |
> |
return 0.0; |
| 298 |
> |
} |
| 299 |
> |
else refVec[2] = doubleData->getData(); |
| 300 |
> |
} |
| 301 |
> |
|
| 302 |
> |
// calculate the theta and omega displacements |
| 303 |
> |
Calc_body_thetaVal( A, refVec ); |
| 304 |
> |
omegaPass = integrableObject->getZangle(); |
| 305 |
> |
Calc_body_omegaVal( omegaPass ); |
| 306 |
> |
|
| 307 |
> |
// uTx... and vTx... are the body-fixed z and y unit vectors |
| 308 |
> |
uTx = 0.0; |
| 309 |
> |
uTy = 0.0; |
| 310 |
> |
uTz = 1.0; |
| 311 |
> |
vTx = 0.0; |
| 312 |
> |
vTy = 1.0; |
| 313 |
> |
vTz = 0.0; |
| 314 |
> |
|
| 315 |
> |
dVdux = 0.0; |
| 316 |
> |
dVduy = 0.0; |
| 317 |
> |
dVduz = 0.0; |
| 318 |
> |
dVdvx = 0.0; |
| 319 |
> |
dVdvy = 0.0; |
| 320 |
> |
dVdvz = 0.0; |
| 321 |
> |
|
| 322 |
> |
if (fabs(theta) > tolerance) { |
| 323 |
> |
dVdux = -(kTheta*theta/sin(theta))*ub0x; |
| 324 |
> |
dVduy = -(kTheta*theta/sin(theta))*ub0y; |
| 325 |
> |
dVduz = -(kTheta*theta/sin(theta))*ub0z; |
| 326 |
> |
} |
| 327 |
> |
|
| 328 |
> |
if (fabs(omega) > tolerance) { |
| 329 |
> |
dVdvx = -(kOmega*omega/sin(omega))*vb0x; |
| 330 |
> |
dVdvy = -(kOmega*omega/sin(omega))*vb0y; |
| 331 |
> |
dVdvz = -(kOmega*omega/sin(omega))*vb0z; |
| 332 |
> |
} |
| 333 |
> |
|
| 334 |
> |
// next we calculate the restraint torques |
| 335 |
> |
restraintTrq[0] = 0.0; |
| 336 |
> |
restraintTrq[1] = 0.0; |
| 337 |
> |
restraintTrq[2] = 0.0; |
| 338 |
> |
|
| 339 |
> |
if (fabs(omega) > tolerance) { |
| 340 |
> |
restraintTrq[0] += 0.0; |
| 341 |
> |
restraintTrq[1] += 0.0; |
| 342 |
> |
restraintTrq[2] += vTy*dVdvx; |
| 343 |
> |
tempPotent += 0.5*(kOmega*omega*omega); |
| 344 |
> |
} |
| 345 |
> |
if (fabs(theta) > tolerance) { |
| 346 |
> |
restraintTrq[0] += (uTz*dVduy); |
| 347 |
> |
restraintTrq[1] += -(uTz*dVdux); |
| 348 |
> |
restraintTrq[2] += 0.0; |
| 349 |
> |
tempPotent += 0.5*(kTheta*theta*theta); |
| 350 |
> |
} |
| 351 |
> |
|
| 352 |
> |
// apply the lambda scaling factor to these torques |
| 353 |
> |
for (j = 0; j < 3; j++) restraintTrq[j] *= factor; |
| 354 |
> |
|
| 355 |
> |
// now we need to convert from body-fixed to space-fixed torques |
| 356 |
> |
spaceTrq[0] = A(0,0)*restraintTrq[0] + A(1,0)*restraintTrq[1] |
| 357 |
> |
+ A(2,0)*restraintTrq[2]; |
| 358 |
> |
spaceTrq[1] = A(0,1)*restraintTrq[0] + A(1,1)*restraintTrq[1] |
| 359 |
> |
+ A(2,1)*restraintTrq[2]; |
| 360 |
> |
spaceTrq[2] = A(0,2)*restraintTrq[0] + A(1,2)*restraintTrq[1] |
| 361 |
> |
+ A(2,2)*restraintTrq[2]; |
| 362 |
> |
|
| 363 |
> |
// now pass this temporary torque vector to the total torque |
| 364 |
> |
integrableObject->addTrq(spaceTrq); |
| 365 |
> |
} |
| 366 |
> |
|
| 367 |
> |
// update the total harmonic potential with this object's contribution |
| 368 |
> |
harmPotent += tempPotent; |
| 369 |
|
} |
| 370 |
< |
|
| 245 |
< |
// next we calculate the restraint forces and torques |
| 246 |
< |
restraintFrc[0] = dVdrx; |
| 247 |
< |
restraintFrc[1] = dVdry; |
| 248 |
< |
restraintFrc[2] = dVdrz; |
| 249 |
< |
tempPotent = 0.5*kDist*(delRx*delRx + delRy*delRy + delRz*delRz); |
| 250 |
< |
|
| 251 |
< |
restraintTrq[0] = 0.0; |
| 252 |
< |
restraintTrq[1] = 0.0; |
| 253 |
< |
restraintTrq[2] = 0.0; |
| 254 |
< |
|
| 255 |
< |
if (fabs(omega) > tolerance) { |
| 256 |
< |
restraintTrq[0] += 0.0; |
| 257 |
< |
restraintTrq[1] += 0.0; |
| 258 |
< |
restraintTrq[2] += vTy*dVdvx; |
| 259 |
< |
tempPotent += 0.5*(kOmega*omega*omega); |
| 260 |
< |
} |
| 261 |
< |
if (fabs(theta) > tolerance) { |
| 262 |
< |
restraintTrq[0] += (uTz*dVduy); |
| 263 |
< |
restraintTrq[1] += -(uTz*dVdux); |
| 264 |
< |
restraintTrq[2] += 0.0; |
| 265 |
< |
tempPotent += 0.5*(kTheta*theta*theta); |
| 266 |
< |
} |
| 267 |
< |
|
| 268 |
< |
for (j = 0; j < 3; j++) { |
| 269 |
< |
restraintFrc[j] *= factor; |
| 270 |
< |
restraintTrq[j] *= factor; |
| 271 |
< |
} |
| 272 |
< |
|
| 273 |
< |
harmPotent += tempPotent; |
| 274 |
< |
|
| 275 |
< |
// now we need to convert from body-fixed torques to space-fixed torques |
| 276 |
< |
spaceTrq[0] = A[0][0]*restraintTrq[0] + A[1][0]*restraintTrq[1] |
| 277 |
< |
+ A[2][0]*restraintTrq[2]; |
| 278 |
< |
spaceTrq[1] = A[0][1]*restraintTrq[0] + A[1][1]*restraintTrq[1] |
| 279 |
< |
+ A[2][1]*restraintTrq[2]; |
| 280 |
< |
spaceTrq[2] = A[0][2]*restraintTrq[0] + A[1][2]*restraintTrq[1] |
| 281 |
< |
+ A[2][2]*restraintTrq[2]; |
| 282 |
< |
|
| 283 |
< |
// now it's time to pass these temporary forces and torques |
| 284 |
< |
// to the total forces and torques |
| 285 |
< |
vecParticles[i]->addFrc(restraintFrc); |
| 286 |
< |
vecParticles[i]->addTrq(spaceTrq); |
| 370 |
> |
|
| 371 |
|
} |
| 288 |
– |
} |
| 289 |
– |
|
| 290 |
– |
// and we can return the appropriately scaled potential energy |
| 291 |
– |
tempPotent = harmPotent * factor; |
| 292 |
– |
return tempPotent; |
| 293 |
– |
} |
| 294 |
– |
|
| 295 |
– |
void Restraints::Store_Init_Info(vector<StuntDouble*> vecParticles){ |
| 296 |
– |
int idealSize; |
| 297 |
– |
double pos[3]; |
| 298 |
– |
double A[3][3]; |
| 299 |
– |
double RfromQ[3][3]; |
| 300 |
– |
double quat0, quat1, quat2, quat3; |
| 301 |
– |
double dot; |
| 302 |
– |
vector<double> tempZangs; |
| 303 |
– |
const char *delimit = " \t\n;,"; |
| 304 |
– |
|
| 305 |
– |
//open the idealCrystal.in file and zAngle.ang file |
| 306 |
– |
strcpy(fileName, "idealCrystal.in"); |
| 307 |
– |
strcpy(angleName, "zAngle.ang"); |
| 308 |
– |
|
| 309 |
– |
ifstrstream crystalIn(fileName); |
| 310 |
– |
ifstrstream angleIn(angleName); |
| 311 |
– |
|
| 312 |
– |
// check to see if these files are present in the execution directory |
| 313 |
– |
if (!crystalIn) { |
| 314 |
– |
sprintf(painCave.errMsg, |
| 315 |
– |
"Restraints Error: Unable to open idealCrystal.in for reading.\n" |
| 316 |
– |
"\tMake sure a ref. crystal file is in the working directory.\n"); |
| 317 |
– |
painCave.severity = OOPSE_ERROR; |
| 318 |
– |
painCave.isFatal = 1; |
| 319 |
– |
simError(); |
| 320 |
– |
} |
| 321 |
– |
|
| 322 |
– |
// it's not fatal to lack a zAngle.ang file, it just means you're starting |
| 323 |
– |
// from the ideal crystal state |
| 324 |
– |
if (!angleIn) { |
| 325 |
– |
sprintf(painCave.errMsg, |
| 326 |
– |
"Restraints Warning: The lack of a zAngle.ang file is mildly\n" |
| 327 |
– |
"\tunsettling... This means the simulation is starting from the\n" |
| 328 |
– |
"\tidealCrystal.in reference configuration, so the omega values\n" |
| 329 |
– |
"\twill all be set to zero. If this is not the case, the energy\n" |
| 330 |
– |
"\tcalculations will be wrong.\n"); |
| 331 |
– |
painCave.severity = OOPSE_WARNING; |
| 332 |
– |
painCave.isFatal = 0; |
| 333 |
– |
simError(); |
| 334 |
– |
} |
| 335 |
– |
|
| 336 |
– |
// A rather specific reader for OOPSE .eor files... |
| 337 |
– |
// Let's read in the perfect crystal file |
| 338 |
– |
crystalIn.getline(inLine,999,'\n'); |
| 339 |
– |
// check to see if the crystal file is the same length as starting config. |
| 340 |
– |
token = strtok(inLine,delimit); |
| 341 |
– |
strcpy(inValue,token); |
| 342 |
– |
idealSize = atoi(inValue); |
| 343 |
– |
if (idealSize != vecParticles.size()) { |
| 344 |
– |
sprintf(painCave.errMsg, |
| 345 |
– |
"Restraints Error: Reference crystal file is not valid.\n" |
| 346 |
– |
"\tMake sure the idealCrystal.in file is the same size as the\n" |
| 347 |
– |
"\tstarting configuration. Using an incompatable crystal will\n" |
| 348 |
– |
"\tlead to energy calculation failures.\n"); |
| 349 |
– |
painCave.severity = OOPSE_ERROR; |
| 350 |
– |
painCave.isFatal = 1; |
| 351 |
– |
simError(); |
| 352 |
– |
} |
| 353 |
– |
// else, the file is okay... let's continue |
| 354 |
– |
crystalIn.getline(inLine,999,'\n'); |
| 355 |
– |
|
| 356 |
– |
for (i=0; i<vecParticles.size(); i++) { |
| 357 |
– |
crystalIn.getline(inLine,999,'\n'); |
| 358 |
– |
token = strtok(inLine,delimit); |
| 359 |
– |
token = strtok(NULL,delimit); |
| 360 |
– |
strcpy(inValue,token); |
| 361 |
– |
cofmPosX.push_back(atof(inValue)); |
| 362 |
– |
token = strtok(NULL,delimit); |
| 363 |
– |
strcpy(inValue,token); |
| 364 |
– |
cofmPosY.push_back(atof(inValue)); |
| 365 |
– |
token = strtok(NULL,delimit); |
| 366 |
– |
strcpy(inValue,token); |
| 367 |
– |
cofmPosZ.push_back(atof(inValue)); |
| 368 |
– |
token = strtok(NULL,delimit); |
| 369 |
– |
token = strtok(NULL,delimit); |
| 370 |
– |
token = strtok(NULL,delimit); |
| 371 |
– |
token = strtok(NULL,delimit); |
| 372 |
– |
strcpy(inValue,token); |
| 373 |
– |
quat0 = atof(inValue); |
| 374 |
– |
token = strtok(NULL,delimit); |
| 375 |
– |
strcpy(inValue,token); |
| 376 |
– |
quat1 = atof(inValue); |
| 377 |
– |
token = strtok(NULL,delimit); |
| 378 |
– |
strcpy(inValue,token); |
| 379 |
– |
quat2 = atof(inValue); |
| 380 |
– |
token = strtok(NULL,delimit); |
| 381 |
– |
strcpy(inValue,token); |
| 382 |
– |
quat3 = atof(inValue); |
| 383 |
– |
|
| 384 |
– |
// now build the rotation matrix and find the unit vectors |
| 385 |
– |
RfromQ[0][0] = quat0*quat0 + quat1*quat1 - quat2*quat2 - quat3*quat3; |
| 386 |
– |
RfromQ[0][1] = 2*(quat1*quat2 + quat0*quat3); |
| 387 |
– |
RfromQ[0][2] = 2*(quat1*quat3 - quat0*quat2); |
| 388 |
– |
RfromQ[1][0] = 2*(quat1*quat2 - quat0*quat3); |
| 389 |
– |
RfromQ[1][1] = quat0*quat0 - quat1*quat1 + quat2*quat2 - quat3*quat3; |
| 390 |
– |
RfromQ[1][2] = 2*(quat2*quat3 + quat0*quat1); |
| 391 |
– |
RfromQ[2][0] = 2*(quat1*quat3 + quat0*quat2); |
| 392 |
– |
RfromQ[2][1] = 2*(quat2*quat3 - quat0*quat1); |
| 393 |
– |
RfromQ[2][2] = quat0*quat0 - quat1*quat1 - quat2*quat2 + quat3*quat3; |
| 372 |
|
|
| 373 |
< |
normalize = sqrt(RfromQ[2][0]*RfromQ[2][0] + RfromQ[2][1]*RfromQ[2][1] |
| 374 |
< |
+ RfromQ[2][2]*RfromQ[2][2]); |
| 375 |
< |
uX0.push_back(RfromQ[2][0]/normalize); |
| 376 |
< |
uY0.push_back(RfromQ[2][1]/normalize); |
| 377 |
< |
uZ0.push_back(RfromQ[2][2]/normalize); |
| 400 |
< |
|
| 401 |
< |
normalize = sqrt(RfromQ[1][0]*RfromQ[1][0] + RfromQ[1][1]*RfromQ[1][1] |
| 402 |
< |
+ RfromQ[1][2]*RfromQ[1][2]); |
| 403 |
< |
vX0.push_back(RfromQ[1][0]/normalize); |
| 404 |
< |
vY0.push_back(RfromQ[1][1]/normalize); |
| 405 |
< |
vZ0.push_back(RfromQ[1][2]/normalize); |
| 373 |
> |
// we can finish by returning the appropriately scaled potential energy |
| 374 |
> |
tempPotent = harmPotent * factor; |
| 375 |
> |
|
| 376 |
> |
return tempPotent; |
| 377 |
> |
|
| 378 |
|
} |
| 379 |
< |
crystalIn.close(); |
| 380 |
< |
|
| 409 |
< |
// now we read in the zAngle.ang file |
| 410 |
< |
if (angleIn){ |
| 411 |
< |
angleIn.getline(inLine,999,'\n'); |
| 412 |
< |
angleIn.getline(inLine,999,'\n'); |
| 413 |
< |
while (!angleIn.eof()) { |
| 414 |
< |
token = strtok(inLine,delimit); |
| 415 |
< |
strcpy(inValue,token); |
| 416 |
< |
tempZangs.push_back(atof(inValue)); |
| 417 |
< |
angleIn.getline(inLine,999,'\n'); |
| 418 |
< |
} |
| 419 |
< |
|
| 420 |
< |
// test to make sure the zAngle.ang file is the proper length |
| 421 |
< |
if (tempZangs.size() == vecParticles.size()) |
| 422 |
< |
for (i=0; i<vecParticles.size(); i++) |
| 423 |
< |
vecParticles[i]->setZangle(tempZangs[i]); |
| 424 |
< |
else { |
| 425 |
< |
sprintf(painCave.errMsg, |
| 426 |
< |
"Restraints Error: the supplied zAngle file is not valid.\n" |
| 427 |
< |
"\tMake sure the zAngle.ang file matches with the initial\n" |
| 428 |
< |
"\tconfiguration (i.e. they're the same length). Using the wrong\n" |
| 429 |
< |
"\tzAngle file will lead to errors in the energy calculations.\n"); |
| 430 |
< |
painCave.severity = OOPSE_ERROR; |
| 431 |
< |
painCave.isFatal = 1; |
| 432 |
< |
simError(); |
| 433 |
< |
} |
| 434 |
< |
} |
| 435 |
< |
angleIn.close(); |
| 436 |
< |
|
| 437 |
< |
return; |
| 438 |
< |
} |
| 439 |
< |
|
| 440 |
< |
void Restraints::Write_zAngle_File(vector<StuntDouble*> vecParticles){ |
| 441 |
< |
|
| 442 |
< |
char zOutName[200]; |
| 443 |
< |
|
| 444 |
< |
strcpy(zOutName,"zAngle.ang"); |
| 445 |
< |
|
| 446 |
< |
ofstream angleOut(zOutName); |
| 447 |
< |
angleOut << "This file contains the omega values for the .eor file\n"; |
| 448 |
< |
for (i=0; i<vecParticles.size(); i++) { |
| 449 |
< |
angleOut << vecParticles[i]->getZangle() << "\n"; |
| 450 |
< |
} |
| 451 |
< |
return; |
| 452 |
< |
} |
| 453 |
< |
|
| 454 |
< |
double Restraints::getVharm(){ |
| 455 |
< |
return harmPotent; |
| 456 |
< |
} |
| 457 |
< |
|
| 379 |
> |
|
| 380 |
> |
}// end namespace oopse |
