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/* |
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* Shapes_FF.cpp |
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* oopse |
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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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* Created by Chris Fennell on 10/20/04. |
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* Copyright 2004 __MyCompanyName__. All rights reserved. |
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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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#include <stdlib.h> |
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#include <stdio.h> |
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#include <string.h> |
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#include "UseTheForce/mpiForceField.h" |
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#endif // is_mpi |
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using namespace std; |
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using namespace oopse; |
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Shapes_FF::~Shapes_FF(){ |
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char readLine[1024]; |
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string fileName; |
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string shapeFileName; |
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string tempString; |
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std::string fileName; |
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std::string shapeFileName; |
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std::string tempString; |
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char *nameToken; |
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char *delim = " ,;\t\n"; |
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int nStrength = 0; |
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int myATID; |
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int isError; |
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string nameString; |
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std::string nameString; |
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AtomType* at; |
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DirectionalAtomType* dat; |
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ShapeAtomType* st; |
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map<string, AtomType*>::iterator iter; |
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std::map<string, AtomType*>::iterator iter; |
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// vectors for shape transfer to fortran |
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vector<RealSphericalHarmonic*> tempSHVector; |
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vector<int> contactL; |
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vector<int> contactM; |
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vector<int> contactFunc; |
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vector<double> contactCoeff; |
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vector<int> rangeL; |
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vector<int> rangeM; |
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vector<int> rangeFunc; |
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vector<double> rangeCoeff; |
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vector<int> strengthL; |
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vector<int> strengthM; |
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vector<int> strengthFunc; |
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vector<double> strengthCoeff; |
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std::vector<RealSphericalHarmonic*> tempSHVector; |
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std::vector<int> contactL; |
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std::vector<int> contactM; |
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std::vector<int> contactFunc; |
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std::vector<double> contactCoeff; |
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std::vector<int> rangeL; |
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std::vector<int> rangeM; |
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std::vector<int> rangeFunc; |
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std::vector<double> rangeCoeff; |
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std::vector<int> strengthL; |
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std::vector<int> strengthM; |
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std::vector<int> strengthFunc; |
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std::vector<double> strengthCoeff; |
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// generate the force file name |
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fileName = "Shapes.frc"; |
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atomTypeMap.insert(make_pair(nameString, st)); |
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} else { |
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// atomType map already contained this string (i.e. it was |
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// atomType map already contained this std::string (i.e. it was |
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// declared in a previous block, and we just need to add |
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// the shape-specific information for this AtomType: |
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void Shapes_FF::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
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int i,j,k; |
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map<string, AtomType*>::iterator iter; |
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std::map<string, AtomType*>::iterator iter; |
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// initialize the atoms |
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DirectionalAtom* dAtom; |
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double ji[3]; |
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double inertialMat[3][3]; |
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Mat3x3d momInt; |
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string myTypeString; |
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std::string myTypeString; |
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bigContact = 0.0; |
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for( i=0; i<nAtoms; i++ ){ |
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myTypeString = the_atoms[i]->getType(); |
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myTypeString = the_atoms[i]->getType().c_str(); |
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iter = atomTypeMap.find(myTypeString); |
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if (iter == atomTypeMap.end()) { |
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sprintf( painCave.errMsg, |
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"AtomType error, %s not found in force file.\n", |
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the_atoms[i]->getType() ); |
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the_atoms[i]->getType().c_str() ); |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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int nTokens; |
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Mat3x3d momInert; |
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RealSphericalHarmonic* rsh; |
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vector<RealSphericalHarmonic*> functionVector; |
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std::vector<RealSphericalHarmonic*> functionVector; |
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ifstrstream shapeFile; |
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string tempString; |
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std::string tempString; |
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shapeFile.open( shapeFileName.c_str() ); |
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