| 1 |
/* |
| 2 |
* Shapes_FF.cpp |
| 3 |
* oopse |
| 4 |
* |
| 5 |
* Created by Chris Fennell on 10/20/04. |
| 6 |
* Copyright 2004 __MyCompanyName__. All rights reserved. |
| 7 |
* |
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*/ |
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|
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#include <stdlib.h> |
| 11 |
#include <stdio.h> |
| 12 |
#include <string.h> |
| 13 |
#include <map> |
| 14 |
#include <cmath> |
| 15 |
#include <iostream> |
| 16 |
|
| 17 |
#ifdef IS_MPI |
| 18 |
#include <mpi.h> |
| 19 |
#endif //is_mpi |
| 20 |
|
| 21 |
#include "UseTheForce/ForceFields.hpp" |
| 22 |
#include "primitives/SRI.hpp" |
| 23 |
#include "utils/simError.h" |
| 24 |
#include "utils/StringUtils.hpp" |
| 25 |
#include "io/basic_ifstrstream.hpp" |
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#include "math/RealSphericalHarmonic.hpp" |
| 27 |
#include "math/SquareMatrix3.hpp" |
| 28 |
#include "types/ShapeAtomType.hpp" |
| 29 |
#include "UseTheForce/DarkSide/atype_interface.h" |
| 30 |
#include "UseTheForce/DarkSide/shapes_interface.h" |
| 31 |
|
| 32 |
#ifdef IS_MPI |
| 33 |
#include "UseTheForce/mpiForceField.h" |
| 34 |
#endif // is_mpi |
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|
| 36 |
using namespace std; |
| 37 |
using namespace oopse; |
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|
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Shapes_FF::~Shapes_FF(){ |
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|
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#ifdef IS_MPI |
| 42 |
if( worldRank == 0 ){ |
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#endif // is_mpi |
| 44 |
|
| 45 |
forceFile.close(); |
| 46 |
|
| 47 |
#ifdef IS_MPI |
| 48 |
} |
| 49 |
#endif // is_mpi |
| 50 |
} |
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|
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|
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void Shapes_FF::calcRcut( void ){ |
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|
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#ifdef IS_MPI |
| 56 |
double tempShapesRcut = shapesRcut; |
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MPI_Allreduce( &tempShapesRcut, &shapesRcut, 1, MPI_DOUBLE, MPI_MAX, |
| 58 |
MPI_COMM_WORLD); |
| 59 |
#endif //is_mpi |
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entry_plug->setDefaultRcut(shapesRcut); |
| 61 |
} |
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|
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|
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void Shapes_FF::initForceField(){ |
| 65 |
initFortran(0); |
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} |
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|
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|
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void Shapes_FF::readParams( void ){ |
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|
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char readLine[1024]; |
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|
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string fileName; |
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string shapeFileName; |
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string tempString; |
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|
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char *nameToken; |
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char *delim = " ,;\t\n"; |
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int nTokens, i; |
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int nContact = 0; |
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int nRange = 0; |
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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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AtomType* at; |
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DirectionalAtomType* dat; |
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ShapeAtomType* st; |
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|
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map<string, AtomType*>::iterator iter; |
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|
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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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|
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// generate the force file name |
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fileName = "Shapes.frc"; |
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|
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// attempt to open the file in the current directory first. |
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forceFile.open( fileName.c_str() ); |
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|
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if( forceFile == NULL ){ |
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|
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tempString = ffPath; |
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tempString += "/"; |
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tempString += fileName; |
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fileName = tempString; |
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|
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forceFile.open( fileName.c_str() ); |
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|
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if( forceFile == NULL ){ |
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|
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sprintf( painCave.errMsg, |
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"Error opening the force field parameter file:\n" |
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"\t%s\n" |
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"\tHave you tried setting the FORCE_PARAM_PATH environment " |
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"variable?\n", |
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fileName.c_str() ); |
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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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|
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// read in the shape types. |
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|
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findBegin( forceFile, "ShapeTypes" ); |
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|
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while( !forceFile.eof() ){ |
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forceFile.getline( readLine, sizeof(readLine) ); |
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|
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// toss comment lines |
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if( readLine[0] != '!' && readLine[0] != '#' ){ |
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|
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if (isEndLine(readLine)) break; |
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|
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nTokens = countTokens(readLine, " ,;\t"); |
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if (nTokens != 0) { |
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if (nTokens < 2) { |
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sprintf( painCave.errMsg, |
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"Not enough data on a ShapeTypes line in file: %s\n", |
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fileName.c_str() ); |
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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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nameToken = strtok( readLine, delim ); |
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shapeFileName = strtok( NULL, delim ); |
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|
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// strings are not char arrays! |
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nameString = nameToken; |
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|
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// does this AtomType name already exist in the map? |
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iter = atomTypeMap.find(nameString); |
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if (iter == atomTypeMap.end()) { |
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// no, it doesn't, so we may proceed: |
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|
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st = new ShapeAtomType(); |
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|
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st->setName(nameString); |
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myATID = atomTypeMap.size(); |
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st->setIdent(myATID); |
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parseShapeFile(shapeFileName, st); |
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st->complete(); |
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atomTypeMap.insert(make_pair(nameString, st)); |
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|
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} else { |
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// atomType map already contained this 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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|
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st = (ShapeAtomType*)(iter->second); |
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parseShapeFile(shapeFileName, st); |
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} |
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} |
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} |
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} |
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|
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#ifdef IS_MPI |
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|
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// looks like all the processors have their ShapeType vectors ready... |
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sprintf( checkPointMsg, |
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"Shapes_FF shape objects read successfully." ); |
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MPIcheckPoint(); |
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|
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#endif // is_mpi |
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|
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// pack up and send the necessary info to fortran |
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for (iter = atomTypeMap.begin(); iter != atomTypeMap.end(); ++iter){ |
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|
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at = (AtomType*)(iter->second); |
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|
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if (at->isDirectional()) { |
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|
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dat = (DirectionalAtomType*)at; |
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|
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if (dat->isShape()) { |
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|
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st = (ShapeAtomType*)at; |
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|
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contactL.clear(); |
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contactM.clear(); |
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contactFunc.clear(); |
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contactCoeff.clear(); |
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|
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tempSHVector = st->getContactFuncs(); |
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|
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nContact = tempSHVector.size(); |
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for (i=0; i<nContact; i++){ |
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contactL.push_back(tempSHVector[i]->getL()); |
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contactM.push_back(tempSHVector[i]->getM()); |
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contactFunc.push_back(tempSHVector[i]->getFunctionType()); |
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contactCoeff.push_back(tempSHVector[i]->getCoefficient()); |
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} |
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|
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rangeL.clear(); |
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rangeM.clear(); |
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rangeFunc.clear(); |
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rangeCoeff.clear(); |
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|
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tempSHVector = st->getRangeFuncs(); |
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|
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nRange = tempSHVector.size(); |
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for (i=0; i<nRange; i++){ |
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rangeL.push_back(tempSHVector[i]->getL()); |
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rangeM.push_back(tempSHVector[i]->getM()); |
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rangeFunc.push_back(tempSHVector[i]->getFunctionType()); |
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rangeCoeff.push_back(tempSHVector[i]->getCoefficient()); |
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} |
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|
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strengthL.clear(); |
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strengthM.clear(); |
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strengthFunc.clear(); |
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strengthCoeff.clear(); |
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|
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tempSHVector = st->getStrengthFuncs(); |
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|
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nStrength = tempSHVector.size(); |
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for (i=0; i<nStrength; i++){ |
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strengthL.push_back(tempSHVector[i]->getL()); |
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strengthM.push_back(tempSHVector[i]->getM()); |
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strengthFunc.push_back(tempSHVector[i]->getFunctionType()); |
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strengthCoeff.push_back(tempSHVector[i]->getCoefficient()); |
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} |
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|
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isError = 0; |
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myATID = at->getIdent(); |
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makeShape( &nContact, &contactL[0], &contactM[0], &contactFunc[0], |
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&contactCoeff[0], |
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&nRange, &rangeL[0], &rangeM[0], &rangeFunc[0], |
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&rangeCoeff[0], |
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&nStrength, &strengthL[0], &strengthM[0], |
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&strengthFunc[0], &strengthCoeff[0], |
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&myATID, |
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&isError); |
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if( isError ){ |
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sprintf( painCave.errMsg, |
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"Error initializing the \"%s\" shape in fortran\n", |
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(iter->first).c_str() ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
| 276 |
} |
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} |
| 278 |
|
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#ifdef IS_MPI |
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sprintf( checkPointMsg, |
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"Shapes_FF atom structures successfully sent to fortran\n" ); |
| 282 |
MPIcheckPoint(); |
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#endif // is_mpi |
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|
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} |
| 286 |
|
| 287 |
void Shapes_FF::cleanMe( void ){ |
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|
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} |
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|
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void Shapes_FF::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
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|
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int i,j,k; |
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map<string, AtomType*>::iterator iter; |
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|
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// initialize the atoms |
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DirectionalAtom* dAtom; |
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AtomType* at; |
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DirectionalAtomType* dat; |
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ShapeAtomType* sat; |
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double sigma; |
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double ji[3]; |
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double inertialMat[3][3]; |
| 304 |
Mat3x3d momInt; |
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string myTypeString; |
| 306 |
|
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for( i=0; i<nAtoms; i++ ){ |
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|
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myTypeString = the_atoms[i]->getType(); |
| 310 |
iter = atomTypeMap.find(myTypeString); |
| 311 |
|
| 312 |
if (iter == atomTypeMap.end()) { |
| 313 |
sprintf( painCave.errMsg, |
| 314 |
"AtomType error, %s not found in force file.\n", |
| 315 |
the_atoms[i]->getType() ); |
| 316 |
painCave.isFatal = 1; |
| 317 |
simError(); |
| 318 |
} else { |
| 319 |
|
| 320 |
at = (AtomType*)(iter->second); |
| 321 |
|
| 322 |
the_atoms[i]->setMass( at->getMass() ); |
| 323 |
the_atoms[i]->setIdent( at->getIdent() ); |
| 324 |
|
| 325 |
if ( at->isShape() ) { |
| 326 |
|
| 327 |
sat = (ShapeAtomType*)at; |
| 328 |
sigma = findLargestContactDistance(sat); |
| 329 |
if (sigma > bigSigma) bigSigma = sigma; |
| 330 |
|
| 331 |
} |
| 332 |
|
| 333 |
the_atoms[i]->setHasCharge(at->isCharge()); |
| 334 |
|
| 335 |
if( at->isDirectional() ){ |
| 336 |
|
| 337 |
dat = (DirectionalAtomType*)at; |
| 338 |
dAtom = (DirectionalAtom *) the_atoms[i]; |
| 339 |
|
| 340 |
momInt = dat->getI(); |
| 341 |
|
| 342 |
// zero out the moments of inertia matrix |
| 343 |
for( j=0; j<3; j++ ) |
| 344 |
for( k=0; k<3; k++ ) |
| 345 |
inertialMat[j][k] = momInt(j,k); |
| 346 |
dAtom->setI( inertialMat ); |
| 347 |
|
| 348 |
ji[0] = 0.0; |
| 349 |
ji[1] = 0.0; |
| 350 |
ji[2] = 0.0; |
| 351 |
dAtom->setJ( ji ); |
| 352 |
|
| 353 |
if (dat->isDipole()) { |
| 354 |
dAtom->setHasDipole( dat->isDipole() ); |
| 355 |
entry_plug->n_dipoles++; |
| 356 |
} |
| 357 |
} |
| 358 |
} |
| 359 |
} |
| 360 |
} |
| 361 |
|
| 362 |
void Shapes_FF::initializeBonds( int nBonds, Bond** BondArray, |
| 363 |
bond_pair* the_bonds ){ |
| 364 |
|
| 365 |
if( nBonds ){ |
| 366 |
sprintf( painCave.errMsg, |
| 367 |
"Shapes_FF does not support bonds.\n" ); |
| 368 |
painCave.isFatal = 1; |
| 369 |
simError(); |
| 370 |
} |
| 371 |
} |
| 372 |
|
| 373 |
void Shapes_FF::initializeBends( int nBends, Bend** bendArray, |
| 374 |
bend_set* the_bends ){ |
| 375 |
|
| 376 |
if( nBends ){ |
| 377 |
sprintf( painCave.errMsg, |
| 378 |
"Shapes_FF does not support bends.\n" ); |
| 379 |
painCave.isFatal = 1; |
| 380 |
simError(); |
| 381 |
} |
| 382 |
} |
| 383 |
|
| 384 |
void Shapes_FF::initializeTorsions( int nTorsions, Torsion** torsionArray, |
| 385 |
torsion_set* the_torsions ){ |
| 386 |
|
| 387 |
if( nTorsions ){ |
| 388 |
sprintf( painCave.errMsg, |
| 389 |
"Shapes_FF does not support torsions.\n" ); |
| 390 |
painCave.isFatal = 1; |
| 391 |
simError(); |
| 392 |
} |
| 393 |
} |
| 394 |
|
| 395 |
void Shapes_FF::parseShapeFile(string shapeFileName, ShapeAtomType* st){ |
| 396 |
const int MAXLEN = 1024; |
| 397 |
char inLine[MAXLEN]; |
| 398 |
char *token; |
| 399 |
char *delim = " ,;\t\n"; |
| 400 |
int nTokens; |
| 401 |
Mat3x3d momInert; |
| 402 |
RealSphericalHarmonic* rsh; |
| 403 |
vector<RealSphericalHarmonic*> functionVector; |
| 404 |
ifstrstream shapeFile; |
| 405 |
string tempString; |
| 406 |
|
| 407 |
shapeFile.open( shapeFileName.c_str() ); |
| 408 |
|
| 409 |
if( shapeFile == NULL ){ |
| 410 |
|
| 411 |
tempString = ffPath; |
| 412 |
tempString += "/"; |
| 413 |
tempString += shapeFileName; |
| 414 |
shapeFileName = tempString; |
| 415 |
|
| 416 |
shapeFile.open( shapeFileName.c_str() ); |
| 417 |
|
| 418 |
if( shapeFile == NULL ){ |
| 419 |
|
| 420 |
sprintf( painCave.errMsg, |
| 421 |
"Error opening the shape file:\n" |
| 422 |
"\t%s\n" |
| 423 |
"\tHave you tried setting the FORCE_PARAM_PATH environment " |
| 424 |
"variable?\n", |
| 425 |
shapeFileName.c_str() ); |
| 426 |
painCave.severity = OOPSE_ERROR; |
| 427 |
painCave.isFatal = 1; |
| 428 |
simError(); |
| 429 |
} |
| 430 |
} |
| 431 |
|
| 432 |
// read in the shape types. |
| 433 |
|
| 434 |
// first grab the values in the ShapeInfo section |
| 435 |
findBegin( shapeFile, "ShapeInfo"); |
| 436 |
|
| 437 |
shapeFile.getline(inLine, MAXLEN); |
| 438 |
while( !shapeFile.eof() ) { |
| 439 |
// toss comment lines |
| 440 |
if( inLine[0] != '!' && inLine[0] != '#' ){ |
| 441 |
// end marks section completion |
| 442 |
if (isEndLine(inLine)) break; |
| 443 |
|
| 444 |
nTokens = countTokens(inLine, delim); |
| 445 |
if (nTokens != 0) { |
| 446 |
if (nTokens < 5) { |
| 447 |
sprintf( painCave.errMsg, |
| 448 |
"Not enough data on a ShapeInfo line in file: %s\n", |
| 449 |
shapeFileName.c_str() ); |
| 450 |
painCave.severity = OOPSE_ERROR; |
| 451 |
painCave.isFatal = 1; |
| 452 |
simError(); |
| 453 |
|
| 454 |
token = strtok(inLine, delim); |
| 455 |
token = strtok(NULL, delim); |
| 456 |
st->setMass(atof(token)); |
| 457 |
token = strtok(NULL, delim); |
| 458 |
momInert(0,0) = atof(token); |
| 459 |
token = strtok(NULL, delim); |
| 460 |
momInert(1,1) = atof(token); |
| 461 |
token = strtok(NULL, delim); |
| 462 |
momInert(2,2) = atof(token); |
| 463 |
st->setI(momInert); |
| 464 |
} |
| 465 |
} |
| 466 |
} |
| 467 |
shapeFile.getline(inLine, MAXLEN); |
| 468 |
} |
| 469 |
|
| 470 |
// now grab the contact functions |
| 471 |
findBegin(shapeFile, "ContactFunctions"); |
| 472 |
functionVector.clear(); |
| 473 |
|
| 474 |
shapeFile.getline(inLine, MAXLEN); |
| 475 |
while( !shapeFile.eof() ) { |
| 476 |
// toss comment lines |
| 477 |
if( inLine[0] != '!' && inLine[0] != '#' ){ |
| 478 |
// end marks section completion |
| 479 |
if (isEndLine(inLine)) break; |
| 480 |
|
| 481 |
nTokens = countTokens(inLine, delim); |
| 482 |
if (nTokens != 0) { |
| 483 |
if (nTokens < 4) { |
| 484 |
sprintf( painCave.errMsg, |
| 485 |
"Not enough data on a ContactFunctions line in file: %s\n", |
| 486 |
shapeFileName.c_str() ); |
| 487 |
painCave.severity = OOPSE_ERROR; |
| 488 |
painCave.isFatal = 1; |
| 489 |
simError(); |
| 490 |
|
| 491 |
// read in a spherical harmonic function |
| 492 |
token = strtok(inLine, delim); |
| 493 |
rsh = new RealSphericalHarmonic(); |
| 494 |
rsh->setL(atoi(token)); |
| 495 |
token = strtok(NULL, delim); |
| 496 |
rsh->setM(atoi(token)); |
| 497 |
token = strtok(NULL, delim); |
| 498 |
if (!strcasecmp("sin",token)) |
| 499 |
rsh->makeSinFunction(); |
| 500 |
else |
| 501 |
rsh->makeCosFunction(); |
| 502 |
token = strtok(NULL, delim); |
| 503 |
rsh->setCoefficient(atof(token)); |
| 504 |
|
| 505 |
functionVector.push_back(rsh); |
| 506 |
} |
| 507 |
} |
| 508 |
} |
| 509 |
shapeFile.getline(inLine, MAXLEN); |
| 510 |
} |
| 511 |
|
| 512 |
// pass contact functions to ShapeType |
| 513 |
st->setContactFuncs(functionVector); |
| 514 |
|
| 515 |
// now grab the range functions |
| 516 |
findBegin(shapeFile, "RangeFunctions"); |
| 517 |
functionVector.clear(); |
| 518 |
|
| 519 |
shapeFile.getline(inLine, MAXLEN); |
| 520 |
while( !shapeFile.eof() ) { |
| 521 |
// toss comment lines |
| 522 |
if( inLine[0] != '!' && inLine[0] != '#' ){ |
| 523 |
// end marks section completion |
| 524 |
if (isEndLine(inLine)) break; |
| 525 |
|
| 526 |
nTokens = countTokens(inLine, delim); |
| 527 |
if (nTokens != 0) { |
| 528 |
if (nTokens < 4) { |
| 529 |
sprintf( painCave.errMsg, |
| 530 |
"Not enough data on a RangeFunctions line in file: %s\n", |
| 531 |
shapeFileName.c_str() ); |
| 532 |
painCave.severity = OOPSE_ERROR; |
| 533 |
painCave.isFatal = 1; |
| 534 |
simError(); |
| 535 |
|
| 536 |
// read in a spherical harmonic function |
| 537 |
token = strtok(inLine, delim); |
| 538 |
|
| 539 |
rsh = new RealSphericalHarmonic(); |
| 540 |
rsh->setL(atoi(token)); |
| 541 |
token = strtok(NULL, delim); |
| 542 |
rsh->setM(atoi(token)); |
| 543 |
token = strtok(NULL, delim); |
| 544 |
if (!strcasecmp("sin",token)) |
| 545 |
rsh->makeSinFunction(); |
| 546 |
else |
| 547 |
rsh->makeCosFunction(); |
| 548 |
token = strtok(NULL, delim); |
| 549 |
rsh->setCoefficient(atof(token)); |
| 550 |
|
| 551 |
functionVector.push_back(rsh); |
| 552 |
} |
| 553 |
} |
| 554 |
} |
| 555 |
shapeFile.getline(inLine, MAXLEN); |
| 556 |
} |
| 557 |
|
| 558 |
// pass range functions to ShapeType |
| 559 |
st->setRangeFuncs(functionVector); |
| 560 |
|
| 561 |
// finally grab the strength functions |
| 562 |
findBegin(shapeFile, "StrengthFunctions"); |
| 563 |
functionVector.clear(); |
| 564 |
|
| 565 |
shapeFile.getline(inLine, MAXLEN); |
| 566 |
while( !shapeFile.eof() ) { |
| 567 |
// toss comment lines |
| 568 |
if( inLine[0] != '!' && inLine[0] != '#' ){ |
| 569 |
// end marks section completion |
| 570 |
if (isEndLine(inLine)) break; |
| 571 |
|
| 572 |
nTokens = countTokens(inLine, delim); |
| 573 |
if (nTokens != 0) { |
| 574 |
if (nTokens < 4) { |
| 575 |
sprintf( painCave.errMsg, |
| 576 |
"Not enough data on a StrengthFunctions line in file: %s\n", |
| 577 |
shapeFileName.c_str() ); |
| 578 |
painCave.severity = OOPSE_ERROR; |
| 579 |
painCave.isFatal = 1; |
| 580 |
simError(); |
| 581 |
|
| 582 |
// read in a spherical harmonic function |
| 583 |
token = strtok(inLine, delim); |
| 584 |
rsh = new RealSphericalHarmonic(); |
| 585 |
rsh->setL(atoi(token)); |
| 586 |
token = strtok(NULL, delim); |
| 587 |
rsh->setM(atoi(token)); |
| 588 |
token = strtok(NULL, delim); |
| 589 |
if (!strcasecmp("sin",token)) |
| 590 |
rsh->makeSinFunction(); |
| 591 |
else |
| 592 |
rsh->makeCosFunction(); |
| 593 |
token = strtok(NULL, delim); |
| 594 |
rsh->setCoefficient(atof(token)); |
| 595 |
|
| 596 |
functionVector.push_back(rsh); |
| 597 |
} |
| 598 |
} |
| 599 |
} |
| 600 |
shapeFile.getline(inLine, MAXLEN); |
| 601 |
} |
| 602 |
|
| 603 |
// pass strength functions to ShapeType |
| 604 |
st->setStrengthFuncs(functionVector); |
| 605 |
|
| 606 |
// we're done reading from this file |
| 607 |
shapeFile.close(); |
| 608 |
} |
| 609 |
|
| 610 |
double Shapes_FF::findLargestContactDistance(ShapeAtomType* st) { |
| 611 |
int i, j, nSteps; |
| 612 |
double theta, thetaStep, thetaMin, costheta; |
| 613 |
double phi, phiStep; |
| 614 |
double sigma, bigSigma; |
| 615 |
|
| 616 |
nSteps = 16; |
| 617 |
|
| 618 |
thetaStep = M_PI / nSteps; |
| 619 |
thetaMin = thetaStep / 2.0; |
| 620 |
phiStep = thetaStep * 2.0; |
| 621 |
bigSigma = 0.0; |
| 622 |
|
| 623 |
for (i = 0; i < nSteps; i++) { |
| 624 |
|
| 625 |
theta = thetaMin + i * thetaStep; |
| 626 |
costheta = cos(theta); |
| 627 |
|
| 628 |
for (j = 0; j < nSteps; j++) { |
| 629 |
|
| 630 |
phi = j*phiStep; |
| 631 |
|
| 632 |
sigma = st->getContactValueAt(costheta, phi); |
| 633 |
|
| 634 |
if (sigma > bigSigma) bigSigma = sigma; |
| 635 |
} |
| 636 |
} |
| 637 |
|
| 638 |
return bigSigma; |
| 639 |
} |
