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chrisfen |
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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 <iostream> |
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using namespace std; |
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif //is_mpi |
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#include "ForceFields.hpp" |
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#include "SRI.hpp" |
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#include "simError.h" |
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#include "fortranWrappers.hpp" |
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#ifdef IS_MPI |
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#include "mpiForceField.h" |
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#endif // is_mpi |
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namespace WATER_NS{ |
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gezelter |
989 |
// Declare the structures that will be passed by the parser and MPI |
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chrisfen |
976 |
|
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typedef struct{ |
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char name[15]; |
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double mass; |
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double epslon; |
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double sigma; |
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double charge; |
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int isDirectional; |
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int isLJ; |
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int isCharge; |
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int ident; |
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int last; // 0 -> default |
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// 1 -> in MPI: tells nodes to stop listening |
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} atomStruct; |
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typedef struct{ |
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char name[15]; |
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gezelter |
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double Ixx; |
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double Iyy; |
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double Izz; |
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chrisfen |
976 |
double dipole; |
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double w0; |
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double v0; |
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double v0p; |
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double rl; |
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double ru; |
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double rlp; |
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double rup; |
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int isDipole; |
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int isSticky; |
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int last; // 0 -> default |
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// 1 -> in MPI: tells nodes to stop listening |
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} directionalStruct; |
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int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ); |
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int parseDirectional( char *lineBuffer, int lineNum, directionalStruct &info ); |
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#ifdef IS_MPI |
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MPI_Datatype mpiAtomStructType; |
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MPI_Datatype mpiDirectionalStructType; |
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#endif |
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class LinkedAtomType { |
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public: |
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LinkedAtomType(){ |
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next = NULL; |
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name[0] = '\0'; |
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} |
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~LinkedAtomType(){ if( next != NULL ) delete next; } |
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LinkedAtomType* find(char* key){ |
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if( !strcmp(name, key) ) return this; |
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if( next != NULL ) return next->find(key); |
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return NULL; |
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} |
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void add( atomStruct &info ){ |
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// check for duplicates |
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if( !strcmp( info.name, name ) ){ |
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sprintf( painCave.errMsg, |
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"Duplicate WATER atom type \"%s\" found in " |
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"the WATER param file./n", |
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name ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if( next != NULL ) next->add(info); |
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else{ |
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next = new LinkedAtomType(); |
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strcpy(next->name, info.name); |
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next->isDirectional = info.isDirectional; |
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next->isLJ = info.isLJ; |
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next->isCharge = info.isCharge; |
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next->mass = info.mass; |
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next->epslon = info.epslon; |
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next->sigma = info.sigma; |
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next->charge = info.charge; |
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next->ident = info.ident; |
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} |
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} |
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#ifdef IS_MPI |
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void duplicate( atomStruct &info ){ |
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strcpy(info.name, name); |
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info.isDirectional = isDirectional; |
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info.isLJ = isLJ; |
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info.isCharge = isCharge; |
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info.mass = mass; |
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info.epslon = epslon; |
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info.sigma = sigma; |
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info.charge = charge; |
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info.ident = ident; |
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info.last = 0; |
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} |
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#endif |
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char name[15]; |
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int isDirectional; |
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int isLJ; |
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int isCharge; |
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double mass; |
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double epslon; |
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double sigma; |
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double charge; |
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int ident; |
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LinkedAtomType* next; |
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}; |
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class LinkedDirectionalType { |
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public: |
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LinkedDirectionalType(){ |
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next = NULL; |
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name[0] = '\0'; |
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} |
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~LinkedDirectionalType(){ if( next != NULL ) delete next; } |
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LinkedDirectionalType* find(char* key){ |
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if( !strcmp(name, key) ) return this; |
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if( next != NULL ) return next->find(key); |
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return NULL; |
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} |
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void add( directionalStruct &info ){ |
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// check for duplicates |
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if( !strcmp( info.name, name ) ){ |
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sprintf( painCave.errMsg, |
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"Duplicate WATER directional type \"%s\" found in " |
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"the WATER param file./n", |
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name ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if( next != NULL ) next->add(info); |
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else{ |
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next = new LinkedDirectionalType(); |
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strcpy(next->name, info.name); |
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next->isDipole = info.isDipole; |
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next->isSticky = info.isSticky; |
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gezelter |
989 |
next->Ixx = info.Ixx; |
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next->Iyy = info.Iyy; |
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next->Izz = info.Izz; |
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next->dipole = info.dipole; |
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chrisfen |
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next->w0 = info.w0; |
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next->v0 = info.v0; |
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next->v0p = info.v0p; |
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next->rl = info.rl; |
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next->ru = info.ru; |
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next->rlp = info.rlp; |
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next->rup = info.rup; |
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} |
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} |
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#ifdef IS_MPI |
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void duplicate( directionalStruct &info ){ |
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strcpy(info.name, name); |
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info.isDipole = isDipole; |
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info.isSticky = isSticky; |
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gezelter |
989 |
info.Ixx = Ixx; |
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info.Iyy = Iyy; |
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info.Izz = Izz; |
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chrisfen |
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info.dipole = dipole; |
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info.w0 = w0; |
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info.v0 = v0; |
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info.v0p = v0p; |
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info.rl = rl; |
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info.ru = ru; |
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info.rlp = rlp; |
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info.rup = rup; |
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info.last = 0; |
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} |
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#endif |
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char name[15]; |
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int isDipole; |
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int isSticky; |
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gezelter |
989 |
double Ixx; |
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double Iyy; |
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double Izz; |
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chrisfen |
976 |
double dipole; |
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double w0; |
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double v0; |
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double v0p; |
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double rl; |
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double ru; |
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double rlp; |
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double rup; |
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LinkedDirectionalType* next; |
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}; |
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LinkedAtomType* headAtomType; |
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LinkedAtomType* currentAtomType; |
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LinkedDirectionalType* headDirectionalType; |
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LinkedDirectionalType* currentDirectionalType; |
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gezelter |
989 |
} // namespace |
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chrisfen |
976 |
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using namespace WATER_NS; |
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//**************************************************************** |
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// begins the actual forcefield stuff. |
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//**************************************************************** |
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WATER::WATER(){ |
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char fileName[200]; |
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char* ffPath_env = "FORCE_PARAM_PATH"; |
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char* ffPath; |
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char temp[200]; |
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headAtomType = NULL; |
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currentAtomType = NULL; |
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headDirectionalType = NULL; |
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currentDirectionalType = NULL; |
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// do the funtion wrapping |
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wrapMeFF( this ); |
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#ifdef IS_MPI |
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int i; |
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// ********************************************************************** |
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// Init the atomStruct mpi type |
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atomStruct atomProto; // mpiPrototype |
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int atomBC[3] = {15,4,5}; // block counts |
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MPI_Aint atomDspls[3]; // displacements |
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MPI_Datatype atomMbrTypes[3]; // member mpi types |
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MPI_Address(&atomProto.name, &atomDspls[0]); |
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MPI_Address(&atomProto.mass, &atomDspls[1]); |
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gezelter |
989 |
MPI_Address(&atomProto.isDirectional, &atomDspls[2]); |
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chrisfen |
976 |
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atomMbrTypes[0] = MPI_CHAR; |
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atomMbrTypes[1] = MPI_DOUBLE; |
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atomMbrTypes[2] = MPI_INT; |
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for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
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MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType); |
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MPI_Type_commit(&mpiAtomStructType); |
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// *********************************************************************** |
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// ********************************************************************** |
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// Init the directionalStruct mpi type |
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directionalStruct directionalProto; // mpiPrototype |
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gezelter |
989 |
int directionalBC[3] = {15,11,3}; // block counts |
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chrisfen |
976 |
MPI_Aint directionalDspls[3]; // displacements |
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MPI_Datatype directionalMbrTypes[3]; // member mpi types |
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MPI_Address(&directionalProto.name, &directionalDspls[0]); |
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gezelter |
989 |
MPI_Address(&directionalProto.Ixx, &directionalDspls[1]); |
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MPI_Address(&directionalProto.isDipole, &directionalDspls[2]); |
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chrisfen |
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directionalMbrTypes[0] = MPI_CHAR; |
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directionalMbrTypes[1] = MPI_DOUBLE; |
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directionalMbrTypes[2] = MPI_INT; |
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for (i=2; i >= 0; i--) directionalDspls[i] -= directionalDspls[0]; |
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MPI_Type_struct(3, directionalBC, directionalDspls, directionalMbrTypes, |
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&mpiDirectionalStructType); |
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MPI_Type_commit(&mpiDirectionalStructType); |
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// *********************************************************************** |
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if( worldRank == 0 ){ |
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#endif |
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// generate the force file name |
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strcpy( fileName, "WATER.frc" ); |
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// fprintf( stderr,"Trying to open %s\n", fileName ); |
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// attempt to open the file in the current directory first. |
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frcFile = fopen( fileName, "r" ); |
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if( frcFile == NULL ){ |
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// next see if the force path enviorment variable is set |
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ffPath = getenv( ffPath_env ); |
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if( ffPath == NULL ) { |
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STR_DEFINE(ffPath, FRC_PATH ); |
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} |
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strcpy( temp, ffPath ); |
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strcat( temp, "/" ); |
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strcat( temp, fileName ); |
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strcpy( fileName, temp ); |
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frcFile = fopen( fileName, "r" ); |
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if( frcFile == NULL ){ |
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sprintf( painCave.errMsg, |
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"Error opening the force field parameter file: %s\n" |
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"Have you tried setting the FORCE_PARAM_PATH environment " |
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"variable?\n", |
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fileName ); |
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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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sprintf( checkPointMsg, "WATER file opened sucessfully." ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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} |
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WATER::~WATER(){ |
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if( headAtomType != NULL ) delete headAtomType; |
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if( headDirectionalType != NULL ) delete headDirectionalType; |
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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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fclose( frcFile ); |
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#ifdef IS_MPI |
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} |
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#endif // is_mpi |
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} |
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void WATER::cleanMe( void ){ |
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#ifdef IS_MPI |
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// keep the linked list in the mpi version |
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#else // is_mpi |
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// delete the linked list in the single processor version |
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if( headAtomType != NULL ) delete headAtomType; |
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if( headDirectionalType != NULL ) delete headDirectionalType; |
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#endif // is_mpi |
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} |
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void WATER::initForceField( int ljMixRule ){ |
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initFortran( ljMixRule, entry_plug->useReactionField ); |
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} |
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void WATER::readParams( void ){ |
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401 |
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int identNum; |
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403 |
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atomStruct atomInfo; |
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directionalStruct directionalInfo; |
405 |
gezelter |
989 |
fpos_t *atomPos; |
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chrisfen |
976 |
|
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atomInfo.last = 1; // initialize last to have the last set. |
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directionalInfo.last = 1; // if things go well, last will be set to 0 |
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atomPos = new fpos_t; |
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bigSigma = 0.0; |
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#ifdef IS_MPI |
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if( worldRank == 0 ){ |
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#endif |
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417 |
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// read in the atom types. |
418 |
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headAtomType = new LinkedAtomType; |
420 |
gezelter |
989 |
headDirectionalType = new LinkedDirectionalType; |
421 |
chrisfen |
976 |
|
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fastForward( "AtomTypes", "initializeAtoms" ); |
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// we are now at the AtomTypes section. |
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|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
427 |
|
|
lineNum++; |
428 |
|
|
|
429 |
|
|
|
430 |
|
|
// read a line, and start parsing out the atom types |
431 |
|
|
|
432 |
|
|
if( eof_test == NULL ){ |
433 |
|
|
sprintf( painCave.errMsg, |
434 |
|
|
"Error in reading Atoms from force file at line %d.\n", |
435 |
|
|
lineNum ); |
436 |
|
|
painCave.isFatal = 1; |
437 |
|
|
simError(); |
438 |
|
|
} |
439 |
|
|
|
440 |
|
|
identNum = 1; |
441 |
|
|
// stop reading at end of file, or at next section |
442 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
443 |
|
|
|
444 |
|
|
// toss comment lines |
445 |
|
|
if( readLine[0] != '!' ){ |
446 |
|
|
|
447 |
|
|
// the parser returns 0 if the line was blank |
448 |
|
|
if( parseAtom( readLine, lineNum, atomInfo ) ){ |
449 |
|
|
atomInfo.ident = identNum; |
450 |
|
|
headAtomType->add( atomInfo ); |
451 |
|
|
if ( atomInfo.isDirectional ) { |
452 |
|
|
|
453 |
|
|
// if the atom is directional, skip to the directional section |
454 |
|
|
// and parse directional info. |
455 |
|
|
fgetpos( frcFile, atomPos ); |
456 |
|
|
sectionSearch( "DirectionalTypes", atomInfo.name, |
457 |
|
|
"initializeDirectional" ); |
458 |
|
|
parseDirectional( readLine, lineNum, directionalInfo ); |
459 |
gezelter |
989 |
headDirectionalType->add( directionalInfo ); |
460 |
chrisfen |
976 |
|
461 |
|
|
// return to the AtomTypes section |
462 |
|
|
fsetpos( frcFile, atomPos ); |
463 |
|
|
} |
464 |
|
|
identNum++; |
465 |
|
|
} |
466 |
|
|
} |
467 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
468 |
|
|
lineNum++; |
469 |
|
|
} |
470 |
|
|
|
471 |
|
|
#ifdef IS_MPI |
472 |
|
|
|
473 |
|
|
// send out the linked list to all the other processes |
474 |
|
|
|
475 |
|
|
sprintf( checkPointMsg, |
476 |
|
|
"WATER atom structures read successfully." ); |
477 |
|
|
MPIcheckPoint(); |
478 |
|
|
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
479 |
|
|
while( currentAtomType != NULL ){ |
480 |
|
|
currentAtomType->duplicate( atomInfo ); |
481 |
|
|
|
482 |
|
|
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
483 |
|
|
|
484 |
|
|
sprintf( checkPointMsg, |
485 |
|
|
"successfully sent WATER force type: \"%s\"\n", |
486 |
|
|
atomInfo.name ); |
487 |
|
|
MPIcheckPoint(); |
488 |
|
|
|
489 |
|
|
currentAtomType = currentAtomType->next; |
490 |
|
|
} |
491 |
gezelter |
989 |
|
492 |
chrisfen |
976 |
atomInfo.last = 1; |
493 |
|
|
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
494 |
|
|
|
495 |
|
|
if ( atomInfo.isDirectional ){ |
496 |
|
|
// send out the linked list to all the other processes |
497 |
|
|
|
498 |
|
|
sprintf( checkPointMsg, |
499 |
|
|
"WATER directional structures read successfully." ); |
500 |
|
|
MPIcheckPoint(); |
501 |
|
|
|
502 |
|
|
currentDirectionalType = headDirectionalType->next; |
503 |
|
|
while( currentDirectionalType != NULL ){ |
504 |
|
|
currentDirectionalType->duplicate( directionalInfo ); |
505 |
|
|
sendFrcStruct( &directionalInfo, mpiDirectionalStructType ); |
506 |
|
|
currentDirectionalType = currentDirectionalType->next; |
507 |
|
|
} |
508 |
|
|
directionalInfo.last = 1; |
509 |
|
|
sendFrcStruct( &directionalInfo, mpiDirectionalStructType ); |
510 |
|
|
} |
511 |
|
|
} |
512 |
gezelter |
989 |
|
513 |
chrisfen |
976 |
else{ |
514 |
|
|
|
515 |
|
|
// listen for node 0 to send out the force params |
516 |
|
|
|
517 |
|
|
MPIcheckPoint(); |
518 |
gezelter |
989 |
|
519 |
chrisfen |
976 |
headAtomType = new LinkedAtomType; |
520 |
|
|
receiveFrcStruct( &atomInfo, mpiAtomStructType ); |
521 |
|
|
|
522 |
|
|
while( !atomInfo.last ){ |
523 |
|
|
|
524 |
|
|
headAtomType->add( atomInfo ); |
525 |
|
|
|
526 |
|
|
MPIcheckPoint(); |
527 |
|
|
|
528 |
|
|
receiveFrcStruct( &atomInfo, mpiAtomStructType ); |
529 |
|
|
} |
530 |
|
|
|
531 |
|
|
if ( atomInfo.isDirectional ) { |
532 |
|
|
// listen for node 0 to send out the force params |
533 |
|
|
|
534 |
|
|
MPIcheckPoint(); |
535 |
|
|
|
536 |
|
|
headDirectionalType = new LinkedDirectionalType; |
537 |
|
|
receiveFrcStruct( &directionalInfo, mpiDirectionalStructType ); |
538 |
|
|
while( !directionalInfo.last ){ |
539 |
|
|
|
540 |
|
|
headDirectionalType->add( directionalInfo ); |
541 |
|
|
receiveFrcStruct( &directionalInfo, mpiDirectionalStructType ); |
542 |
|
|
} |
543 |
|
|
|
544 |
|
|
sprintf( checkPointMsg, |
545 |
|
|
"WATER directional structures broadcast successfully." ); |
546 |
|
|
MPIcheckPoint(); |
547 |
|
|
} |
548 |
|
|
} |
549 |
|
|
|
550 |
|
|
#endif // is_mpi |
551 |
|
|
|
552 |
|
|
// call new A_types in fortran |
553 |
|
|
|
554 |
|
|
int isError; |
555 |
|
|
|
556 |
|
|
// dummy variables |
557 |
|
|
int isGB = 0; |
558 |
|
|
int isEAM = 0; |
559 |
gezelter |
989 |
int notDipole = 0; |
560 |
|
|
int notSSD = 0; |
561 |
|
|
double noDipMoment = 0.0; |
562 |
|
|
|
563 |
|
|
|
564 |
|
|
currentAtomType = headAtomType->next; |
565 |
|
|
currentDirectionalType = headDirectionalType->next; |
566 |
|
|
|
567 |
chrisfen |
976 |
while( currentAtomType != NULL ){ |
568 |
|
|
|
569 |
|
|
if( currentAtomType->isLJ ) entry_plug->useLJ = 1; |
570 |
gezelter |
989 |
if( currentAtomType->isCharge ) entry_plug->useCharges = 1; |
571 |
chrisfen |
976 |
if( currentAtomType->isDirectional ){ |
572 |
gezelter |
989 |
// only directional atoms can have dipoles or be sticky |
573 |
|
|
if ( currentDirectionalType->isDipole ) entry_plug->useDipoles = 1; |
574 |
|
|
if ( currentDirectionalType->isSticky ) { |
575 |
chrisfen |
976 |
entry_plug->useSticky = 1; |
576 |
gezelter |
989 |
set_sticky_params( &(currentDirectionalType->w0), |
577 |
|
|
&(currentDirectionalType->v0), |
578 |
|
|
&(currentDirectionalType->v0p), |
579 |
|
|
&(currentDirectionalType->rl), |
580 |
|
|
&(currentDirectionalType->ru), |
581 |
|
|
&(currentDirectionalType->rlp), |
582 |
|
|
&(currentDirectionalType->rup)); |
583 |
chrisfen |
976 |
} |
584 |
gezelter |
989 |
if( currentAtomType->name[0] != '\0' ){ |
585 |
|
|
isError = 0; |
586 |
|
|
makeAtype( &(currentAtomType->ident), |
587 |
|
|
&(currentAtomType->isLJ), |
588 |
|
|
&(currentDirectionalType->isSticky), |
589 |
|
|
&(currentDirectionalType->isDipole), |
590 |
|
|
&isGB, |
591 |
|
|
&isEAM, |
592 |
|
|
&(currentAtomType->isCharge), |
593 |
|
|
&(currentAtomType->epslon), |
594 |
|
|
&(currentAtomType->sigma), |
595 |
|
|
&(currentAtomType->charge), |
596 |
|
|
&(currentDirectionalType->dipole), |
597 |
|
|
&isError ); |
598 |
|
|
if( isError ){ |
599 |
|
|
sprintf( painCave.errMsg, |
600 |
|
|
"Error initializing the \"%s\" atom type in fortran\n", |
601 |
|
|
currentAtomType->name ); |
602 |
|
|
painCave.isFatal = 1; |
603 |
|
|
simError(); |
604 |
|
|
} |
605 |
|
|
} |
606 |
|
|
currentDirectionalType->next; |
607 |
chrisfen |
976 |
} |
608 |
gezelter |
989 |
|
609 |
|
|
else { |
610 |
|
|
// use all dummy variables if this is not a directional atom |
611 |
|
|
if( currentAtomType->name[0] != '\0' ){ |
612 |
|
|
isError = 0; |
613 |
|
|
makeAtype( &(currentAtomType->ident), |
614 |
|
|
&(currentAtomType->isLJ), |
615 |
|
|
¬SSD, |
616 |
|
|
¬Dipole, |
617 |
|
|
&isGB, |
618 |
|
|
&isEAM, |
619 |
|
|
&(currentAtomType->isCharge), |
620 |
|
|
&(currentAtomType->epslon), |
621 |
|
|
&(currentAtomType->sigma), |
622 |
|
|
&(currentAtomType->charge), |
623 |
|
|
&noDipMoment, |
624 |
|
|
&isError ); |
625 |
|
|
if( isError ){ |
626 |
|
|
sprintf( painCave.errMsg, |
627 |
|
|
"Error initializing the \"%s\" atom type in fortran\n", |
628 |
|
|
currentAtomType->name ); |
629 |
|
|
painCave.isFatal = 1; |
630 |
|
|
simError(); |
631 |
|
|
} |
632 |
chrisfen |
976 |
} |
633 |
|
|
} |
634 |
|
|
currentAtomType = currentAtomType->next; |
635 |
|
|
} |
636 |
|
|
|
637 |
|
|
#ifdef IS_MPI |
638 |
|
|
sprintf( checkPointMsg, |
639 |
|
|
"WATER atom structures successfully sent to fortran\n" ); |
640 |
|
|
MPIcheckPoint(); |
641 |
|
|
#endif // is_mpi |
642 |
|
|
|
643 |
|
|
} |
644 |
|
|
|
645 |
|
|
|
646 |
|
|
void WATER::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
647 |
|
|
|
648 |
gezelter |
989 |
int i,j; |
649 |
chrisfen |
976 |
|
650 |
|
|
// initialize the atoms |
651 |
gezelter |
989 |
DirectionalAtom* dAtom; |
652 |
|
|
double inertialMat[3][3]; |
653 |
chrisfen |
976 |
|
654 |
|
|
for( i=0; i<nAtoms; i++ ){ |
655 |
gezelter |
989 |
fprintf(stderr, "flag 1\n"); |
656 |
chrisfen |
976 |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
657 |
gezelter |
989 |
fprintf(stderr, "%s is the type\n", the_atoms[i]->getType()); |
658 |
chrisfen |
976 |
if( currentAtomType == NULL ){ |
659 |
|
|
sprintf( painCave.errMsg, |
660 |
|
|
"AtomType error, %s not found in force file.\n", |
661 |
|
|
the_atoms[i]->getType() ); |
662 |
|
|
painCave.isFatal = 1; |
663 |
|
|
simError(); |
664 |
|
|
} |
665 |
gezelter |
989 |
fprintf(stderr, "flag 2\n"); |
666 |
|
|
if( currentAtomType->isLJ ) the_atoms[i]->setLJ(); |
667 |
|
|
if( currentAtomType->isCharge ) the_atoms[i]->setCharged(); |
668 |
chrisfen |
976 |
the_atoms[i]->setMass( currentAtomType->mass ); |
669 |
|
|
the_atoms[i]->setIdent( currentAtomType->ident ); |
670 |
gezelter |
989 |
fprintf(stderr, "flag 3\n"); |
671 |
|
|
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
672 |
chrisfen |
976 |
|
673 |
gezelter |
989 |
if( currentAtomType->isDirectional ){ |
674 |
|
|
fprintf(stderr, "flag 4\n"); |
675 |
|
|
currentDirectionalType = |
676 |
|
|
headDirectionalType->find( the_atoms[i]->getType() ); |
677 |
|
|
fprintf(stderr, "%s is the type\n", the_atoms[i]->getType()); |
678 |
|
|
if( currentDirectionalType == NULL ){ |
679 |
|
|
sprintf( painCave.errMsg, |
680 |
|
|
"DirectionalType error, %s not found in force file.\n", |
681 |
|
|
the_atoms[i]->getType() ); |
682 |
|
|
painCave.isFatal = 1; |
683 |
|
|
simError(); |
684 |
|
|
} |
685 |
chrisfen |
976 |
|
686 |
gezelter |
989 |
// zero out the moments of inertia matrix |
687 |
|
|
for( i=0; i<3; i++ ) |
688 |
|
|
for( j=0; j<3; j++ ) |
689 |
|
|
inertialMat[i][j] = 0.0; |
690 |
chrisfen |
976 |
|
691 |
gezelter |
989 |
// load the force file moments of inertia |
692 |
|
|
inertialMat[0][0] = currentDirectionalType->Ixx; |
693 |
|
|
inertialMat[1][1] = currentDirectionalType->Iyy; |
694 |
|
|
inertialMat[2][2] = currentDirectionalType->Izz; |
695 |
|
|
fprintf(stderr, "Let's try pointing to isDirectional\n"); |
696 |
|
|
fprintf(stderr, "%i what is this\n",the_atoms[i]->isDirectional()); |
697 |
|
|
dAtom = (DirectionalAtom *) the_atoms[i]; |
698 |
|
|
fprintf(stderr, "%i is isDipole\n", currentDirectionalType->isDipole); |
699 |
|
|
dAtom->setHasDipole( currentDirectionalType->isDipole ); |
700 |
|
|
dAtom->setMu( currentDirectionalType->dipole ); |
701 |
|
|
fprintf(stderr, "flag 5\n"); |
702 |
|
|
dAtom->setMu( currentDirectionalType->dipole ); |
703 |
|
|
fprintf(stderr,"flag 6\n"); |
704 |
|
|
// if it's sticky then it's an SSD type |
705 |
|
|
dAtom->setSSD( currentDirectionalType->isSticky ); |
706 |
|
|
dAtom->setJx( 0.0 ); |
707 |
|
|
dAtom->setJy( 0.0 ); |
708 |
|
|
dAtom->setJz( 0.0 ); |
709 |
|
|
dAtom->setI( inertialMat ); |
710 |
|
|
fprintf(stderr, "flag 7\n"); |
711 |
|
|
entry_plug->n_dipoles++; |
712 |
|
|
fprintf(stderr, "flag 8\n"); |
713 |
|
|
} |
714 |
|
|
else{ |
715 |
|
|
sprintf( painCave.errMsg, |
716 |
|
|
"WATER error: Atom \"%s\" is directional, yet no standard" |
717 |
|
|
" orientation was specifed in the BASS file.\n", |
718 |
|
|
currentAtomType->name ); |
719 |
chrisfen |
976 |
painCave.isFatal = 1; |
720 |
|
|
simError(); |
721 |
|
|
} |
722 |
|
|
} |
723 |
|
|
} |
724 |
|
|
|
725 |
|
|
void WATER::initializeBonds( int nBonds, Bond** BondArray, |
726 |
|
|
bond_pair* the_bonds ){ |
727 |
|
|
|
728 |
|
|
if( nBonds ){ |
729 |
|
|
sprintf( painCave.errMsg, |
730 |
|
|
"WATER does not support bonds.\n" ); |
731 |
|
|
painCave.isFatal = 1; |
732 |
|
|
simError(); |
733 |
|
|
} |
734 |
|
|
} |
735 |
|
|
|
736 |
|
|
void WATER::initializeBends( int nBends, Bend** bendArray, |
737 |
|
|
bend_set* the_bends ){ |
738 |
|
|
|
739 |
|
|
if( nBends ){ |
740 |
|
|
sprintf( painCave.errMsg, |
741 |
|
|
"WATER does not support bends.\n" ); |
742 |
|
|
painCave.isFatal = 1; |
743 |
|
|
simError(); |
744 |
|
|
} |
745 |
|
|
} |
746 |
|
|
|
747 |
|
|
void WATER::initializeTorsions( int nTorsions, Torsion** torsionArray, |
748 |
|
|
torsion_set* the_torsions ){ |
749 |
|
|
|
750 |
|
|
if( nTorsions ){ |
751 |
|
|
sprintf( painCave.errMsg, |
752 |
|
|
"WATER does not support torsions.\n" ); |
753 |
|
|
painCave.isFatal = 1; |
754 |
|
|
simError(); |
755 |
|
|
} |
756 |
|
|
} |
757 |
|
|
|
758 |
|
|
void WATER::fastForward( char* stopText, char* searchOwner ){ |
759 |
|
|
|
760 |
|
|
int foundText = 0; |
761 |
|
|
char* the_token; |
762 |
|
|
|
763 |
|
|
rewind( frcFile ); |
764 |
|
|
lineNum = 0; |
765 |
|
|
|
766 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
767 |
|
|
lineNum++; |
768 |
|
|
if( eof_test == NULL ){ |
769 |
|
|
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
770 |
|
|
" file is empty.\n", |
771 |
|
|
searchOwner ); |
772 |
|
|
painCave.isFatal = 1; |
773 |
|
|
simError(); |
774 |
|
|
} |
775 |
|
|
|
776 |
|
|
|
777 |
|
|
while( !foundText ){ |
778 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
779 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
780 |
|
|
lineNum++; |
781 |
|
|
} |
782 |
|
|
if( eof_test == NULL ){ |
783 |
|
|
sprintf( painCave.errMsg, |
784 |
|
|
"Error fast forwarding force file for %s at " |
785 |
|
|
"line %d: file ended unexpectedly.\n", |
786 |
|
|
searchOwner, |
787 |
|
|
lineNum ); |
788 |
|
|
painCave.isFatal = 1; |
789 |
|
|
simError(); |
790 |
|
|
} |
791 |
|
|
|
792 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
793 |
|
|
foundText = !strcmp( stopText, the_token ); |
794 |
|
|
|
795 |
|
|
if( !foundText ){ |
796 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
797 |
|
|
lineNum++; |
798 |
|
|
|
799 |
|
|
if( eof_test == NULL ){ |
800 |
|
|
sprintf( painCave.errMsg, |
801 |
|
|
"Error fast forwarding force file for %s at " |
802 |
|
|
"line %d: file ended unexpectedly.\n", |
803 |
|
|
searchOwner, |
804 |
|
|
lineNum ); |
805 |
|
|
painCave.isFatal = 1; |
806 |
|
|
simError(); |
807 |
|
|
} |
808 |
|
|
} |
809 |
|
|
} |
810 |
|
|
} |
811 |
|
|
|
812 |
|
|
void WATER::sectionSearch( char* secHead, char* stopText, char* searchOwner ){ |
813 |
|
|
|
814 |
|
|
int foundSection = 0; |
815 |
|
|
int foundText = 0; |
816 |
|
|
char* the_token; |
817 |
gezelter |
989 |
fpos_t *tempPos; |
818 |
chrisfen |
976 |
|
819 |
|
|
rewind( frcFile ); |
820 |
|
|
lineNum = 0; |
821 |
gezelter |
989 |
tempPos = new fpos_t; |
822 |
chrisfen |
976 |
|
823 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
824 |
|
|
lineNum++; |
825 |
|
|
if( eof_test == NULL ){ |
826 |
|
|
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
827 |
|
|
" file is empty.\n", |
828 |
|
|
searchOwner ); |
829 |
|
|
painCave.isFatal = 1; |
830 |
|
|
simError(); |
831 |
|
|
} |
832 |
|
|
|
833 |
|
|
while( !foundSection ){ |
834 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
835 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
836 |
|
|
lineNum++; |
837 |
|
|
} |
838 |
|
|
if( eof_test == NULL ){ |
839 |
|
|
sprintf( painCave.errMsg, |
840 |
|
|
"Error fast forwarding force file for %s at " |
841 |
|
|
"line %d: file ended unexpectedly.\n", |
842 |
|
|
searchOwner, |
843 |
|
|
lineNum ); |
844 |
|
|
painCave.isFatal = 1; |
845 |
|
|
simError(); |
846 |
|
|
} |
847 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
848 |
|
|
foundSection = !strcmp( secHead, the_token ); |
849 |
|
|
|
850 |
|
|
if( !foundSection ){ |
851 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
852 |
|
|
lineNum++; |
853 |
|
|
|
854 |
|
|
if( eof_test == NULL ){ |
855 |
|
|
sprintf( painCave.errMsg, |
856 |
|
|
"Error section searching force file for %s at " |
857 |
|
|
"line %d: file ended unexpectedly.\n", |
858 |
|
|
searchOwner, |
859 |
|
|
lineNum ); |
860 |
|
|
painCave.isFatal = 1; |
861 |
|
|
simError(); |
862 |
|
|
} |
863 |
|
|
} |
864 |
gezelter |
989 |
} |
865 |
chrisfen |
976 |
|
866 |
|
|
while( !foundText ){ |
867 |
gezelter |
989 |
|
868 |
|
|
fgetpos( frcFile, tempPos ); |
869 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
870 |
|
|
lineNum++; |
871 |
|
|
|
872 |
|
|
if( eof_test == NULL ){ |
873 |
|
|
sprintf( painCave.errMsg, |
874 |
|
|
"Error fast forwarding force file for %s at " |
875 |
|
|
"line %d: file ended unexpectedly.\n", |
876 |
|
|
searchOwner, |
877 |
|
|
lineNum ); |
878 |
|
|
painCave.isFatal = 1; |
879 |
chrisfen |
976 |
simError(); |
880 |
gezelter |
989 |
} |
881 |
chrisfen |
976 |
|
882 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
883 |
gezelter |
989 |
if( the_token != NULL ){ |
884 |
|
|
foundText = !strcmp( stopText, the_token ); |
885 |
|
|
} |
886 |
chrisfen |
976 |
} |
887 |
gezelter |
989 |
fsetpos( frcFile, tempPos ); |
888 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
889 |
|
|
lineNum++; |
890 |
chrisfen |
976 |
} |
891 |
|
|
|
892 |
|
|
|
893 |
|
|
int WATER_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
894 |
|
|
|
895 |
|
|
char* the_token; |
896 |
|
|
|
897 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
898 |
|
|
if( the_token != NULL ){ |
899 |
|
|
|
900 |
|
|
strcpy( info.name, the_token ); |
901 |
|
|
|
902 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
903 |
|
|
sprintf( painCave.errMsg, |
904 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
905 |
|
|
painCave.isFatal = 1; |
906 |
|
|
simError(); |
907 |
|
|
} |
908 |
|
|
|
909 |
|
|
info.isDirectional = atoi( the_token ); |
910 |
|
|
|
911 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
912 |
|
|
sprintf( painCave.errMsg, |
913 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
914 |
|
|
painCave.isFatal = 1; |
915 |
|
|
simError(); |
916 |
|
|
} |
917 |
|
|
|
918 |
|
|
info.isLJ = atoi( the_token ); |
919 |
|
|
|
920 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
921 |
|
|
sprintf( painCave.errMsg, |
922 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
923 |
|
|
painCave.isFatal = 1; |
924 |
|
|
simError(); |
925 |
|
|
} |
926 |
|
|
|
927 |
|
|
info.isCharge = atoi( the_token ); |
928 |
|
|
|
929 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
930 |
|
|
sprintf( painCave.errMsg, |
931 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
932 |
|
|
painCave.isFatal = 1; |
933 |
|
|
simError(); |
934 |
|
|
} |
935 |
|
|
|
936 |
|
|
info.mass = atof( the_token ); |
937 |
|
|
|
938 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
939 |
|
|
sprintf( painCave.errMsg, |
940 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
941 |
|
|
painCave.isFatal = 1; |
942 |
|
|
simError(); |
943 |
|
|
} |
944 |
|
|
|
945 |
|
|
info.epslon = atof( the_token ); |
946 |
|
|
|
947 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
948 |
|
|
sprintf( painCave.errMsg, |
949 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
950 |
|
|
painCave.isFatal = 1; |
951 |
|
|
simError(); |
952 |
|
|
} |
953 |
|
|
|
954 |
|
|
info.sigma = atof( the_token ); |
955 |
|
|
|
956 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
957 |
|
|
sprintf( painCave.errMsg, |
958 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
959 |
|
|
painCave.isFatal = 1; |
960 |
|
|
simError(); |
961 |
|
|
} |
962 |
|
|
|
963 |
|
|
info.charge = atof( the_token ); |
964 |
|
|
|
965 |
|
|
return 1; |
966 |
|
|
} |
967 |
|
|
else return 0; |
968 |
|
|
} |
969 |
|
|
|
970 |
|
|
int WATER_NS::parseDirectional( char *lineBuffer, int lineNum, directionalStruct &info ){ |
971 |
|
|
|
972 |
|
|
char* the_token; |
973 |
|
|
|
974 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
975 |
|
|
if( the_token != NULL ){ |
976 |
|
|
|
977 |
|
|
strcpy( info.name, the_token ); |
978 |
|
|
|
979 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
980 |
|
|
sprintf( painCave.errMsg, |
981 |
|
|
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
982 |
|
|
painCave.isFatal = 1; |
983 |
|
|
simError(); |
984 |
|
|
} |
985 |
|
|
|
986 |
|
|
info.isDipole = atoi( the_token ); |
987 |
|
|
|
988 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
989 |
|
|
sprintf( painCave.errMsg, |
990 |
|
|
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
991 |
|
|
painCave.isFatal = 1; |
992 |
|
|
simError(); |
993 |
|
|
} |
994 |
|
|
|
995 |
|
|
info.isSticky = atoi( the_token ); |
996 |
|
|
|
997 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
998 |
|
|
sprintf( painCave.errMsg, |
999 |
|
|
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
1000 |
|
|
painCave.isFatal = 1; |
1001 |
|
|
simError(); |
1002 |
|
|
} |
1003 |
|
|
|
1004 |
gezelter |
989 |
info.Ixx = atof( the_token ); |
1005 |
chrisfen |
976 |
|
1006 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1007 |
|
|
sprintf( painCave.errMsg, |
1008 |
|
|
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
1009 |
|
|
painCave.isFatal = 1; |
1010 |
|
|
simError(); |
1011 |
|
|
} |
1012 |
|
|
|
1013 |
gezelter |
989 |
info.Iyy = atof( the_token ); |
1014 |
chrisfen |
976 |
|
1015 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1016 |
|
|
sprintf( painCave.errMsg, |
1017 |
|
|
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
1018 |
|
|
painCave.isFatal = 1; |
1019 |
|
|
simError(); |
1020 |
|
|
} |
1021 |
|
|
|
1022 |
gezelter |
989 |
info.Izz = atof( the_token ); |
1023 |
chrisfen |
976 |
|
1024 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1025 |
|
|
sprintf( painCave.errMsg, |
1026 |
|
|
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
1027 |
|
|
painCave.isFatal = 1; |
1028 |
|
|
simError(); |
1029 |
|
|
} |
1030 |
|
|
|
1031 |
|
|
|
1032 |
|
|
info.dipole = atof( the_token ); |
1033 |
|
|
|
1034 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1035 |
|
|
sprintf( painCave.errMsg, |
1036 |
|
|
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
1037 |
|
|
painCave.isFatal = 1; |
1038 |
|
|
simError(); |
1039 |
|
|
} |
1040 |
|
|
|
1041 |
|
|
info.w0 = atof( the_token ); |
1042 |
|
|
|
1043 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1044 |
|
|
sprintf( painCave.errMsg, |
1045 |
|
|
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
1046 |
|
|
painCave.isFatal = 1; |
1047 |
|
|
simError(); |
1048 |
|
|
} |
1049 |
|
|
|
1050 |
|
|
info.v0 = atof( the_token ); |
1051 |
|
|
|
1052 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1053 |
|
|
sprintf( painCave.errMsg, |
1054 |
|
|
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
1055 |
|
|
painCave.isFatal = 1; |
1056 |
|
|
simError(); |
1057 |
|
|
} |
1058 |
|
|
|
1059 |
|
|
info.v0p = atof( the_token ); |
1060 |
|
|
|
1061 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1062 |
|
|
sprintf( painCave.errMsg, |
1063 |
|
|
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
1064 |
|
|
painCave.isFatal = 1; |
1065 |
|
|
simError(); |
1066 |
|
|
} |
1067 |
|
|
|
1068 |
|
|
info.rl = atof( the_token ); |
1069 |
|
|
|
1070 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1071 |
|
|
sprintf( painCave.errMsg, |
1072 |
|
|
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
1073 |
|
|
painCave.isFatal = 1; |
1074 |
|
|
simError(); |
1075 |
|
|
} |
1076 |
|
|
|
1077 |
|
|
info.ru = atof( the_token ); |
1078 |
|
|
|
1079 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1080 |
|
|
sprintf( painCave.errMsg, |
1081 |
|
|
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
1082 |
|
|
painCave.isFatal = 1; |
1083 |
|
|
simError(); |
1084 |
|
|
} |
1085 |
|
|
|
1086 |
|
|
info.rlp = atof( the_token ); |
1087 |
|
|
|
1088 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1089 |
|
|
sprintf( painCave.errMsg, |
1090 |
|
|
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
1091 |
|
|
painCave.isFatal = 1; |
1092 |
|
|
simError(); |
1093 |
|
|
} |
1094 |
|
|
|
1095 |
|
|
info.rup = atof( the_token ); |
1096 |
|
|
|
1097 |
|
|
return 1; |
1098 |
|
|
} |
1099 |
|
|
else return 0; |
1100 |
|
|
} |